Methods for determining interaction between PROTEINS.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
Any method used for determining the location of and relative distances between genes on a chromosome.
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A species of protozoa that is the causal agent of falciparum malaria (MALARIA, FALCIPARUM). It is most prevalent in the tropics and subtropics.
A protozoan disease caused in humans by four species of the PLASMODIUM genus: PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PLASMODIUM OVALE; and PLASMODIUM MALARIAE; and transmitted by the bite of an infected female mosquito of the genus ANOPHELES. Malaria is endemic in parts of Asia, Africa, Central and South America, Oceania, and certain Caribbean islands. It is characterized by extreme exhaustion associated with paroxysms of high FEVER; SWEATING; shaking CHILLS; and ANEMIA. Malaria in ANIMALS is caused by other species of plasmodia.
Malaria caused by PLASMODIUM FALCIPARUM. This is the severest form of malaria and is associated with the highest levels of parasites in the blood. This disease is characterized by irregularly recurring febrile paroxysms that in extreme cases occur with acute cerebral, renal, or gastrointestinal manifestations.
Proteins found in any species of protozoan.
Any part or derivative of any protozoan that elicits immunity; malaria (Plasmodium) and trypanosome antigens are presently the most frequently encountered.
A federal area located between Maryland and Virginia on the Potomac river; it is coextensive with Washington, D.C., which is the capital of the United States.
A genus of protozoa that comprise the malaria parasites of mammals. Four species infect humans (although occasional infections with primate malarias may occur). These are PLASMODIUM FALCIPARUM; PLASMODIUM MALARIAE; PLASMODIUM OVALE, and PLASMODIUM VIVAX. Species causing infection in vertebrates other than man include: PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; P. vinckei, and PLASMODIUM YOELII in rodents; P. brasilianum, PLASMODIUM CYNOMOLGI; and PLASMODIUM KNOWLESI in monkeys; and PLASMODIUM GALLINACEUM in chickens.
Libraries in which a major proportion of the resources are available in machine-readable format, rather than on paper or MICROFORM.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
A purplish-red, light-sensitive pigment found in RETINAL ROD CELLS of most vertebrates. It is a complex consisting of a molecule of ROD OPSIN and a molecule of 11-cis retinal (RETINALDEHYDE). Rhodopsin exhibits peak absorption wavelength at about 500 nm.
A heterotrimeric GTP-binding protein that mediates the light activation signal from photolyzed rhodopsin to cyclic GMP phosphodiesterase and is pivotal in the visual excitation process. Activation of rhodopsin on the outer membrane of rod and cone cells causes GTP to bind to transducin followed by dissociation of the alpha subunit-GTP complex from the beta/gamma subunits of transducin. The alpha subunit-GTP complex activates the cyclic GMP phosphodiesterase which catalyzes the hydrolysis of cyclic GMP to 5'-GMP. This leads to closure of the sodium and calcium channels and therefore hyperpolarization of the rod cells. EC 3.6.1.-.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
Collections of systematically acquired and organized information resources, and usually providing assistance to users. (ERIC Thesaurus, http://www.eric.ed.gov/ accessed 2/1/2008)
The use of automatic machines or processing devices in libraries. The automation may be applied to library administrative activities, office procedures, and delivery of library services to users.
That segment of commercial enterprise devoted to the design, development, and manufacture of chemical products for use in the diagnosis and treatment of disease, disability, or other dysfunction, or to improve function.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Structured vocabularies describing concepts from the fields of biology and relationships between concepts.
A specified list of terms with a fixed and unalterable meaning, and from which a selection is made when CATALOGING; ABSTRACTING AND INDEXING; or searching BOOKS; JOURNALS AS TOPIC; and other documents. The control is intended to avoid the scattering of related subjects under different headings (SUBJECT HEADINGS). The list may be altered or extended only by the publisher or issuing agency. (From Harrod's Librarians' Glossary, 7th ed, p163)
A center in the PUBLIC HEALTH SERVICE which is primarily concerned with the collection, analysis, and dissemination of health statistics on vital events and health activities to reflect the health status of people, health needs, and health resources.
Sequential operating programs and data which instruct the functioning of a digital computer.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
A species of the genus FLAVIVIRUS which causes an acute febrile and sometimes hemorrhagic disease in man. Dengue is mosquito-borne and four serotypes are known.
An acute febrile disease transmitted by the bite of AEDES mosquitoes infected with DENGUE VIRUS. It is self-limiting and characterized by fever, myalgia, headache, and rash. SEVERE DENGUE is a more virulent form of dengue.
A virulent form of dengue characterized by THROMBOCYTOPENIA and an increase in vascular permeability (grades I and II) and distinguished by a positive pain test (e.g., TOURNIQUET PAIN TEST). When accompanied by SHOCK (grades III and IV), it is called dengue shock syndrome.
The class Insecta, in the phylum ARTHROPODA, whose members are characterized by division into three parts: head, thorax, and abdomen. They are the dominant group of animals on earth; several hundred thousand different kinds having been described. Three orders, HEMIPTERA; DIPTERA; and SIPHONAPTERA; are of medical interest in that they cause disease in humans and animals. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p1)
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.
A genus of mosquitoes (CULICIDAE) frequently found in tropical and subtropical regions. YELLOW FEVER and DENGUE are two of the diseases that can be transmitted by species of this genus.
Diseases that are underfunded and have low name recognition but are major burdens in less developed countries. The World Health Organization has designated six tropical infectious diseases as being neglected in industrialized countries that are endemic in many developing countries (HELMINTHIASIS; LEPROSY; LYMPHATIC FILARIASIS; ONCHOCERCIASIS; SCHISTOSOMIASIS; and TRACHOMA).
The branch of medicine concerned with diseases, mainly of parasitic origin, common in tropical and subtropical regions.
A ZINC FINGER MOTIF protein that recognizes and interacts with damaged DNA. It is a DNA-binding protein that plays an essential role in NUCLEOTIDE EXCISION REPAIR. Mutations in this protein are associated with the most severe form of XERODERMA PIGMENTOSUM.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A rare, pigmentary, and atrophic autosomal recessive disease. It is manifested as an extreme photosensitivity to ULTRAVIOLET RAYS as the result of a deficiency in the enzyme that permits excisional repair of ultraviolet-damaged DNA.
Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.

A novel in vivo assay for the analysis of protein-protein interaction. (1/5726)

The Ras Recruitment System (RRS) is a method for identification and isolation of protein-protein interaction. The method is based on translocation of cytoplasmic mammalian Ras protein to the inner leaflet of the plasma membrane through protein-protein interaction. The system is studied in a temperature-sensitive yeast strain where the yeast Ras guanyl nucleotide exchange factor is inactive at 36 degrees C. Protein-protein interaction results in cell growth at the restrictive temperature. We developed a gene reporter assay for the analysis of protein-protein interaction in mammalian cells. Ras activation in mammalian cells induces the mitogen-activated kinase cascade (MAPK), which can be monitored using Ras-dependent reporter genes. This greatly extends the usefulness of the system and provides a novel assay for protein-protein interaction in mammalian cells.  (+info)

The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms. (2/5726)

Forkhead-associated (FHA) domains are a class of ubiquitous signaling modules that appear to function through interactions with phosphorylated target molecules. We have used oriented peptide library screening to determine the optimal phosphopeptide binding motifs recognized by several FHA domains, including those within a number of DNA damage checkpoint kinases, and determined the X-ray structure of Rad53p-FHA1, in complex with a phospho-threonine peptide, at 1.6 A resolution. The structure reveals a striking similarity to the MH2 domains of Smad tumor suppressor proteins and reveals a mode of peptide binding that differs from SH2, 14-3-3, or PTB domain complexes. These results have important implications for DNA damage signaling and CHK2-dependent tumor suppression, and they indicate that FHA domains play important and unsuspected roles in S/T kinase signaling mechanisms in prokaryotes and eukaryotes.  (+info)

The beta-slip: a novel concept in transthyretin amyloidosis. (3/5726)

Transthyretin is a tetrameric plasma protein associated with two forms of amyloid disease. The structure of the highly amyloidogenic transthyretin triple mutant TTRG53S/E54D/L55S determined at 2.3 A resolution reveals a novel conformation: the beta-slip. A three-residue shift in beta strand D places Leu-58 at the position normally occupied by Leu-55 now mutated to serine. The beta-slip is best defined in two of the four monomers, where it makes new protein-protein interactions to an area normally involved in complex formation with retinol-binding protein. This interaction creates unique packing arrangements, where two protein helices combine to form a double helix in agreement with fiber diffraction and electron microscopy data. Based on these findings, a novel model for transthyretin amyloid formation is presented.  (+info)

C/EBP beta and Elk-1 synergistically transactivate the c-fos serum response element. (4/5726)

BACKGROUND: The serum response element (SRE) in the c-fos promoter is a convergence point for several signaling pathways that regulate induction of the c-fos gene. Many transcription factors regulate the SRE, including serum response factor (SRF), ternary complex factor (TCF), and CCAAT/enhancer binding protein-beta (C/EBPbeta). Independently, the TCFs and C/EBPbeta have been shown to interact with SRF and to respond to Ras-dependent signaling pathways that result in transactivation of the SRE. Due to these common observations, we addressed the possibility that C/EBPbeta and Elk-1 could both be necessary for Ras-stimulated transactivation of the SRE. RESULTS: In this report, we demonstrate that Elk-1 and C/EBPbeta functionally synergize in transactivation of both a Gal4 reporter plasmid in concert with Gal4-SRF and in transactivation of the SRE. Interestingly, this synergy is only observed upon activation of Ras-dependent signaling pathways. Furthermore, we show that Elk-1 and C/EBPbeta could interact both in an in vitro GST-pulldown assay and in an in vivo co-immunoprecipitation assay. The in vivo interaction between the two proteins is dependent on the presence of activated Ras. We have also shown that the C-terminal domain of C/EBPbeta and the N-terminal domain of Elk-1 are necessary for the proteins to interact. CONCLUSIONS: These data show that C/EBPbeta and Elk-1 synergize in SRF dependent transcription of both a Gal-4 reporter and the SRE. This suggests that SRF, TCF, and C/EBPbeta are all necessary for maximal induction of the c-fos SRE in response to mitogenic signaling by Ras.  (+info)

Simultaneous modelling of metabolic, genetic and product-interaction networks. (5/5726)

The creation of cell models from annotated genome information, as well as additional data from other databases, requires both a format and medium for its distribution. Standards are described for the representation of the data in the form of Document Type Definitions (DTDs) for XML files. Separate DTDs are detailed for genetic, metabolic and gene product-interaction networks, which can be used to hold information on individual subsystems, or which may be combined to create a whole cell DTD. In the execution of this work, a fifth DTD was also created for a metabolite thesaurus, which allows incorporation of metabolite synonyms and generic nomenclature data into the models. A gene-regulation classification scheme was also created, to facilitate incorporation of gene regulatory information in an efficient manner. The work is described with particular reference to the metabolic network of Escherichia coli, which contains 808 individual enzymes. The assignment of confidence levels to these data, through the use of Gene Ontology evidence codes, is highlighted. In silico investigations may now be performed using the mathematical simulation workbench, DBsolve, which incorporates the facility to introduce data directly from XML.  (+info)

Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands. (6/5726)

The binding of a nitroxide spin-labeled analog of N-acetyllactosamine to galectin-3, a mammalian lectin of 26 kD size, is studied to map the binding sites of this small oligosaccharide on the protein surface. Perturbation of intensities of cross-peaks in the (15)N heteronuclear single quantum coherence (HSQC) spectrum of full-length galectin-3 owing to the bound spin label is used qualitatively to identify protein residues proximate to the binding site for N-acetyllactosamine. A protocol for converting intensity measurements to a more quantitative determination of distances between discrete protein amide protons and the bound spin label is then described. This protocol is discussed as part of a drug design strategy in which subsequent perturbation of chemical shifts of distance mapped amide cross-peaks can be used effectively to screen a library of compounds for other ligands that bind to the target protein at distances suitable for chemical linkage to the primary ligand. This approach is novel in that it bypasses the need for structure determination and resonance assignment of the target protein.  (+info)

Domain-domain interactions of HtpG, an Escherichia coli homologue of eukaryotic HSP90 molecular chaperone. (7/5726)

In the present study, we investigated the domain structure and domain-domain interactions of HtpG, an Escherichia coli homologue of eukaryotic HSP90. Limited proteolysis of recombinant HtpG, revealed three major tryptic sites, i.e. Arg7-Gly8, Arg336-Glu337 and Lys552-Leu553, of which the latter two were located at the positions equivalent to the major cleavage sites of human HSP90alpha. A similar pattern was obtained by papain treatment under nondenaturing conditions but not under denaturing conditions. Thus, HtpG consists of three domains, i.e. Domain A, Met1-Arg336; domain B, Glu337-Lys552; and domain C, Leu553-Ser624, as does HSP90. The domains of HtpG were expressed and their interactions were estimated on polyacrylamide gel electrophoresis under nondenaturing conditions. As a result, two kinds of domain-domain interactions were revealed: domain B interaction with domain A of the same polypeptide and domain C of one partner with domain B of the other in the dimer. Domain B could be structurally and functionally divided into two subdomains, the N-terminal two-thirds (subdomain BI) that interacted with domain A and the C-terminal one-third (subdomain BII) that interacted with domain C. The C-terminal two-thirds of domain A, i.e. Asp116-Arg336, were sufficient for the binding to domain B. We finally propose the domain organization of an HtpG dimer.  (+info)

Mapping the energy surface of transmembrane helix-helix interactions. (8/5726)

Transmembrane helices are no longer believed to be just hydrophobic segments that exist solely to anchor proteins to a lipid bilayer, but rather they appear to have the capacity to specify function and structure. Specific interactions take place between hydrophobic segments within the lipid bilayer whereby subtle mutations that normally would be considered innocuous can result in dramatic structural differences. That such specificity takes place within the lipid bilayer implies that it may be possible to identify the most favorable interaction surface of transmembrane alpha-helices based on computational methods alone, as shown in this study. Herein, an attempt is made to map the energy surface of several transmembrane helix-helix interactions for several homo-oligomerizing proteins, where experimental data regarding their structure exist (glycophorin A, phospholamban, Influenza virus A M2, Influenza virus C CM2, and HIV vpu). It is shown that due to symmetry constraints in homo-oligomers the computational problem can be simplified. The results obtained are mostly consistent with known structural data and may additionally provide a view of possible alternate and intermediate configurations.  (+info)

We have recently shown by formally modelling human protein interaction networks (PINs) as metric spaces and classified proteins into zones based on their distance from the topological centre that hub proteins are primarily centrally located. We also showed that zones closest to the network centre are enriched for critically important proteins and are also functionally very specialised for specific house keeping functions. We proposed that proteins closest to the network centre may present good therapeutic targets. Here, we present multiple pieces of novel functional evidence that provides strong support for this hypothesis. We found that the human PINs has a highly connected signalling core, with the majority of proteins involved in signalling located in the two zones closest to the topological centre. The majority of essential, disease related, tumour suppressor, oncogenic and approved drug target proteins were found to be centrally located. Similarly, the majority of proteins consistently expressed
Title:Are Topological Properties of Drug Targets Based on Protein-Protein Interaction Network Ready to Predict Potential Drug Targets?. VOLUME: 19 ISSUE: 2. Author(s):Shiliang Li, Xiaojuan Yu, Chuanxin Zou, Jiayu Gong and Xiaofeng Liu. Affiliation:School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.. Keywords:Drug targets, protein-protein interactions network, support vector machine, network topological properties.. Abstract:Identification of potential druggable targets utilizing protein-protein interactions network (PPIN) has been emerging as a hotspot in drug discovery and development research. However, it remains unclear whether the currently used PPIN topological properties are enough to discriminate the drug targets from non-drug targets. In this study, three-step classification models using different network topological properties were designed and implemented using support vector machine (SVM) to compare the enrichment of known drug targets from ...
TY - JOUR. T1 - Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network. AU - Vaggi, Federico. AU - Dodgson, James. AU - Bajpai, Archana. AU - Chessel, Anatole. AU - Jordán, Ferenc. AU - Sato, Masamitsu. AU - Carazo-Salas, Rafael Edgardo. AU - Csikász-Nagy, Attila. PY - 2012/10. Y1 - 2012/10. N2 - The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify linker proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key ...
How many ways protein protein interactions are regulated? - posted in Biochemistry: I wonder how many ways protein-protein interactions are regulated. I know a lot of protein protein interactions are modified by phosphorylaton or other modification. Is there other ways that mediate the protein protein interaction? Thanks!
Receptor tyrosine kinase EGFR is usually localized on plasma membrane inducing the progression of many cancers including malignancy in children (Bodey et al. In Vivo. 2005, 19:931-41), but it contains a nuclear localization signal (NLS) that mediates EGFR nuclear translocation (Lin et al. Nat Cell Biol. 2001, 3:802-8). In this report, we claim that NLS of EGFR has an old evolutionary origin. In particular, our analysis of protein-protein interaction maps reveals that nuclear EGFR (nEGFR) pathways are different from that of membrane EGFR and EGF is not found in nEGFR network, while androgen receptor (AR) is found, which suggests the evolution of prostate cancer, a well-known AR driven cancer, through changes in androgen- or EGF-dependence. Database analysis shows that nEGFR correlates with the tumor grades especially in prostate cancer patients. Structural prediction analysis indicates that NLS can compromise the differential protein binding to EGFR through stretch linkers with evolutionary ...
TY - JOUR. T1 - Association rulemining from yeast protein inetraction to assist protein-protein interaction prediction. AU - Chiu, Hung-Wen. AU - Hung , Fei-Hung PY - 2008. Y1 - 2008. N2 - Protein protein interaction (PPI) is very important information for constructing biological pathways in this systems biology era. Recently many PPI-related databases have been created by high-throughput wet-lab methods. However, in-silico methods developed to predict PPIs are significant techniques for obtaining the whole aspect of PPI networks. Functional regions of a protein defined by specific amino-acid sequences are the key components on determining the role the protein play in a biological process. Association rule mining is a popular data mining skill for finding the association of components in an itemset. Therefore, to mining the associations of functional regions of two interacting proteins will be helpful for PPI prediction. In this study, we collected yeast PPI data from DIP and IntAct, and ...
Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to
The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms. We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted
Understanding the roles and consequences of protein-protein interactions is a fundamental goal in cellular biology and a prerequisite for the development of molecular systems biology. The endeavor of cataloging protein interactions is primarily hindered by the throughput and reproducibility of existing technologies. Different techniques for mapping protein interactions are available, such as the two‐hybrid approach (Chien et al, 1991) and the LUMIER approach (Barrios‐Rodiles et al, 2005) and assay whether two proteins interact in a pair‐wise fashion. We have developed a high‐throughput platform combining immunoprecipitation and high‐throughput mass spectrometry (IP‐HTMS) to rapidly identify potentially novel protein interactions for a bait protein of interest. We (Ho et al, 2002) and others (Gavin et al, 2002) previously used this approach to map protein-protein interactions in yeast, creating invaluable data sets for yeast biology and extrapolation into mammalian biology.. Mapping ...
Profacgen provides One-Stop-Service on protein-protein interaction analysis, including Yeast two-hybrid, Pull-downs and Surface Plasmon Resonance (SPR) assay etc., to facilitate your scientific research. Our service can be tailored according to your specific requirements.
TY - JOUR. T1 - A top-down approach to infer and compare domain-domain interactions across eight model organisms. AU - Guda, Chittibabu. AU - King, Brian R.. AU - Pal, Lipika R.. AU - Guda, Purnima. PY - 2009/3/31. Y1 - 2009/3/31. N2 - Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer functionally relevant DDIs from PPI data. We created a comprehensive, non-redundant dataset of 209,165 experimentally-derived PPIs by combining datasets from five major interaction databases. We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting ...
Towards Inter- and Intra- Cellular Protein Interaction Analysis: Applying the Betweenness Centrality Graph Measure for Node Importance
In recent years, protein-protein interaction (PPI) datasets have been recognized as important resources to elucidate various biological processes and cellular mechanisms. The prediction of protein complexes from PPIs (see, for example, survey papers [1-3]) is one of the most challenging inference problems from PPIs because protein complexes are essential entities in the cell. Proteins functions are manifested in the form of a protein complex. Thus, the identification of protein complexes is necessary for the precise description of biological systems.. For protein complex prediction, many computational methods have been proposed, which were directly or indirectly designed based on the observation that densely connected subgraphs, or clusters of proteins, of a whole PPI network often overlap with known complexes. This observation is often valid for relatively large protein complexes. However, small complexes, consisting of two or three proteins, form a major category of the known complexes of an ...
Cancer stem cells (CSCs) are a small subpopulation of cells within tumors with stem cell property. Increased evidence suggest that CSCs could be responsible for chemoresistance and recurrence in colorectal cancer (CRC). However, a reliable therapeutic target on CSCs is still lacking. Here we describe a two-step strategy to generate CSC targets with high selectivity for colon stem cell markers, specific proteins that are interacted with CSC markers were selected and subsequently validated in a survival analysis. TMEM17 protein was found and its biological functions in CRC cells were further examined. Finally, we utilized the Gene Set Enrichment Analysis (GSEA) to investigate the potential mechanisms of TMEM17 in CRC. By combining protein-protein interaction (PPI) database and high-throughput gene profiles, network analysis revealed a cluster of colon CSCs related genes. In the cluster, TMEM17 was identified as a novel CSCs related gene. The results of in-vitro functional study demonstrated that TMEM17
Protein Interaction Analysis ProteOn XPR36 Protein Interaction Array System 248 Instrument 248 Software 249 Regulatory Tools 249 Sensor Chips 250 Kits, Reagents, and Consumables 250 Ordering Information
단백질 상호 작용은 세포의 기능의 핵심이다. 열량 및 분광 기술은 일반적으로 그 특성을하는 데 사용됩니다. 여기에서 우리는 Shwachman - 다이아몬드 증후군 (SBDS)에 돌연변이 단백질과 신장 인자 같은 1는 GTPase (EFL1) ...
TY - JOUR. T1 - A markov clustering based link clustering method to identify overlapping modules in protein-protein interaction networks. AU - Wang, Yan. AU - Wang, Guishen. AU - Meng, Di. AU - Huang, Lan. AU - Blanzieri, Enrico. AU - Cui, Juan. PY - 2016/4/1. Y1 - 2016/4/1. N2 - Previous studies indicated that many overlapping structures exist among the modular structures in protein-protein interaction (PPI) networks, which may reflect common functional components shared by different biological processes. In this paper, a Markov clustering based Link Clustering (MLC) method for the identification of overlapping modular structures in PPI networks is proposed. Firstly, MLC method calculates the extended link similarity and derives a similarity matrix to represent the relevance among the protein interactions. Then it employs markov clustering to partition the link similarity matrix and obtains overlapping network modules with significantly less parameters and threshold constraints compared to most ...
Researchers from the Institut Curie and from the Paris-based biotechnology company Hybrigenics announced today that they have built a protein-protein interaction map of the fruit fly, Drosophila melanogaster. This simple model organism allows them to study a reference set of proteins that includes most of those known to be involved in human cancer. Since proteins function in networks, the systematic identification of the physical interactions that occur between proteins will help understanding their biological function, and improve our capacity to intervene and, ultimately, to discover novel, more specific therapeutic targets. Their results are published in the March 1st issue of Genome Research ...
TY - GEN. T1 - Combining gene expression profiles and protein-protein interactions for identifying functional modules. AU - Wang, Dingding. AU - Ogihara, Mitsunori. AU - Zeng, Erliang. AU - Li, Tao. PY - 2012/12/1. Y1 - 2012/12/1. N2 - Identifying functional modules from protein-protein interaction networks is an important and challenging task. This paper presents a new approach called PPIBM which is designed to integrate gene expression data analysis and clustering of protein-protein interactions. The proposed approach relies on a Bayesian model which uses as its base protein-protein interactions given as part of input. The proposed method is evaluated with standard measures and its performance is compared with the state-of-the-art network analysis methods. Experimental results on both real-world data and synthetic data demonstrate the effectiveness of the proposed approach.. AB - Identifying functional modules from protein-protein interaction networks is an important and challenging task. This ...
Defining protein complexes is critical to virtually all aspects of cell biology because most cellular processes are regulated by stable or more dynamic protein interactions. Elucidation of the protein-protein interaction network around transcription factors is essential to fully understand their function and regulation. In the last decade, new technologies have emerged to study protein-protein interactions under near-physiological conditions. We have developed a high-throughput tandem affinity purification (TAP)/mass spectrometry (MS) platform for cell suspension cultures to analyze protein complexes in Arabidopsis thaliana. This streamlined platform follows an integrated approach comprising generic Gateway-based vectors with high cloning flexibility, the fast generation of transgenic suspension cultures, TAP adapted for plant cells, and tandem matrix-assisted laser desorption ionization MS for the identification of purified proteins. Recently, we evaluated the GS tag, originally developed to ...
SVM and RF contributed 15 and 10 unique predictions, respectively, that were confirmed experimentally. Thus, the two methods were somewhat complementary and, if used together, may provide better coverage of true predictions. On the other hand, using the overlap of predictions from both SVM and RF provides a more conservative and, hence, more reliable list of protein interactions that could be used as a starting point for further investigations.. The Cbf11 interactors predicted were significantly enriched for the experimentally determined targets, both in the case of SVM (Fishers exact test, P = 10−14), RF (Fishers P = 10−28), and in the overlap of the two methods (Fishers P = 10−28). So far, there are no known genetic interactions for Cbf11 and no functional interactions due to the protein not being conserved in budding yeast. For this reason, our method for predicting its physical association partners can only be compared with selecting proteins at random from the whole genome. The ...
Eukaryotic cells have evolved an intricate system to resolve DNA damage to prevent its transmission to daughter cells. This system, collectively known as the DNA damage response (DDR) network, includes many proteins that detect DNA damage, promote repair, and coordinate progression through the cell cycle. Because defects in this network can lead to cancer, this network constitutes a barrier against tumorigenesis. The modular BRCA1 carboxyl-terminal (BRCT) domain is frequently present in proteins involved in the DDR, can exist either as an individual domain or as tandem domains (tBRCT), and can bind phosphorylated peptides. We performed a systematic analysis of protein-protein interactions involving tBRCT in the DDR by combining literature curation, yeast two-hybrid screens, and tandem affinity purification coupled to mass spectrometry. We identified 23 proteins containing conserved BRCT domains and generated a human protein-protein interaction network for seven proteins with tBRCT. This study ...
Some experimental protocols, such as tandem affinity purification (TAP), generate complex data sets, depicting interactions in which more than two proteins are involved at the same time (n-ary interactions).. However, interaction data are often stored in tabular formats that aim to be amenable to quick, comprehensive searches. It may be desirable to convert these complexes into sets of binary interactions to simplify and speed up searches. There are two algorithms that will perform such conversion: the matrix model and the spoke model 2, as depicted in Figure 10. In this hypothetical example, take the bottom right protein complex (marked reality). A tandem affinity experiment (far left) might tell you that each of the other five proteins interact with the red bait protein in the middle. In reality, the red protein has only one interactor, which is the yellow protein. As you can see, both algorithms are somewhat mis-leading, but as the spoke model generates up to 3 times fewer false positives ...
Abstract Background Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. Description DroID, the Drosophila Interactions Database, is a comprehensive interactions database designed specifically for Drosophila. DroID houses published physical protein interactions, genetic interactions, and computationally predicted
Macromolecular assemblies play an important role in almost all cellular processes. However, despite several large-scale studies, our current knowledge about protein complexes is still quite limited, thus advocating the use of in silico predictions to gather information on complex composition in model organisms. Since protein-protein interactions present certain constraints on the functional divergence of macromolecular assemblies during evolution, it is possible to predict complexes based on orthology data. Here, we show that incorporating interaction information through network alignment significantly increases the precision of orthology-based complex prediction. Moreover, we performed a large-scale in silico screen for protein complexes in human, yeast and fly, through the alignment of hundreds of known complexes to whole organism interactomes. Systematic comparison of the resulting network alignments to all complexes currently known in those species revealed many conserved complexes, as well as
Background The individual contribution of genes in the HLA region to the risk of developing type 1 diabetes (T1D) is confounded by the high linkage disequilibrium (LD) in this region. Using a novel approach we have combined genetic association data with information on functional protein-protein interactions to elucidate risk independent of LD and to place the genetic association into a functional context. Methodology/Principal Findings Genetic association data from 2300 single nucleotide polymorphisms (SNPs) in the HLA region was analysed in 2200 T1D family trios divided into six risk groups based on HLA-DRB1 genotypes. The best SNP signal in each gene was mapped to proteins in a human protein interaction network and their significance of clustering in functional network modules was evaluated. The significant network modules identified through this approach differed between the six HLA risk groups, which could be divided into two groups based on carrying the DRB1*0301 or the DRB1*0401 allele. Proteins
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): The rapid adoption of Internet technology has accelerated the establishment of platforms for virtual interaction that overcome the inherent time and space limitations of face-to-face communication. The objective of this study is to investigate the individual and network level mechanisms that characterize interactions on these electronic knowledge networks (EKNs). Toward that goal, we develop a simulation model of a thread-based asynchronous EKN and provide results based on 330 runs of the model (simulating a total of 3,643,942 messages generated by 38,860 authors). This study contributes to our understanding of electronic knowledge networks by demonstrating the importance of structural characteristics in influencing participant behaviors. We focus specifically on the role of preferential attachment (the tendency to associate with the most popular participants) and mutuality (the tendency to maintain symmetry in relationships
Many nonsynonymous single nucleotide polymorphisms (nsSNPs) are disease causing due to effects at protein-protein interfaces. We have integrated a database of the three-dimensional (3D) structures of human protein/protein complexes and the humsavar database of nsSNPs. We analyzed the location of nsSNPS in terms of their location in the protein core, at protein-protein interfaces, and on the surface when not at an interface. Disease-causing nsSNPs that do not occur in the protein core are preferentially located at protein-protein interfaces rather than surface noninterface regions when compared to random segregation. The disruption of the protein-protein interaction can be explained by a range of structural effects including the loss of an electrostatic salt bridge, the destabilization due to reduction of the hydrophobic effect, the formation of a steric clash, and the introduction of a proline altering the main-chain conformation. ...
Here, we described the multiplex in vivo measurement of 1,379 protein-protein interactions in 14 environmental conditions, to our knowledge the most extensive direct study of how protein interaction networks respond dynamically to extrinsic environmental perturbations. The most striking finding was the prevalence of dynamic binary complexes. More than half of the PPIs we considered (757 of 1,379) responded to at least one perturbation. The environmental perturbations that yielded the largest number of changes relative to our reference condition were respiratory growth in ethanol, heat shock, oxidative stress, and DNA damage. That these responses were the most profound might have been expected, as these conditions are likely to have been frequently experienced in the evolutionary history of yeast (Gasch & Werner‐Washburne, 2002; Gasch, 2007), allowing for selection and maintenance of a complex adaptive regulatory strategy. We observed that proteins with certain functions were more likely to ...
VisualComplexity.com is a unified resource space for anyone interested in the visualization of complex networks. The projects main goal is to leverage a critical understanding of different visualization methods, across a series of disciplines, as diverse as Biology, Social Networks or the World Wide Web.
Computational Framework for Analysis of Prey-Prey Associations in Interaction Proteomics Identifies Novel Human Protein-Protein Interactions and Networks
Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins. Come learn web-based gene annotation, gene ID conversion, pathway enrichment, and protein-protein interaction networks and automate the process ...
An online database that integrates the extracellular protein interaction network. ARNIE allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters using the drop-down menus. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.
Noncoding genetic variation is a major driver of phenotypic diversity, but functional interpretation is challenging. To better understand common genetic variation associated with brain diseases, we defined noncoding regulatory regions for major cell types of the human brain. Whereas psychiatric disorders were primarily associated with variants in transcriptional enhancers and promoters in neurons, sporadic Alzheimers disease (AD) variants were largely confined to microglia enhancers. Interactome maps connecting disease-risk variants in cell-type-specific enhancers to promoters revealed an extended microglia gene network in AD. Deletion of a microglia-specific enhancer harboring AD-risk variants ablated BIN1 expression in microglia, but not in neurons or astrocytes. These findings revise and expand the list of genes likely to be influenced by noncoding variants in AD and suggest the probable cell types in which they function. ...
Predicting Protein Functions from Protein Interaction Networks: 10.4018/978-1-60566-398-2.ch012: Functional characterization of genes and their protein products is essential to biological and clinical research. Yet, there is still no reliable way of
Specific protein-protein interactions form a major part of the basic organization of living cells. The structure of a protein complex holds information about the relative mutual organization of two proteins in a frozen state, but not about the kinetic or thermodynamic parameters that are central to their function. For many years I have been interested in understanding the relationships between the structures of transient protein-protein interactions and their binding activity. To address this, I adopted a multidisciplinary approach including: wet biophysical bench work, protein-design and engineering, bioinformatics, and algorithm development and applied the gained knowledge and techniques to address biological questions. As part of this I-CORE I am investigating structure/function aspects of type I interferon-receptor interactions and how these are related to signaling. Through a comprehensive analysis of the structure, energetics and dynamics of IFN recognition by its receptor subunits, and of ...
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (Oct 2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature. 437 (7062): 1173-8. doi:10.1038/nature04209. PMID 16189514 ...
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (October 2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature. 437 (7062): 1173-8. doi:10.1038/nature04209. PMID 16189514 ...
Rual JF، Venkatesan K، Hao T، Hirozane-Kishikawa T، Dricot A، Li N، Berriz GF، Gibbons FD، Dreze M، Ayivi-Guedehoussou N، Klitgord N، Simon C، Boxem M، Milstein S، Rosenberg J، Goldberg DS، Zhang LV، Wong SL، Franklin G، Li S، Albala JS، Lim J، Fraughton C، Llamosas E، Cevik S، Bex C، Lamesch P، Sikorski RS، Vandenhaute J، Zoghbi HY، Smolyar A، Bosak S، Sequerra R، Doucette-Stamm L، Cusick ME، Hill DE، Roth FP، Vidal M (2005). Towards a proteome-scale map of the human protein-protein interaction network.. Nature. 437 (7062): 1173-8. PMID 16189514. doi:10.1038/nature04209. ...
Mass spectrometry is a powerful analytical technique that can accurately measure the molecular masses of individual biomolecules, including peptides, proteins, and large intact protein assemblies. Chaits lab specializes in the development of mass spectrometers and other tools and methods for investigating a variety of biological and biochemical phenomena. Knowledge of the makeup, structure, and dynamics of protein assemblies is key to understanding many cellular processes. The Chait lab devises new tools, including those based on quantitative mass spectrometry, to identify and study the protein interactions within these assemblies. Another primary goal of the lab is to derive a functional definition of cellular protein assemblies.. The lab has recently developed potent approaches for elucidating proximal, distal, and transient protein-protein interactions in cellular milieus, and for determining distance restraints between amino-acid residues within large protein assemblies by chemical ...
Sandrock, TM, ODell, J L and Adams, A E M (1997) Allele-specific suppression by formation of new protein-protein interactions. Genetics, 147 (4). pp. 1635-42. Full text not available from this repository ...
Sigma-Aldrich offers abstracts and full-text articles by [D Trisciuoglio, M Desideri, V Farini, T De Luca, M Di Martile, M G Tupone, A Urbani, S DAguanno, D Del Bufalo].
To understand living cells one must study them as systems rather than as a collection of individual molecules. The abstract representation of intracellular systems as networks is fruitful, because it provides the ability to study these systems as a whole by ignoring details of individual components, but retaining the complexity of the interactions. This chapter will review the discoveries made through application of approaches from the science of complex networks to Protein Interaction Networks, i.e. undirected networks in which the nodes represent proteins, and pairs are connected by edges if the proteins physically interact. Over the last decade the experimental techniques for measuring protein interactions has been highly improved and large numbers of new protein interactions have been elucidated. Therefore, along with the reviewed concepts and discoveries, we provide a re-evaluation of several previous conclusions by analyzing a set of high quality networks from the organism S. ...
The study of cytosolic protein complexes, calledsystems or functional proteomics, is complicated by the challenges associated with purifying unadulterated, functional complexes, and with developing analytical methods for studying protein structure that can accommodate high molecular masses, or weak and transient protein-protein interactions
Signal transmission progresses via a series of transient protein-protein interactions and protein movements, which require diffusion within a cell packed with different molecules. Yeast Hog1, the effector protein kinase of the High Osmolarity Glycerol pathway, translocates transiently from the cytosol to the nucleus during adaptation to high external osmolarity. We followed the dynamics of osmostress-induced cell volume loss and Hog1 nuclear accumulation upon exposure of cells to different NaCl concentrations. While Hog1 nuclear accumulation peaked within five minutes following mild osmotic shock it was delayed up to six-fold under severe stress. The timing of Hog1 nuclear accumulation correlated with the degree of cell volume loss and the cells capacity to recover. Also the nuclear translocation of Msn2, the transcription factor of the general stress response pathway, is delayed upon severe osmotic stress suggesting a general phenomenon. We show by direct measurements that the general diffusion rate of
MedAI, provides customers with professional prediction of protein-protein interaction solutions according to their detailed requirements.
The yeast Saccharomyces cerevisiae is the model organism in which protein interactions have been most extensively analyzed. The vast majority of these interactions have been characterized by a variety of sophisticated high-throughput techniques probing different aspects of protein association. This chapter summarizes the major techniques, highlights their complementary nature, discusses the data they produce, and highlights some of the biases from which they suffer. A main focus is the key role played by computational methods for processing, analyzing, and validating the large body of noisy data produced by the experimental procedures. It also describes how computational methods are used to extend the coverage and reliability of protein interaction data by integrating information from heterogeneous sources and reviews the current status of literature-curated data on yeast protein interactions stored in specialized databases.. ...
In a differential gene experiment, a cell perturbation can be measured on a microarray before and after the perturbation. The information from these microarrays can then be used to inference genetic pathways and protein-protein interaction networks. In this paper we reverse this idea somewhat and measure a cell perturbation through microarrays and then rely on a protein interaction map to assess which proteins are most likely influenced by the specific perturbation. This in turn helps to elucidate the functional effect the perturbation has on the cell system. The first part of the paper focuses on the propagation model we developed to obtain this information. The second part of the paper reports on a specific experiment that was driven by the interpretation we obtained through such a gene influence network. We applied a PC12 cell line that allows doxocyclin-dependent expression of constitutive active mitogen-activated protein kinase-activated protein kinase (MAPKAPK5 or MK5) to compare the
Within the cell, biosynthetic pathways are embedded in protein-protein interaction networks. In Arabidopsis, the biosynthetic pathways of aliphatic and indole glucosinolate defense compounds are well-characterized. However, little is known about the spatial orchestration of these enzymes and their interplay with the cellular environment. To address these aspects, we applied two complementary, untargeted approaches - split-ubiquitin yeast 2-hybrid and co-immunoprecipitation screens - to identify proteins interacting with CYP83A1 and CYP83B1, two homologous enzymes specific for aliphatic and indole glucosinolate biosynthesis, respectively. Our analyses reveal distinct functional networks with substantial interconnection among the identified interactors for both pathway-specific markers, and add to our knowledge about how biochemical pathways are connected to cellular processes. Specifically, a group of protein interactors involved in cell death and the hypersensitive response provides a potential link
Genetics and biochemistry have been used to map many of the individual pathways that establish and maintain cell polarity in yeast, but Drees et al. (page 549) have now produced the equivalent of an aerial photograph of these processes. Using a high-throughput yeast two-hybrid screen, the authors assayed the universe of likely protein-protein interactions involved in cell polarity development. The resulting protein interaction map provides tantalizing insights and identifies dozens of potential mechanistic connections worth closer examination.. The authors used 68 yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases as baits in parallel two-hybrid screens covering ∼90% of the predicted Saccharomyces cerevisiae ORFs. The screen uncovered 128 novel protein-protein interactions, including 44 involving previously uncharacterized proteins. The appearance of known interactions in the screen, along with subcellular localization studies, ...
TY - JOUR. T1 - Protein interaction networks revealed by proteome coevolution. AU - Cong, Qian. AU - Anishchenko, Ivan. AU - Ovchinnikov, Sergey. AU - Baker, David. N1 - Funding Information: This project has been funded in part with Washington Research Foundation, National Institute of General Medical Sciences (grant no. R01-GM092802-07), National Institute of Allergy and Infectious Diseases (contract no. HHSN272201700059C), and Office of the Director of the National Institutes of Health (grant no. DP5OD026389). This research used resources of the National Energy Research Scientific Computing Center (contract no. DE-AC02-05CH11231).. PY - 2019. Y1 - 2019. N2 - Residue-residue coevolution has been observed across a number of protein-protein interfaces, but the extent of residue coevolution between protein families on the whole-proteome scale has not been systematically studied. We investigate coevolution between 5.4 million pairs of proteins in Escherichia coli and between 3.9 millions pairs in ...
mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate the interactome. menthas approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli ...
Although protein-peptide interactions are estimated to constitute up to 40% of all protein interactions, relatively little information is available for the structural details of these interactions. Peptide-mediated interactions are a prime target for drug design because they are predominantly present in signaling and regulatory networks. A reliable data set of nonredundant protein-peptide complexes is indispensable as a basis for modeling and design, but current data sets for protein-peptide interactions are often biased towards specific types of interactions or are limited to interactions with small ligands. In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. The final ...
virus mentha archives evidence about viral interactions collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. virus mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate the interactome. virus menthas approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching ...
The primary constituent of the amyloid plaque, beta-amyloid (Abeta), is thought to be the causal toxic moiety of Alzheimers disease. However, despite much work focused on both Abeta and its parent protein, amyloid precursor protein (APP), the functional roles of APP and its cleavage products remain to be fully elucidated. Protein-protein interaction networks can provide insight into protein function, however, high-throughput data often report false positives and are in frequent disagreement with low-throughput experiments. Moreover, the complexity of the CNS is likely to be under represented in such databases. Therefore, we curated the published work characterizing both APP and Abeta to create a protein interaction network of APP and its proteolytic cleavage products, with annotation, where possible, to the level of APP binding domain and isoform. This is the first time that an interactome has been refined to domain level, essential for the interpretation of APP due to the presence of ...
Looking for online definition of Reduced expression in cancer protein in the Medical Dictionary? Reduced expression in cancer protein explanation free. What is Reduced expression in cancer protein? Meaning of Reduced expression in cancer protein medical term. What does Reduced expression in cancer protein mean?
We have mapped SARS CoV-2 human Protein-Protein Interactions from A SARS-CoV-2 protein interaction map reveals targets for drug repurposing human drug target interacted with SARS CoV-2 are highlighted in black arrow. ...
Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine the reason for the low overlap. Low overlap can arise from either …
CTD curates specific chemical-gene and -protein interactions in vertebrates and invertebrates from published references. You may search for specific types of interactions by selecting a term or terms in this field. Each interaction has a degree and type as defined below. Degree. Each chemical-gene interaction is qualified by a degree: increases, decreases, affects, or does not affect (e.g., Chemical X increases expression of Gene Y mRNA). The affects degree is used when the reference does not describe a more specific degree. Interactions having the does not affect degree are excluded from our public data. An interaction type must be selected in order to filter by degree(s). At least one degree must be checked. Type. To select or deselect multiple interaction types, hold the Ctrl key (PC) or ⌘/Open-Apple/Command key (Mac) while clicking. Interaction types are searched in this hierarchy: ...
Some 30 years after its discovery, phage display remains one of the most widely used methods of in vitro selection. Initially developed to revolutionize the generation of therapeutic antibodies, phage display is now the first choice for screening artificial binding proteins. Artificial binding proteins can be used as reagents to study protein-protein interactions, target posttranslational modifications, and distinguish between homologous proteins. They can also be used as research and affinity reagents, for diagnostic purposes, and as therapeutics. However, the ability to identify isoform-specific reagents remains highly challenging. We describe an adapted phage display protocol using an artificial binding protein (Affimer) for the selection of isoform-selective binding proteins. ...
Proteome is a complement of proteins expressed in a cell at given time and proteomics means global analysis of this protein complement. Proteomics investigates the global changes of proteins in cells and tissues in response to a stimulus (for example temperature change, drug or nutrient treatment, or growth phase). It also studies protein-protein interactions. Proteomics came into prominence after 1997 and quickly became a popular research avenue, holding much greater importance than scientists initially suspected. The main reason for this is the fact that based on the genomic sequence it is impossible to predict how the gene products (proteins) are going to behave. Proteins are regulated at the level of protein translation, subsequently they can be modified by addition of various molecules (sugar, for example). Proteins can have varying half-lives, and their intracellular distribution can be predicted only with limited certainty.. ...
Background Schizophrenia (SZ) is a heritable, complex mental disorder. We have seen limited success in finding causal genes for schizophrenia from numerous conventional studies. Protein interaction network and pathway-based analysis may provide us an alternative and effective approach to investigating the molecular mechanisms of schizophrenia. Methodology/Principal Findings We selected a list of schizophrenia candidate genes (SZGenes) using a multi-dimensional evidence-based approach. The global network properties of proteins encoded by these SZGenes were explored in the context of the human protein interactome while local network properties were investigated by comparing SZ-specific and cancer-specific networks that were extracted from the human interactome. Relative to cancer genes, we observed that SZGenes tend to have an intermediate degree and an intermediate efficiency on a perturbation spreading throughout the human interactome. This suggested that schizophrenia might have different pathological
Video articles in JoVE about g2 phase include Cell Cycle Analysis in the C. elegans Germline with the Thymidine Analog EdU, Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols, Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM), Analysis of Combinatorial miRNA Treatments to Regulate Cell Cycle and Angiogenesis.
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the NEFL protein, and the other against the APP protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0062) - Products - Abnova
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the HGF protein, and the other against the MET protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0046) - Products - Abnova
Wiki-Pi: a web resource for human protein-protein interactions. It shows genes and PPIs with information about pathways, protein-protein interactions (PPIs), Gene Ontology (GO) annotations including cellular localization, molecular function and biological process, drugs, diseases, genome-wide association studies (GWAS), GO enrichments, PDB ID, Uniprot ID, HPRD ID, and word cloud from pubmed abstracts.
Wiki-Pi: a web resource for human protein-protein interactions. It shows genes and PPIs with information about pathways, protein-protein interactions (PPIs), Gene Ontology (GO) annotations including cellular localization, molecular function and biological process, drugs, diseases, genome-wide association studies (GWAS), GO enrichments, PDB ID, Uniprot ID, HPRD ID, and word cloud from pubmed abstracts.
Significance Analysis of INTeractome (SAINT) is a software package for scoring protein‐protein interactions based on label‐free quantitative proteomics data (e
BRIEF DESCRIPTION:. The PhD student post will be part of an interdisciplinary team working on the quantitative and systems analysis of signaling networks in colon cancer. This study is funded through Science Foundation Ireland (SFI). The project will investigate how signalling and protein interaction networks are context-specific quantitatively modulated in (patho)physiologically-relevant primary cells and in vivo-like 3D model systems. Specifically, we will study how protein interactions control cellular phenotypes by investigating (i) how they generate cell type specific vs. general functions; (ii) how pathogenic mutations affect these interactions and downstream signalling; and (iii) how signal flow changes can be validated by generating mutations that rewire networks in a designed fashion.. The student will gain valuable knowledge in the analysis of signal transduction networks in colon cancer, protein analysis techniques, and standard methods used in molecular and cell biology. The student ...
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular ...
The superiority of KNN over KM is not surprising. With KNN, a protein of interest is clustered with the top K most signature-similar proteins in the network. With KM, a protein of interest is clustered with a signature-closest centre protein, i.e. with the centre protein having the highest signature similarity with it (see §3). However, the signature-closest centre protein is not necessarily the most signature-similar protein in the network. Additionally, KNN allows for overlap between clusters, whereas KM does not. Thus, with KNN, known cancer genes can be positioned in multiple clusters, and therefore the number of possible clusters that are significantly enriched with cancer genes might be higher for KNN than for KM. Additionally, proteins perform the function or participate in a disease by interacting with other proteins within a functional module, but also with proteins across modules. Thus, it might be biologically relevant to allow for the overlap between clusters. The better performance ...
Creative Biolabs offers high-throughput X-ray crystallography or Protein crystallography services for protein-protein interaction assays.
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Understanding the underlying architecture of gene regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics as it can provide insights in disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs, which are small subgraphs of specific types and appear more abundantly in GRNs than in other randomized networks. In fact, such motifs are considered to be the building blocks of GRNs (and other complex networks) and they help achieve the underlying robustness demonstrated by most biological networks. The goal of this thesis is to design biological network (specifically, GRN) growing models. As the motif distribution in networks grown using preferential attachment based algorithms do not match that of the GRNs seen in model organisms like E. coli and yeast, we hypothesize that such models at a single node level may not properly reproduce the observed degree and motif distributions of
Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, OConnor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931 ...
TY - JOUR. T1 - Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle. AU - Wang, Haiying. AU - Zheng, Huiru. PY - 2014/12/4. Y1 - 2014/12/4. N2 - The organization of global protein interaction networks (PINs) has been extensively studied and heatedly debated. We revisited this issue in the context of the analysis of dynamic organization of a PIN in the yeast cell cycle. Statistically significant bimodality was observed when analyzing the distribution of the differences in expression peak between periodically expressed partners. A close look at their behavior revealed that date and party hubs derived from this analysis have some distinct features. There are no significant differences between them in terms of protein essentiality, expression correlation and semantic similarity derived from Gene Ontology (GO) biological process hierarchy. However, date hubs exhibit significantly greater values than party hubs in terms of semantic similarity ...
Modules that switch protein-protein interactions on and off are important to develop artificial biology; for instance, to assemble orthogonal signaling pathways, to manage synthetic protein constructions dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system {couples} nucleotide-dependent switching of MinD dimerization to membrane targeting to set off spatiotemporal sample formation. Here …. De novo design of a reversible phosphorylation-dependent switch for membrane targeting Read More ». ...
A challenge for biomedical scientists today is to arrive at an understanding of cellular behavior on a global scale. The advent of DNA microarrays has greatly facilitated discovery of gene expression profiles associated with different cellular states. The problem of understanding cellular signaling at the level of the interacting proteins is in some ways more challenging. Ashman et al. discuss the current methods available for studying protein interactions on a global scale, as well as directions for the future. Technical hurdles exist at many stages, from the isolation of protein complexes, to the determination of their composition, to the software and databases needed to analyze the results of large-scale, high-throughput datasets. Ashman et al. suggest that, with advances in technology and cooperation among academia and industry, a global protein interaction map that underlies cellular behavior will emerge as an essential resource for basic and applied research.. ...
The discovery of new Protein-Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. The lead peptide, CAM7117, prevents the formation of the holoenzyme assembly in vitro, slows down proliferation, induces apoptosis in cancer cells and is stable in human serum. CAM7117 could aid the development of novel CK2 inhibitors acting at the interface and help to fully understand the intracellular pathways involving CK2. Importantly, the approach adopted herein could be ...
Homopolymeric amino acids repeats (AARs), which are widespread in proteomes, have often been viewed simply as spacers between protein domains, or even as junk sequences with no obvious function but with a potential to cause harm upon expansion as in genetic diseases associated with polyglutamine or polyalanine expansions, including Huntington disease and cleidocranial dysplasia. A growing body of evidence indicates however that at least some AARs can form organized, functional protein structures and can regulate protein function. In particular, certain AARs can mediate protein-protein interactions, either through homotypic AAR-AAR contacts or through heterotypic contacts with other protein domains. It is still unclear however, whether AARs may have a generalized, proteome-wide role in shaping protein-protein interaction networks. Therefore, we have undertaken here a bioinformatics screening of the human proteome and interactome in search of quantitative evidence of such a role. We first identified the
When a cell is perturbed by external stimuli, it responds by adjusting the amount at which different types of proteins are needed. Transcriptional regulatory networks form the core of this cellular response system. However, the static wiring of these networks does not reveal which parts of the network are active under certain conditions and how perturbations are propagated through the network. For this reason there has been much interest in integrating the static network topology with gene expression data which reflect the dynamical or functional state of the network. In a pioneering paper, large changes were identified in the subnetworks of the transcriptional regulatory network of S. cerevisiae active under five different conditions [1]. In reality, the transcriptional regulatory network cannot be considered in isolation, but it is integrated with other networks such as the protein-protein interaction network [2]. In [3], a framework was developed which integrates protein-protein and ...
We have initiated an effort to exhaustively map interactions between HTLV-1 Tax and host cellular proteins. The resulting Tax interactome will have significant utility toward defining new and understanding known activities of this important viral protein. In addition, the completion of a full Tax interactome will also help shed light upon the functional consequences of these myriad Tax activities. The physical mapping process involved the affinity isolation of Tax complexes followed by sequence identification using tandem mass spectrometry. To date we have mapped 250 cellular components within this interactome. Here we present our approach to prioritizing these interactions via an in silico culling process. We first constructed an in silico Tax interactome comprised of 46 literature-confirmed protein-protein interactions. This number was then reduced to four Tax-interactions suspected to play a role in DNA damage response (Rad51, TOP1, Chk2, 53BP1). The first-neighbor and second-neighbor interactions of
Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach fo
Associate Professor of Biomedical Informatics and Intelligent Systems, University of Pittsburgh - Cited by 1,733 - Translational Bioinformatics - Networks Analysis - Machine Learning - Protein-Protein Interaction Prediction
Transcriptional regulation complexes are large, multicomponent assemblies involving proteins with various enzymatic activities, adaptor functions and DNA recognition modules. We are looking at interplay between the components of these assemblies in order to understand the structural logic of how these complexes carry out intricate biological activities.. We are studying a family of BTB-zinc finger transcriptional regulators that include proteins implicated in development and/or in cancer. In these proteins, the BTB domain is a protein-protein interaction module that recruits activator and/or corepressor complexes to promoter sites recognized by the C-terminal zinc-finger regions. Our objective is to understand and characterize the protein-protein interaction network of these proteins.. For example, we have determined crystal structures of complexes between the BTB domain of BCL6 and the minimal binding region of the SMRT, NCoR and BCoR corepressors. BCL6 is a key oncoprotein in B-cell lymphoma ...
Gopinath, S.C.B. (2009). "Mapping of RNA-protein interactions". Analytica Chimica Acta. 636 (2): 117-128. doi:10.1016/j.aca. ... It can thus be used to probe the interactions involved with the secondary structure and other binding interactions of RNA and ...
ISBN 0-8247-0562-9. Pelletier J, Sidhu S (August 2001). "Mapping protein-protein interactions with combinatorial biology ... This could involve the protein being fused to the M13 minor coat protein pIII, with the gene encoding this protein being held ... which are generated and screened by physically linking a gene encoding a protein and a copy of said protein. ... In biotechnology, combinatorial biology is the creation of a large number of compounds (usually proteins or peptides) through ...
Genomewide mapping of in vivo protein-DNA interactions. Science. 316:1497-1502. Chen X et al. 2008. Integration of external ... The first ChIA-PET was developed by Fullwood et al.. (2009) to generate a map of the interactions between chromatin bound by ... It is a genome-wide strategy for finding de novo long-range interactions between DNA elements bound by protein factors. ... ChIA-PET is an unbiased way to analyze interactions and higher-order chromatin structures because it can detect interactions ...
"Epstein-Barr virus and virus human protein interaction maps". Proceedings of the National Academy of Sciences of the United ... Protein. Protein. Protein. Protein. Protein. Protein. Protein. Protein. Protein. ncRNAs Latency I. +. -. -. -. -. -. -. -. -. ... Protein/genes[edit]. Protein/gene/antigen Stage Description EBNA-1 latent+lytic EBNA-1 protein binds to a replication origin ( ... These genes also bind the host RBP-Jκ protein. LMP-1 latent LMP-1 is a six-span transmembrane protein that is also essential ...
Protein-protein interaction Interactome data; Genetic regulatory relationships; Details of intra- and inter-specific sequence ... Genetic maps, markers and polymorphisms; The C. elegans physical map; Gene expression profiles (stage, tissue and cell) from ... The protein products of gene are created by translating the CDS sequences. Each unique protein sequence is given a unique ... Examples of the protein identifier names for each species in WormBase is given in the table, below. It is possible for two CDS ...
Although protein-protein interaction maps containing several thousand binary interactions are now available for several species ... "Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and ... such as those among proteins, also known as protein-protein interactions, PPIs; or between small molecules and proteins[1]) but ... Protein function prediction[edit]. Protein interaction networks have been used to predict the function of proteins of unknown ...
Kim, Jognhwan (2005). "Genome- wide mapping of DNA- protein interactions in eukaryotes". University of Austin Texas. "Ensembl ... than the normal human protein and is mostly conserved within its orthologous proteins. KIAA1704 has protein orthologs extending ... KIAA1704, also known as LSR7 (lipopolysaccharide-specific response protein 7), is a protein that in humans is encoded by the ... Negative Orientation Nuclear Fragile X Mental Retardation Protein Interacting Protein 1 (NUFIp1) shows RNA-binding activity ...
"Genome-Wide Mapping of in Vivo Protein-DNA Interactions". Science. 316 (5830): 1497-1502. doi:10.1126/science.1141319. Johnson ... These maps can determine the binding sites of many DNA-binding proteins like transcription factors and also chromatin ... J.D. Lieb, X. Liu, D. Botstein, P.O. Brown, Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA ... In the future, as ChIP-on-chip arrays become more and more advanced, high resolution whole genome maps of DNA-binding proteins ...
Structural consequences and effects on protein-protein interactions". The Journal of Biological Chemistry. 276 (44): 41399-406 ... Meza JE, Brzovic PS, King MC, Klevit RE (Feb 1999). "Mapping the functional domains of BRCA1. Interaction of the ring finger ... Structural consequences and effects on protein-protein interactions". The Journal of Biological Chemistry. 276 (44): 41399-406 ... protein homodimerization activity. • kinase binding. • RNA binding. • protein heterodimerization activity. • ubiquitin-protein ...
... is a technique that is used to map genome-wide interactions between small molecules and their protein targets in the ... Johnson, DS; Mortazavi, A; Myers, RM; Wold, B (Jun 8, 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). ... elicit their effects by binding specific proteins associated with the genome. Mapping the global interactions of these chemical ... assay was used to map the sites of interaction of metabolic compounds in the yeast genome, but Chem-seq is the first method to ...
Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science ... It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common ... The performance of ChIP-seq was then compared to the alternative protein-DNA interaction methods of ChIP-PCR and ChIP-chip. ... ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin ...
Johnson et al., (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science. (316); 1497-502. Kuo & Allis, (1999 ... 2009), used ChIA-PET to detect and map the chromatin interaction network mediated by estrogen receptor alpha (ER-alpha) in ... By creating ChIA-PET interactome maps for DNA-binding regulatory proteins and promoter regions, we can better identify unique ... Dry-lab portion of the workflow: PET extraction, mapping, and statistical analyses The PET tags are extracted and mapped to the ...
August 2016). "Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function". Molecular Cell. ... has been identified as a protein that specifically binds ETF and this interaction has been indicated to inactivate ETF by ... The native ETF protein contains one molecule of FAD and one molecule of AMP, respectively. First reports on the ETF protein ... This interaction triggers conformational changes and the highly mobile redox active FAD domain of ETF swings to the FAD domain ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134 ... "Molecular interaction between human tumor marker protein p150, the largest subunit of eIF3, and intermediate filament protein ... Eukaryotic translation initiation factor 3 subunit A (eIF3a) is a protein that in humans is encoded by the EIF3A gene.[5][6][7] ... protein binding. • structural molecule activity. • translation initiation factor activity. • receptor tyrosine kinase binding. ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... Interactions[edit]. MYO6 has been shown to interact with GIPC1[6][7] and DAB2.[8][9] ... protein complex. • apical part of cell. • clathrin-coated vesicle membrane. • ruffle. • cytosol. • extracellular exosome. • ... protein binding. • minus-end directed microfilament motor activity. • ADP binding. • actin binding. • nucleotide binding. • ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration". Cell. 125 (4): ... The protein encoded by this gene is a member of the keratin gene family. As a type I hair keratin, it is an acidic protein ... Keratin, type I cuticular Ha1 is a protein that in humans is encoded by the KRT31 gene. ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... GTP-dependent protein binding. • GTPase activity. • enzyme binding. • protein binding. • thioesterase binding. • protein kinase ... protein phosphorylation. • Rho protein signal transduction. • regulation of lamellipodium assembly. • Rac protein signal ... "Interaction of Nck-associated protein 1 with activated GTP-binding protein Rac". The Biochemical Journal. 322 (3): 873-8. doi: ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... This protein contains ankyrin repeats involved in protein-protein interactions. Mutations in this gene have been linked to bare ... DNA-binding protein RFXANK is a protein that in humans is encoded by the RFXANK gene.[5][6][7] ... The protein encoded by this gene, along with regulatory factor X-associated protein and regulatory factor-5, forms a complex ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3: 89. PMC 1847948 ... protein dimerization activity. • transcription factor activity, sequence-specific DNA binding. • protein complex binding. • ... "Interactions of the DNA mismatch repair proteins MLH1 and MSH2 with c-MYC and MAX". Oncogene. 22 (6): 819-25. PMID 12584560. ... protein complex. • nucleolus. • nucleus. • nuclear chromatin. Biological process. • Notch signaling pathway. • chromatin ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... Structural maintenance of chromosomes protein 2 (SMC-2) also known as chromosome-associated protein E (CAP-E) is a protein that ... Przewloka MR, Pardington PE, Yannone SM, Chen DJ, Cary RB (Feb 2003). "In vitro and in vivo interactions of DNA ligase IV with ... SMC-2 is a subunit of condensin I and II, large protein complexes involved in chromosome condensation. SMC2 has been shown to ...
"Mapping specific protein-protein interactions within the core component of the breast cell DNA synthesome". Oncol. Res. 9 (11- ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... binding proteins in human cell lysates. Identification of the human CHL12/RFCs2-5 complex as a novel PCNA-binding protein". J. ... Post SM, Tomkinson AE, Lee EY (Oct 2003). "The human checkpoint Rad protein Rad17 is chromatin-associated throughout the cell ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ... aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this ... "A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway". Nature Cell Biology. 6 (2): 97- ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134 ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... "Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture ( ... nuclear autoantigen are members of a novel family of calmodulin-binding proteins that associate with protein phosphatase 2A". J ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... Pickwell GV, Shih H, Quattrochi LC (Apr 2003). "Interaction of upstream stimulatory factor proteins with an E-box located ... "Cross-family interaction between the bHLHZip USF and bZip Fra1 proteins results in down-regulation of AP1 activity". Oncogene. ... "Cross-family interaction between the bHLHZip USF and bZip Fra1 proteins results in down-regulation of AP1 activity". Oncogene. ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... Ligatin, otherwise known as eIF2D, is a protein that in humans is encoded by the LGTN gene. This protein is not a component of ... This protein contains single PUA and SUI1 domains and these domains may function in RNA binding and translation initiation, ... This gene encodes a protein receptor that localizes phosphoglycoproteins within endosomes and at the cell periphery. This ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... Cellular nucleic acid-binding protein is a protein that in humans is encoded by the CNBP gene. The ZNF9 protein contains 7 zinc ... "Mouse cellular nucleic acid binding proteins: a highly conserved family identified by genetic mapping and sequencing". Genomics ... Lusis AJ, Rajavashisth TB, Klisak I, Heinzmann C, Mohandas T, Sparkes RS (Oct 1990). "Mapping of the gene for CNBP, a finger ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of ... In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. BRG1 works to ... "Selective interaction between the chromatin-remodeling factor BRG1 and the heterochromatin-associated protein HP1alpha". The ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. doi: ... "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome ... Serine/threonine-protein phosphatase 4 regulatory subunit 3B is an enzyme that in humans is encoded by the SMEK2 gene. SMEK2 ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... Myosin phosphatase Rho-interacting protein is an enzyme that in humans is encoded by the MPRIP gene. M-RIP has been shown to ... The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 5 (6): 355-64. doi: ... "Entrez Gene: M-RIP myosin phosphatase-Rho interacting protein". Gebbink MF, Kranenburg O, Poland M, van Horck FP, Houssa B, ...
It stays associated with the membrane through protein-protein interactions of itself and other membrane associated proteins, ... Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10. Somat. Cell Mol. Genet. March 1993, 19 (2): ... endoplasmic reticulum unfolded protein response. · protein localization to nucleus. · sterol regulatory element binding protein ... activation of signaling protein activity involved in unfolded protein response. · mitotic nuclear envelope disassembly. · ...
"Road maps of interactions or grist for theoretical development?" (PDF). Ecology. 69 (6): 1648-1654. doi:10.2307/1941141. ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... Food webs are the road-maps through Darwin's famous 'entangled bank' and have a long history in ecology. Like maps of ... Links in food webs map the feeding connections (who eats whom) in an ecological community. Food cycle is an obsolete term that ...
MN1 is a gene found on human chromosome 22, with gene map locus 22q12.3-qter.[5] Its official full name is meningioma ( ... MN1 is a transcription coregulator that enhances or represses RAR/RXR-mediated gene transcription through interaction with RAC3 ...
The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars than, ... two-dimensional maps". The Plant Journal. 57 (1): 195-205. doi:10.1111/j.1365-313X.2008.03678.x. PMID 18785998.. ... Interactions with other organismsEdit. Some insects, like Kallima inachus, mimic leaves ... further processed by chemical synthesis into more complex organic molecules such as proteins or cellulose, the basic structural ...
The channels are regulated by G protein-coupled receptors that can activate or inhibit the NALCN channels depending on the ... These characteristics show the interaction between the parafacial respiratory group and the pre-Bötzinger complex, which allows ... through cross-correlation and antidromic mapping techniques. The inhibitory connections discovered indicate their ability to ... Since NALCN sodium leak channels appear to contribute to the depolarization of neurons, their regulation by G-protein coupled ...
O'Donovan (1999). „Physical mapping of the CXC chemokine locus on human chromosome 4.". Cytogenet. Cell Genet. 84: 39-42. PMID ... cAMP-zavisna regulatorna aktivnost protein kinaza. Celularna komponenta. • ekstracelularni region. • ekstracelularni prostor. • ... Booth (2002). „The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions.". Biochemistry. 41. PMID 12173928 ... Angiolillo (1995). „Human interferon-inducible protein 10 is a potent inhibitor of angiogenesis in vivo". J. Exp. Med. 182: 155 ...
This membrane protein-related article is a stub. You can help Wikipedia by expanding it.. *v ... McLean PJ, Farb DH, Russek SJ (Aug 1995). "Mapping of the alpha 4 subunit gene (GABRA4) to human chromosome 4 defines an alpha ... "Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism". Am. J. Hum. ... Gamma-aminobutyric acid receptor subunit alpha-4 is a protein that in humans is encoded by the GABRA4 gene.[5][6] ...
ribosomal proteins. tRNAs. nicotiana tabacum. edit · image. Chloroplast DNA Interactive gene map of chloroplast DNA from ... Sandelius AS (2009). The Chloroplast: Interactions with the Environment. Springer. p. 18. ISBN 978-3-540-68696-5. .. ... Protein targeting and importEdit. See also: Protein targeting. The movement of so many chloroplast genes to the nucleus means ... A protein kinase drifting around on the outer chloroplast membrane can use ATP to add a phosphate group to the Toc34 protein, ...
GO:0001948 protein binding. • carbohydrate binding. • identical protein binding. • receptor ligand activity. • extracellular ... Bleil JD, Wassarman PM (1980). "Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae ... and maps closely to this gene.[5] ... Zona pellucida sperm-binding protein 3, also known as zona ... The protein encoded by this gene is a major structural component of the ZP and functions in primary binding and stimulation of ...
Most species are solitary when not mating,[66] though a few are known to occur in high densities and with frequent interactions ... Editing is concentrated in the nervous system and affects proteins involved in neural excitability and neuronal morphology. ... the complex motor skills of octopuses are not organised in their brain via an internal somatotopic map of its body, instead ... the proteins that guide the connections neurons make with each other. The California two-spot octopus has had its genome ...
Kurstaki Insect Control Protein". Nature Biotechnology. 7 (12): 1265-1269. doi:10.1038/nbt1289-1265.. ... Tomato as a model system: I. Genetic and physical mapping of jointless". MGG Molecular & General Genetics. 242 (6). doi:10.1007 ... "Fruit Cell Wall Proteins Help Fungus Turn Tomatoes From Ripe To Rotten". Science Daily. Jan 31, 2008. Retrieved 29 August 2010. ... Tomatoes have been used as a model in map-based cloning, where transgenic plants must be created to prove that a gene has been ...
The PAX genes give instructions for making proteins that attach themselves to certain areas of DNA.[6] This nuclear protein is ... InteractionsEdit. PAX8 has been shown to interact with NK2 homeobox 1.[16] ... Pilz AJ, Povey S, Gruss P, Abbott CM (1993). "Mapping of the human homologs of the murine paired-box-containing genes". ... These mutations can affect different functions of the protein including DNA biding, gene activation, protein stability, and ...
"Lyme Disease risk areas map". Risk of Lyme disease to Canadians. Government of Canada. 27 January 2015. Archived from the ... A hexavalent (OspA) protein subunit-based vaccine candidate VLA15 was granted fast track designation by the U.S. Food and Drug ... Host Interaction and Pathogenesis. Caister Academic Press. ISBN 978-1-904455-58-5. .. ... CDC map showing the risk of Lyme disease in the United States, particularly its concentration in the Northeast Megalopolis and ...
"Towards a proteome-scale map of the human protein-protein interaction network.". Nature. 437 (7062): 1173-8. PMID 16189514. doi ... Vallenius T، Mäkelä TP (2003). "Clik1: a novel kinase targeted to actin stress fibers by the CLP-36 PDZ-LIM protein.". J. Cell ... Wang H، Harrison-Shostak DC، Lemasters JJ، Herman B (1996). "Cloning of a rat cDNA encoding a novel LIM domain protein with ... Vallenius T، Luukko K، Mäkelä TP (2000). "CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4 ...
"Selective interactions of Kruppel-like factor 9/basic transcription element-binding protein with progesterone receptor isoforms ... "The progesterone receptor gene maps to human chromosome band 11q13, the site of the mammary oncogene int-2". Proceedings of ... protein binding. • enzyme binding. • receptor binding. • lipid binding. • RNA polymerase II transcription factor activity, ... The progesterone receptor (PR), also known as NR3C3 or nuclear receptor subfamily 3, group C, member 3, is a protein found ...
Hsu SC، Hazuka CD، Roth R، Foletti DL، Heuser J، Scheller RH (June 1998). "Subunit composition, protein interactions, and ... "A human gene similar to Drosophila melanogaster peanut maps to the DiGeorge syndrome region of 22q11". Human Genetics. 101 (1 ... "A protein interaction framework for human mRNA degradation". Genome Research. 14 (7): 1315-23. PMC 442147. . PMID 15231747. doi ... protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1". Proceedings of the National ...
"More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen" (PDF). Molecular ... Interaction with humans. Whaling. Main articles: Whaling and History of whaling. Whale Fishing: Woodcut by Thevet, Paris, 1574 ... World map showing International Whaling Commission (IWC) members in blue. Whaling decreased substantially after 1946 when, in ...
Simple genotype-phenotype map that only shows additive pleiotropy effects. G1, G2, and G3 are different genes that contribute ... The HBB gene encodes information to make the beta-globin subunit of hemoglobin, which is the protein red blood cells use to ... Foods with high levels of protein must be avoided. These include breast milk, eggs, chicken, beef, pork, fish, nuts, and other ... A special PKU formula can be obtained in order for the body to have protein.[30] ...
Antagonistic and synergistic interactions between these two vitamins have been reported, as they relate to skeletal health. ... it was thought that the sole important retinoid delivery pathway to tissues involved retinol bound to retinol-binding protein ( ... "Mawson and Mertz: a re-evaluation of their ill-fated mapping journey during the 1911-1914 Australasian Antarctic Expedition" ...
Hodgkin used advanced techniques to crystallize proteins, allowing their structures to be elucidated by X-ray crystallography, ... like most English maps at the time, the prime meridian is centred on St Paul's cathedral (a system the vestiges of which can be ...
"A structural perspective on protein-protein interactions" (PDF). Current Opinion in Structural Biology 14. Páxs. 313-324. ... Michael S. Waterman (1995). Introduction to Computational Biology: Sequences, Maps and Genomes (en inglés). CRC Press. ISBN 0- ... "Protein Engineering 7 (7). ISSN 1741-0134, Páxs. 841-848.. *↑ 70,0 70,1 Thompson, J. D.; et al. (1994). "CLUSTAL W: improving ... 2005). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (en inglés) (third edition ed.). Wiley. ISBN 0- ...
Alpha-adducin is a protein that in humans is encoded by the ADD1 gene. Adducins are a family of cytoskeleton proteins encoded ... 1993). "Cloning and mapping of the alpha-adducin gene close to D4S95 and assessment of its relationship to Huntington disease ... Mangeat PH (1989). "Interaction of biological membranes with the cytoskeletal framework of living cells". Biol. Cell. 64 (3): ... 1997). "Transcript map of the human chromosome 4p16.3 consisting of 627 cDNA clones derived from 1 Mb of the Huntington's ...
positive regulation of protein phosphorylation. • positive regulation of MAP kinase activity. • positive regulation of ... "Interaction of presenilins with the filamin family of actin-binding proteins". J. Neurosci. 18 (3): 914-22. PMC 2042137. PMID ... protein processing. • protein maturation. • myeloid dendritic cell differentiation. • autophagy. • protein glycosylation. • ... positive regulation of protein kinase activity. • T cell activation involved in immune response. • cellular protein metabolic ...
"Map: Biochemistry Free & Easy (Ahern and Rajagopal)". Biology LibreTexts. 2014-12-24. Retrieved 2017-11-02.. ... The active site is a region on an enzyme which a particular protein or substrate can bind to. The active site will only allow ... "Functional Design of Proteins". Molecular Cell Biology. 4th edition. W. H. Freeman. ...
"Analysis of murine Brca2 reveals conservation of protein-protein interactions but differences in nuclear localization signals ... "Domain mapping of the Rad51 paralog protein complexes". Nucleic Acids Res. 32 (1): 169-78. doi:10.1093/nar/gkg925. PMC 373258 ... protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2[10] and RAD52. ...
"Interaction of Sesbania Mosaic Virus Movement Protein with VPg and P10: Implication to Specificity of Genome Recognition". PLoS ... sequencing of radiochemically modified protein allows mapping of the gene on B RNA. The EMBO Journal, 3(7), 1629-1634. PMC ... The rest of the genome encodes structural proteins at the 5' end and non-structural proteins at the 3' end in a single ... The 1A, 1B, 1C, and 1D proteins are the capsid proteins VP4, VP2, VP3, and VP1, respectively.Virus-coded proteases perform the ...
Interactive pathway map[edit]. Click on genes, proteins and metabolites below to link to respective Wikipedia articles. [§ 1] ... The Calcium/Calmodulin binding to the C-terminal pre-IQ domain of the Cav1.2 channel promotes interaction between channels that ... Calcium channel, voltage-dependent, L type, alpha 1C subunit (also known as Cav1.2) is a protein that in humans is encoded by ... protein binding. • alpha-actinin binding. • voltage-gated calcium channel activity. • voltage-gated calcium channel activity ...
UNKL: encoding protein RING finger protein unkempt-like. *VAT1L: encoding protein Vesicle amine transport protein 1 homolog (T ... Gilbert F (1999). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 16". Genet Test. 3 (2): 243-54. ... LINC00273 encoding protein Long intergenic non-protein coding RNA 273. *LOC124220: encoding protein Zymogen granule protein 16 ... SHCBP1: encoding protein SHC SH2 domain-binding protein 1. *SLZ1: encoding protein SLX1 structure-specific endonuclease subunit ...
... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... "Genomic maps and comparative analysis of histone modifications in human and mouse". Cell. 120 (2): 169-81. doi:10.1016/j.cell. ... Histones undergo posttranslational modifications that alter their interaction with DNA and nuclear proteins. The H3 and H4 ... Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a ...
Important information on protein synthesis, ligand binding and RNA interaction can be obtained using this novel technique at ... Various software programs are available that allow viewing the 3D maps. These often enable the user to manually dock in protein ... This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell. Fatty acid synthase ... Proteins in vitreous ice usually adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic ...
A comprehensive mapping of interactions among Epstein-Barr virus (EBV) proteins and interactions of EBV proteins with human ... a more detailed mapping of their interactions with core herpesvirus proteins, other gamma-specific proteins, and human proteins ... proteome-scale mapping of EBV-EBV and EBV-human direct protein-protein interactions. Such maps represent a rich source of ... Map of the EBV Interactome Network.. To map interactions among EBV proteins, a library or ORFeome of 80 full and 107 partial ...
To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin ... In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. ... However, the protein has eight zinc fingers in its DNA binding domain, and other C2H2 zinc finger proteins such as Zif268 bind ... of which about half mapped to single sites in the human genome (table S1). Sequence reads that map to multiple sites in the ...
This image represents a zoomed region of the Yeast Protein Interaction Map in 3D (VRML) ...
Researchers have produced a detailed map that outlines thousands of physical interactions that take place between proteins ... Researchers have produced a detailed map that outlines thousands of physical interactions that take place between proteins ... From these assays, the scientists identified 2,846 protein-protein interactions, most of which included a protein whose ... Thus, mapping the multitude of interactions among proteins is likely to lead to new insights about drug targets or ...
... to map protein-gene interactions involved in Alzheimers disease. ... Researchers Map Protein-Gene Interactions Involved in Alzheimers Disease By doing so, UC San Diego scientists hope to create a ... Home / Newsroom / Releases / Researchers Map Protein-Gene Interactions Involved in Alzheimers Disease ... The new study combined analyses of gene perturbations and protein interactions, said senior author Robert Rissman, PhD, ...
... data analysis and protein structure modeling. Over the past three years, we have developed tailored experimental methods for ... mass spectrometry and modeling method called MS3D to the structure determination of the rhodopsin-transducin membrane protein ... all steps in the MS3D method for rhodopsin, including protein purification, a functional assay, cross-linking, proteolysis and ... complex (RTC). Herein we describe experimental progress made to adapt the MS3D approach for characterizing membrane protein ...
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Global views of the protein-interaction map. Two global views of protein interaction network are illustrated: a protein class/ ... Confidence scores for protein-protein interactions (A) Drosophila protein-protein interactions have been binned according to ... Global views of the protein-interaction map. (A) Protein family/human disease ortholog view. Proteins are color-coded according ... Statistical properties of the refined Drosophila interaction map. The high-confidence Drosophila protein-protein interactions ...
The study has identified over 2,300 protein interactions. The full dataset and the resulting protein interaction map can be ... By assigning specific functions to cancer-related proteins, this protein-protein interaction map constitutes a first step ... A protein interaction map for a better insight in cancer development. 01.03.2005 ... The number of interactions between proteins is thought to be huge. Exploration of these complex protein networks requires ...
Drug Interaction Knowledge Base Ontology LOOM http://www.biopax.org/release/biopax-level3.owl#Protein Drug Interaction ... http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#protein Protein-ligand interaction ontology LOOM ... Create New Mapping Delete. Mapping To. Ontology. Source. http://www.bioassayontology.org/bao#BAO_0000175 BioAssay Ontology LOOM ... http://psink.de/scio/Protein Spinal Cord Injury Ontology LOOM http://purl.obolibrary.org/obo/MI_0326 Molecular Interactions ...
The interaction networks presented here provide a set of hypothesis for further experimental investigation into the DENV life ... Dengue virus manipulates cellular processes to its advantage through specific interactions with the hosts protein interaction ... Mapping protein interactions between Dengue virus and its human and insect hosts PLoS Negl Trop Dis. 2011 Feb 15;5(2):e954. doi ... Protein-protein interactions between the virus and its host are one avenue through which dengue can connect and exploit these ...
Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 ... Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) by J F Rual, K Venkatesan, T ... In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction ... In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction ...
The fraction of interactions detected in independent screens can be very small, and an outstanding challenge is to determine ... Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. ... Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps PLoS Comput Biol. 2007 Nov ... Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. The fraction of ...
Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus. Jiangwei Song, ... Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus ... Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus ... Mapping the Nonstructural Protein Interaction Network of Porcine Reproductive and Respiratory Syndrome Virus ...
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all ... Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all ... Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all ... Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all ...
Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase ... Ste5p, a protein of unknown biochemical function, interacted with protein kinases that operate at each step of the MAP kinase ... We have used the two-hybrid system of Fields and Song to identify protein-protein interactions that occur in the pheromone ... All of the interactions we detected involved at least one member of the MAP kinase cascade that is a central element of the ...
Further investigation of these predicted protein-protein interactions should provide targets to combat the clinical ... In this work, we used a computational method based on protein structures to predict interactions between DENV and its human and ... proteins encoded by DENV must interact with and alter the behavior of protein networks in both of these hosts. ... We predict numerous interactions, with many involved in known cell death, stress, and immune system pathways. ...
C-reactive protein. AAIM. antibody-array interaction mapping. KNG. kininogen. SAP. serum amyloid P component. Bis-Tris. 2-[bis( ... Antibody-Array Interaction Mapping, a New Method to Detect Protein Complexes Applied to the Discovery and Study of Serum ... Antibody-Array Interaction Mapping, a New Method to Detect Protein Complexes Applied to the Discovery and Study of Serum ... Antibody-Array Interaction Mapping, a New Method to Detect Protein Complexes Applied to the Discovery and Study of Serum ...
... chemical shift mapping and 15N NMR relaxation studies. ... Interactions of human nucleotide excision repair protein XPA ... INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION ... Pre-calculated protein structure alignments at the RCSB PDB website. Bioinformatics 26: 2983-2985 ...
Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR ... INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION ... 3D Interactions. ZN. Query on ZN. Download Ideal Coordinates CCD File Download Instance Coordinates *SDF format, chain B [auth ... NUCLEOTIDE EXCISION REPAIR PROTEIN XPA (XPA-MBD). A. 111. Homo sapiens. Mutation(s): 0 Gene Names: XPA, XPAC. ...
Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase ... Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase ... Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase ... Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase ...
Studies into interactions between MAP kinase and MAP kinase kinase proteins of Arabidopsis ... In this study, the yeast two -hybrid system was used to identify protein-protein interactions between all Arabidopsis MAPKs and ... The Arabidopsis thaliana genome contains genes encoding 10 MAP kinase kinase (MKK) and 20 Map kinase (MAPK) proteins, however ... the result from the qualitative β-galactosidase filter assay showed that 6 MAPK proteins interacted with 6 MKK proteins. ...
Self-Association and Mapping of the Interaction Domain of Hepatitis E Virus ORF3 Protein. Shweta Tyagi, Shahid Jameel, Sunil K ... Self-Association and Mapping of the Interaction Domain of Hepatitis E Virus ORF3 Protein ... Self-Association and Mapping of the Interaction Domain of Hepatitis E Virus ORF3 Protein ... Self-Association and Mapping of the Interaction Domain of Hepatitis E Virus ORF3 Protein ...
Coupled with next generation sequencing, ChIP-seq experiments map protein-DNA... ... is the most widely used method to analyze protein-DNA interactions in vivo. ... Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502 ... Xu C., Corces V.G. (2018) Genome-Wide Mapping of Protein-DNA Interactions on Nascent Chromatin. In: Vavouri T., Peinado M. (eds ...
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. Kate Sokolina, Saranya Kittanakom, Jamie ... Moonlighting proteins and proteinprotein interactions as neurotherapeutic targets in the G protein‐coupled receptor field. ... Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I (2015) Fundamentals of protein interaction network mapping. Mol ... Hamdan FF, Percherancier Y, Breton B, Bouvier M (2006) Monitoring proteinprotein interactions in living cells by ...
This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial ... of human mitochondrial RNA and thereby identify specific regions within mitochondrial transcripts that are bound by proteins. ... Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting. Abstract. Human mitochondrial DNA is ... This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial ...
We detected 1,814 reproducible interactions among 488 proteins. The map includes a large number of novel interactions with ... Informative regions of the map could be highlighted by searching for paralogous interactions and by clustering proteins on the ... The substantial number of new interactions discovered here supports the conclusion that previous interaction mapping studies ... a Gal4-based two-hybrid system was used recently to detect over 20,000 interactions among Drosophila proteins. Although these ...
Cell‐based protein-protein interaction assay. The full‐length cDNA of yellow fluorescent protein (YFP) was split at position ... Protein-protein interactions influence all aspects of cellular life and the most direct mechanism through which proteins can ... based on direct physical interaction resulted in low number of hits. Thus, it is likely that a protein-protein interaction‐ ... Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. András Zeke, ...
... we generated the protein-protein interaction maps on EGFR (48). The analysis of protein interaction maps revealed some proteins ... The protein-protein interaction maps of nuclear EGFR and membrane EGFR in Human. The maps were generated by the SRTING 10.0a ( ... The protein structures predicate the driving force of NLS in protein-protein interactions during evolution. Protein structures ... Protein-protein interaction maps of nEGFR and membrane EGFR in different species revealed several proteins being involved in ...
We are the leaders of Accurate Protein Interactions Analysis by Mass Spec. ... CovalX is a global company offering leading products and services for Epitope Mapping by both Crosslinking Mass Spectrometry ... Using MALDI-TOF MS coupled with a high-mass detector to directly analyze intact proteins in thyroid tissues. Sci China ... Wiley, Journal of Molecular Recognition, June 2018. CovalXs MALDI technology used to analyze the proteins, page 5, item 2.12. ...
  • Such systematically derived protein-protein interaction or "interactome" maps could be combined with other gene-level biological information to formulate hypotheses about specific roles of EBV proteins of various functional and evolutionary classes and reveal more global properties of EBV and EBV-human interactomes. (pnas.org)
  • Specific hypotheses about the role of EBV and human protein interactions should emerge by correlating an unbiased EBV interactome data set with available functional annotations. (pnas.org)
  • Over the past three years, we have developed tailored experimental methods for all steps in the MS3D method for rhodopsin, including protein purification, a functional assay, cross-linking, proteolysis and mass spectrometry. (unt.edu)
  • Protein-protein interactions play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough understanding of the cell. (pnas.org)
  • It is well recognized that protein-protein interactions play key roles in structural and functional organization of the cell. (pnas.org)
  • Hence increasing attention is being paid to protein-protein interactions in both structural and functional studies. (pnas.org)
  • Therefore, the study of protein-protein interactions is one of the most important issues in functional genomics. (pnas.org)
  • We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein-protein interactions for their validation in vitro and in cell‐based assays. (embopress.org)
  • Integrating Gene and Protein Expression Reveals Perturbed Functional Networks in Alzheimer's Disease. (mindzilla.com)
  • We probe kinase identity by asking whether we can use recruitment interactions to force other MAPKK catalytic domains to play the functional role of the mating MAPKK, Ste7. (escholarship.org)
  • These results indicate recruitment interactions can play a dominant role in defining functional identity within a family, and is consistent with a model in which new kinase functions can arise through recombination of existing catalytic domains with new interaction modules. (escholarship.org)
  • Altogether, these results indicate that although recruitment interactions can be utilized as a powerful tool to alter functional identity, evolution may have always insured pathway fidelity in some instances through the intrinsic contributions of kinase catalytic domains. (escholarship.org)
  • The lambda protein network connects 12 proteins of unknown function with well characterized proteins, which should shed light on the functional associations of these uncharacterized proteins. (vcu.edu)
  • Proteins interact to form functional complexes that can be tricky to study. (nih.gov)
  • Intermolecular interactions in the gaseous ions of two protein-ligand complexes, a single chain antibody (scFv) and its trisaccharide ligand (α-D-Galp-(1→2)-[α-D-Abep-(1→3)]-α-Manp-OCH3, L1) and streptavidin homotetramer (S4) and biotin (B), were investigated using a collision-induced dissociation (CID)-functional group replacement (FGR) strategy. (ualberta.ca)
  • Intermolecular interactions were identified from decreases in the collision energy required to dissociate 50 % of the reactant ion (Ec50) upon modification of protein residues or ligand functional groups. (ualberta.ca)
  • Nav1.7, known to regulate opioid receptor efficacy, interacts with the G protein-regulated inducer of neurite outgrowth (Gprin1), an opioid receptor-binding protein, demonstrating a physical and functional link between Nav1.7 and opioid signalling. (ox.ac.uk)
  • The absence-of-interference approach will allow high-throughput mapping of protein interaction sites suitable for functional studies and protein docking. (cf.ac.uk)
  • The significant enrichment of RBP sites across some lncRNA classes is suggestive that these interactions might be important in understanding the functional role of lncRNA. (frontiersin.org)
  • The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. (cshl.edu)
  • Functional experiments showed that this interaction has the capacity to render GATA-dependent transcription responsive to treatment with a combination of all- trans retinoic acid and the histone deacetylase inhibitor trichostatin A (TSA). (bloodjournal.org)
  • At the 60th Experimental Nuclear Magnetic Resonance Conference (ENC, www.enc-conference.org ), Bruker announced today a breakthrough in ultra-high field high-resolution NMR spectroscopy applied to structural biology and the study of functional intrinsically disordered proteins. (news-medical.net)
  • Here, a method for rapid in vivo functional analysis of engineered proteins was developed using Physcomitrella patens. (osti.gov)
  • The assay distinguished mutations that generate fully functional, nonfunctional, and partially functional proteins. (osti.gov)
  • article{osti_1345832, title = {A complementation assay for in vivo protein structure/function analysis in Physcomitrella patens (Funariaceae)}, author = {Scavuzzo-Duggan, Tess R. and Chaves, Arielle M. and Roberts, Alison W.}, abstractNote = {Here, a method for rapid in vivo functional analysis of engineered proteins was developed using Physcomitrella patens. (osti.gov)
  • Identification and Functional Testing of Novel Interacting Protein Partners for the Stress Sensors Wsc1p and Mid2p of Saccharomyces cerevisiae . (nih.gov)
  • The cell is a busy place where many biological processes are regulated by physical or functional protein-protein interaction networks. (frontiersin.org)
  • Many proteins share functional properties despite vast sequence differences because of the shapes that they fold into. (wikibooks.org)
  • These results offer a roadmap for further functional characterizations of the protein factors, and for building models when testing the genetic contributions of these genes in plant growth and development. (biomedcentral.com)
  • To better understand the relationships of proteins in Arabidopsis ( Arabidopsis thaliana ), we have developed a genome-wide protein interaction network (AraPPINet) that is inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins. (plantphysiol.org)
  • abstract = "The genome exerts its functions through interactions with proteins. (elsevier.com)
  • Mapping membrane protein interactions in cell signaling systems. (unt.edu)
  • We proposed to apply a chemical cross-linking, mass spectrometry and modeling method called MS3D to the structure determination of the rhodopsin-transducin membrane protein complex (RTC). (unt.edu)
  • Herein we describe experimental progress made to adapt the MS3D approach for characterizing membrane protein systems, and computational progress in experimental design, data analysis and protein structure modeling. (unt.edu)
  • Membrane proteins have higher false-discovery rates on average, and signal transduction proteins have lower rates. (nih.gov)
  • However, despite the poor colocalization relationship in cotransfected cells, both nsp9 and nsp10 came together with membrane proteins (e.g., nsp2) at the viral replication and transcription complexes (RTC) in PRRSV-infected cells. (asm.org)
  • Thus, our results indicate the existence of a complex interaction network among PRRSV nsps and raise the possibility that the recruitment of key replicase proteins to membrane-associated nsps may involve some regulatory mechanisms during infection. (asm.org)
  • In particular, our analysis of protein-protein interaction maps reveals that nuclear EGFR (nEGFR) pathways are different from that of membrane EGFR and EGF is not found in nEGFR network, while androgen receptor (AR) is found, which suggests the evolution of prostate cancer, a well-known AR driven cancer, through changes in androgen- or EGF-dependence. (jcancer.org)
  • Structural prediction analysis indicates that NLS can compromise the differential protein binding to EGFR through stretch linkers with evolutionary mutation from N to V. In the experiment, elevation of nEGFR but not membrane EGFR was found in castration resistant prostate cancer cells. (jcancer.org)
  • Membrane Protein Complexes Obtained from Chemical Cross-Linking and High-Mass MALDI Mass Spectrometry. (covalx.com)
  • Novel NaV1.7 protein interactors including membrane-trafficking protein synaptotagmin-2 (Syt2), L-type amino acid transporter 1 (Lat1) and transmembrane P24-trafficking protein 10 (Tmed10) together with Scn3b and Crmp2 were validated by co-immunoprecipitation (Co-IP) from sensory neuron extract. (ox.ac.uk)
  • The technique was designed especially to serve as a tool for studying membrane proteins, Suchanek explained. (genomeweb.com)
  • In terms of proteins, there are the least tools for studying membrane proteins, so that's why we chose those amino acids from the beginning," Suchanek said. (genomeweb.com)
  • Commonly, micelles (spherical aggregates formed by short-chain lipids above a critical micelle concentration) or bicelles (discoidal aggregates formed by mixing short- and long-chained lipids) solubilise and stabilise membrane proteins for crystallisation and solution state Nuclear Magnetic Resonance (NMR) analysis. (mappingignorance.org)
  • The known membrane protein structures, derived mainly by crystallography, provide little insight into lipid-protein interactions as bound lipid molecules are rarely visible. (mappingignorance.org)
  • NMR spectroscopy, contrarily, does not require molecular order and lipid-protein contacts may be sampled at low resolution to gauge protein insertion into the lipid layer, e.g. by use of paramagnetic agents that perturb the NMR signals of nearby membrane protein atoms. (mappingignorance.org)
  • For instance, H/F substitution alters the charge distribution in the acyl chain, Also, interaction with membrane proteins may be affected As a drawback for NMR studies, H/F substitution reduces the 1 H density and, thus, coverage of (fluoro)lipid-protein contacts via 1 H, 1 H NOE signals. (mappingignorance.org)
  • A minimal fluorination scheme for acyl chains is derived, and it is shown that a single hydrogen-to-fluorine substitution induces a fully resolved 1 H spectrum for 4F-DHPC 7 , a representative fluorolipid, without impairing micelle formation or stabilisation of the model membrane protein pSRII. (mappingignorance.org)
  • Researchers at St. Jude Children's Research Hospital have discovered the way toxic proteins linked to the most common forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) incapacitate membrane-less organelles inside cells. (news-medical.net)
  • Slit diaphragms, considered specialized adherens junctions, contain both unique membrane proteins ( e.g ., nephrin, podocin, and Neph1) and typical adherens junction proteins ( e.g . (asnjournals.org)
  • Several integral membrane proteins, including nephrin, 7 podocin, 8 and Neph1, 9 not found in other junctions, have been identified as slit diaphragm components. (asnjournals.org)
  • Based on their derivation from typical tight junctions 2 and the fact that they are replaced by tight junctions in nephrosis, 4 , 6 we reasoned that slit diaphragms might also contain membrane proteins normally associated with tight junctions. (asnjournals.org)
  • V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. (uniprot.org)
  • In addition, our study shows that the cAMP-based two-hybrid system is particularly appropriate for analyzing molecular interactions between membrane proteins. (asm.org)
  • The majority of the Fts proteins are anchored to the cell membrane, and most of them appear to localize to the bacterial septum in a sequential order (for reviews, see references 5 , 33 , 35 , and 40 ). (asm.org)
  • In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. (sciencemag.org)
  • Such measurements are important for systems-level studies because they provide a global map of candidate gene network input connections. (sciencemag.org)
  • When malaria fragments that interact were brought together, a telltale marker gene was then triggered by the regulatory protein - detected by growth of yeast cells on a Petri plate. (hhmi.org)
  • That analysis revealed groups of proteins implicated in processes such as chromosome modification and gene activation, as well as those involved in invading host cells. (hhmi.org)
  • Their findings suggest that integrating protein interactions with gene perturbations can generate a comprehensive framework for characterizing alterations in the molecular network related to AD. (ucsd.edu)
  • With the completion of the genome sequence of a number of organisms, analysis of the gene products, the proteins, is the on-going challenge. (innovations-report.com)
  • What we do know is that a single gene can contain information to build different 'forms' of a protein. (innovations-report.com)
  • This approach provides a range of insights into the contribution of RNA-binding proteins to the regulation of mitochondrial gene expression. (garvan.org.au)
  • The bacteriophage T4 59 protein (gp59) plays a vital role in recombination and replication by promoting the assembly of the gene 41 helicase (gp41) onto DNA, thus enabling replication as well as strand exchange in recombination. (elsevier.com)
  • Mapping protein interactions of sodium channel NaV1.7 using epitope-tagged gene-targeted mice. (ox.ac.uk)
  • Protein-protein interactions (PPIs) play essential roles in almost all cellular processes, including gene regulation, metabolic control, signal transduction, and cell communication. (indianaheadlines.com)
  • Moreover, Omega [a ParB-like protein which has a Ribbon-Helix-Helix (RHH) structure] recognizes multiple centromeric sequences located in the promoters of δ , ω and copS (copy-number control gene). (microbiologyresearch.org)
  • We cloned the fl3 gene and determined that it encodes a PLATZ (plant AT-rich sequence and zinc binding) protein. (plantcell.org)
  • To investigate the role of cellular proteins interacting with nsP2, gene silencing experiments were performed in cells infected by a recombinant CHIKV expressing Renilla luciferase as a reporter. (pasteur.fr)
  • In the initial stages of the project, members of Ecker's lab led by research technician Mary Galli converted most of their accumulated library of Arabidopsis protein-coding gene clones into a form useful for protein-interaction tests. (thefreedictionary.com)
  • Recently, it has been shown that signalingentropy, an overall measure of signaling pathway promiscuity and computable fromintegrating a sample's gene expression profile with a protein interactionnetwork, correlates with phenotypic plasticity and is increased in cancer comparedto normal tissue. (nature.com)
  • We demonstrate that the increasedsignaling entropy of cancer is driven by two factors: (i) the scale-free (or nearscale-free) topology of the interaction network and (ii) a subtle positivecorrelation between differential gene expression and node connectivity. (nature.com)
  • Signalling entropyis computed from integrating a sample's genome-wide gene expression profilewith a protein interaction network and, as shown by us, provides a surprisingly goodestimate of a sample's height in Waddingtons's differentiationlandscape, with human embryonic stem cells (hESCs) exhibiting the highest levels ofentropy 10 . (nature.com)
  • p>Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors. (uniprot.org)
  • Here we report a comprehensive pairwise protein-protein interaction mapping and gene expression profiling of the mRNA polyadenylation protein machinery in Arabidopsis. (biomedcentral.com)
  • To aid these comparisons, a coordinate re-mapping program and data are available from: http://wiki.wormbase.org/index.php/Converting_Coordinates_between_releases All the gene-sets of the WormBase species were initially generated by gene prediction programs. (wikipedia.org)
  • This gene encodes a member of the DEAD box protein family. (wikipedia.org)
  • Alpha-sarcoglycan is a protein that in humans is encoded by the SGCA gene. (wikipedia.org)
  • Synthesis of the viral RNA is directed by replication/transcription complexes (RTC) that are mainly composed of a network of PRRSV nonstructural proteins (nsps) and likely cellular proteins. (asm.org)
  • Protein-protein interactions are fundamentally important in biological processes, but the existing analytical tools have limited ability to sensitively and precisely measure the dynamic composition of protein complexes in biological samples. (mcponline.org)
  • These results demonstrate a versatile platform for measuring the dynamic composition of protein complexes in biological samples that should have value for studies of normal and disease-related signaling networks, multiprotein clusters, or enzymatic cascades. (mcponline.org)
  • The principle of the methodology consists in covalently binding DNA-bound proteins by chemical process, fragmenting chromatin, isolating DNA-protein complexes by immunoprecipitation in the presence of the antibody of interest. (france-genomique.org)
  • Taken together, these results suggest that the CID-FGR method, as implemented here, does not represent a reliable approach for identifying interactions in the gaseous protein-ligand complexes. (ualberta.ca)
  • Analysis of NaV1.7 complexes affinity-purified under native conditions by mass spectrometry revealed 267 proteins associated with Nav1.7 in vivo The sodium channel β3 (Scn3b), rather than the β1 subunit, complexes with Nav1.7, and we demonstrate an interaction between collapsing-response mediator protein (Crmp2) and Nav1.7, through which the analgesic drug lacosamide regulates Nav1.7 current density. (ox.ac.uk)
  • The expert contributors explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. (springer.com)
  • A protein complex assembly can result in the formation of homo-oligomeric or hetero-oligomeric complexes. (wikipedia.org)
  • In addition to the conventional complexes, as enzyme-inhibitor and antibody-antigen, interactions can also be established between domain-domain and domain-peptide. (wikipedia.org)
  • Homo-oligomers are macromolecular complexes constituted by only one type of protein subunit. (wikipedia.org)
  • EBV-EBV and EBV-human protein interaction, or "interactome" maps provided a framework for hypotheses of protein function. (pnas.org)
  • Our EBV-EBV interactome map is enriched for interactions among proteins in the same evolutionary class. (pnas.org)
  • Furthermore, human proteins targeted by EBV proteins were enriched for highly connected or "hub" proteins and for proteins with relatively short paths to all other proteins in the human interactome network. (pnas.org)
  • Indeed, interactome network maps have revealed global topological and dynamic features that relate to biological properties ( 6 ). (pnas.org)
  • Finally, if high-quality protein-DNA interactome measurements can be performed routinely and at reasonable cost, it will open the way to detailed studies of interactome dynamics in response to specific signaling stimuli or genetic mutations. (sciencemag.org)
  • Researchers created a draft map of over 1 million protein interactions-an "interactome"-across more than 100 animal species, including people. (nih.gov)
  • Recently released protein-protein interaction or "interactome" maps for multicellular organisms have helped us to start imagining how complex cellular networks are organized. (wiley.com)
  • Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein-small molecule interactome in the model yeast Saccharomyces cerevisiae. (edu.sa)
  • According to an empirical estimation of the size of the protein interactome, experimentally determined interactions represent a small fraction (approximately 6%) of the entire protein interactome, and the relationships among most proteins remain to be discovered ( Arabidopsis Interactome Mapping Consortium, 2011 ). (plantphysiol.org)
  • Interactions of EBV proteins with each other and with human proteins were assessed by using a stringent high-throughput yeast two-hybrid system. (pnas.org)
  • In searching for interactions between proteins, the scientists used a technique known as the yeast two-hybrid assay, which Fields invented. (hhmi.org)
  • Using advanced analytical systems developed by Prolexys, the researchers performed more than 32,000 yeast two-hybrid screens to identify interacting malaria proteins. (hhmi.org)
  • Yeast two-hybrid screens are an important method for mapping pairwise physical interactions between proteins. (nih.gov)
  • Here, we mapped the interaction network among PRRSV nsps by using yeast two-hybrid screening in conjunction with coimmunoprecipitation (co-IP) and cotransfection assays. (asm.org)
  • Despite the need for comprehensive studies on protein-protein interactions, no efforts for a genome-wide scale screening have ever been reported, although pioneering works using the yeast two-hybrid system ( 2 ) were reported on Drosophila cell cycle regulators ( 3 ), proteins of T7 phage ( 4 ), and yeast proteins involved in mRNA splicing ( 5 ). (pnas.org)
  • In this study, the yeast two -hybrid system was used to identify protein-protein interactions between all Arabidopsis MAPKs and MKKs. (bl.uk)
  • In the yeast two- hybrid assay, the result from the qualitative β-galactosidase filter assay showed that 6 MAPK proteins interacted with 6 MKK proteins. (bl.uk)
  • Results of interactions of ORF3 deletion mutants with full-length ORF3, in the yeast two-hybrid system. (asm.org)
  • In order to map lambda's interactions, we have cloned 68 out of 73 lambda open reading frames (the "ORFeome") into Gateway vectors and systematically tested all proteins for interactions using exhaustive array-based yeast two-hybrid screens. (vcu.edu)
  • We developed a new experimental strategy called the 'absence of interference' approach to determine surface residues involved in protein-protein interaction of established yeast two-hybrid pairs of interacting proteins. (cf.ac.uk)
  • We have used a Gateway cloning approach coupled with yeast two-hybrid, RNAi and 2D DiGE to define a protein-protein interaction network taking place in this structure. (ox.ac.uk)
  • Here we describe the extensive use of high-throughput yeast two-hybrid (HT-Y2H) assays to characterize interactions between CHIKV and human proteins. (pasteur.fr)
  • In addition, we showed that CHIKV nsP2 induces a cellular shutoff, as previously reported for other Old World alphaviruses, and determined that among binding partners identified by yeast two-hybrid methods, the tetratricopeptide repeat protein 7B (TTC7B) plays a significant role in this activity. (pasteur.fr)
  • Out of 320 pair-wise protein-protein interaction assays done using the yeast two-hybrid system, 56 (~17%) showed positive interactions. (biomedcentral.com)
  • Researchers from the Institut Curie and from the Paris-based biotechnology company Hybrigenics announced today that they have built a protein-protein interaction map of the fruit fly, Drosophila melanogaster. (innovations-report.com)
  • As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. (nature.com)
  • Furthermore, these related proteins can be part of similar or, conversely, different biological pathways and thus can convey very diverse biological functions. (innovations-report.com)
  • Protein-protein interactions between the virus and its host are one avenue through which dengue can connect and exploit these host cellular pathways and processes. (nih.gov)
  • It also should be emphasized that recent studies of protein-protein interactions, in particular, those involved in signal transduction, uncovered a number of protein-binding domains or motifs, which are evolutionarily conserved and used in various signaling pathways ( 1 ). (pnas.org)
  • Often, the signaling proteins in these pathways use shared interaction elements, both catalytic domains and protein-protein interactions. (escholarship.org)
  • Within the yeast Saccharomyces cerevisae, four distinct mitogen activated protein kinase kinases (MAPKKs) share closely related catalytic domains yet act in separate critical pathways. (escholarship.org)
  • NCS-1-D2 receptor interaction may serve to couple dopamine and calcium signaling pathways, thereby providing a critical component in the regulation of dopaminergic signaling in normal and diseased brain. (jneurosci.org)
  • The transcriptome is dramatically altered in fl3 mutants, in which the downregulated genes are primarily enriched in pathways related to translation, ribosome, misfolded protein responses, and nutrient reservoir activity. (plantcell.org)
  • Within the cell, biosynthetic pathways are embedded in protein-protein interaction networks. (frontiersin.org)
  • Within the crowded intracellular environment where proteins are constantly coming into physical contact, it is an open question how multi-enzyme pathways are orchestrated in response to developmental and exogenous cues. (frontiersin.org)
  • Additionally, how do specific pathways couple to surrounding protein-protein interaction networks within the cell? (frontiersin.org)
  • We identified a total of 24 novel interactions and found that the interactions were centered on open reading frame 1b (ORF1b)-encoded nsps that were mainly connected by the transmembrane proteins nsp2, nsp3, and nsp5. (asm.org)
  • Interestingly, the interactions of the core enzymes nsp9 and nsp10 with transmembrane proteins did not occur in a straightforward manner, as they worked in the co-IP assay but were poorly capable of finding each other within intact mammalian cells. (asm.org)
  • The major limitation is that because they are incorporated into this hydrophobic interaction, it's good for transmembrane proteins, but it may not be good for hydrosolic proteins. (genomeweb.com)
  • Several of these Fts proteins are intrinsic transmembrane proteins whose functions are largely unknown. (asm.org)
  • In the assay used in the Nature study, the researchers inserted the genes for malaria protein fragments into yeast cells and induced the yeast to produce those fragments. (hhmi.org)
  • These interactions also suggest directions one may take for more detailed phenotypic examination of mutants for the novel genes. (pnas.org)
  • The Arabidopsis thaliana genome contains genes encoding 10 MAP kinase kinase (MKK) and 20 Map kinase (MAPK) proteins, however the exact relationship between upstream MKK activators and downstream MAPK protein partners has not fully elucidated. (bl.uk)
  • DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. (sharedproteomics.com)
  • Research scientists at Karolinska Institutet are planning an international initiative to map out the relationships between health, genes and lifestyle. (news-medical.net)
  • Protein-protein interactions ( PPI s) are essential to almost all cellular processes, including DNA replication and transcription, signal transduction, and metabolic cycles. (plantphysiol.org)
  • To further study these processes, we used an affinity tag purification mass spectrometry (AP-MS) approach to identify 187 Mtb-human protein-protein interactions (PPIs) involving 34 secreted Mtb proteins. (altmetric.com)
  • To address this, we cloned, tagged, and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), identifying 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). (asiliconvalleyinsider.com)
  • Protein-protein interactions in the yeast pheromone response pathway: Ste5p interacts with all members of the MAP kinase cascade. (nih.gov)
  • All of the interactions we detected involved at least one member of the MAP kinase cascade that is a central element of the response pathway. (nih.gov)
  • Ste5p, a protein of unknown biochemical function, interacted with protein kinases that operate at each step of the MAP kinase cascade, specifically with Ste11p (an MEKK), Ste7p (an MEK), and Fus3p (a MAP kinase). (nih.gov)
  • This finding suggests that one role of Ste5p is to serve as a scaffold to facilitate interactions among members of the kinase cascade. (nih.gov)
  • Ste5p may also help minimize cross-talk with other MAP kinase cascades and thus ensure the integrity of the pheromone response pathway. (nih.gov)
  • This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase‐mediated partnerships evolved over time. (embopress.org)
  • Coimmunoprecipitation experiments from striatal neurons reveal that NCS-1 is found in association with both the D2 receptor and G-protein-coupled receptor kinase 2, a regulator of D2 receptor desensitization. (jneurosci.org)
  • Therefore, it is likely that the mechanism underlying receptor desensitization, including the desensitization of subtypes of dopamine receptors, is modulated by the activity of proteins that can interact with both the receptor and its kinase. (jneurosci.org)
  • Activates the PBS2 MAP kinase kinase by phosphorylation. (uniprot.org)
  • Protein-protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. (wikipedia.org)
  • Many molecular processes within a cell are carried out by molecular machines that are built from numerous protein components organized by their PPIs. (wikipedia.org)
  • These physiological interactions make up the so-called interactomics of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as Creutzfeldt-Jakob and Alzheimer's diseases. (wikipedia.org)
  • What's more, as clusters of interacting proteins are mapped, multiple unknown proteins can be considered likely candidates to take part in the same biological function, he said. (hhmi.org)
  • Since proteins function in networks, the systematic identification of the physical interactions that occur between proteins will help understanding their biological function, and improve our capacity to intervene and, ultimately, to discover novel, more specific therapeutic targets. (innovations-report.com)
  • While not exhaustive, this study focuses on a 'reference set' of proteins from this 'simplified' biological model and includes most of the proteins implicated in human cancer developmen(1). (innovations-report.com)
  • Uncovering of protein interaction schemes often sheds light on molecular mechanisms underlying biological processes. (pnas.org)
  • For such novel proteins, interactions with known proteins serve as invaluable clues to their functions or biological roles. (pnas.org)
  • In addition, a huge amount of knowledge in molecular cell biology, genetics, and biochemistry is accumulated for this simple eukaryotic organism to help evaluate the biological relevance of the identified interactions. (pnas.org)
  • Ishmael, F , Alley, SC & Benkovic, S 2001, ' Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking ', Journal of Biological Chemistry , vol. 276, no. 27, pp. 25236-25242. (elsevier.com)
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • Protein-protein interactions are critical to most biological processes, and locating protein-protein interfaces on protein structures is an important task in molecular biology. (cf.ac.uk)
  • Due to the vital biological importance of RNA and proteins functioning together within a cell, a protocol volume describing experimental procedures to study their interactions should find a home in many laboratories. (springer.com)
  • Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. (nature.com)
  • Emerging trends in computational structure prediction combine algorithms with biological knowledge to take a "smart search" approach, only focusing on areas of proteins that are most likely to be biologically significant. (wikibooks.org)
  • A comprehensive mapping of interactions among Epstein-Barr virus (EBV) proteins and interactions of EBV proteins with human proteins should provide specific hypotheses and a broad perspective on EBV strategies for replication and persistence. (pnas.org)
  • Core herpesvirus proteins are necessary for genome replication, packaging, and delivery in all cells. (pnas.org)
  • Noncore herpesvirus proteins are thought to adapt the core herpesvirus replication program to specific niches. (pnas.org)
  • In addition to the role of core herpesviruses proteins in replication, core proteins may interact with noncore proteins to adapt replication to specific cell types or enable more complex pathophysiologic strategies such as modification of innate or acquired immune responses. (pnas.org)
  • Using this structure, the surface of XPA-MBD which interacts with DNA and a fragment of the largest subunit of replication protein A (RPA70 Delta C327: M1-Y326) was determined using chemical shift mapping. (rcsb.org)
  • Petruk S, Sedkov Y, Johnston DM, Hodgson JW, Black KL, Kovermann SK et al (2012) TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. (springer.com)
  • Sirbu BM, Couch FB, Cortez D (2012) Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA. (springer.com)
  • The results support a model in which gp59 binds to gp32 on a replication fork, destabilizing the gp32-single-stranded DNA interaction concomitant with the oligomerization of gp59 that results in a switching of gp41 for gp32 at the replication fork. (elsevier.com)
  • Altogether, this report provides the first interaction map between CHIKV and human proteins and describes new host cell proteins involved in the replication cycle of this virus. (pasteur.fr)
  • Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins. (uniprot.org)
  • Several enzymes, carrier proteins, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers. (wikipedia.org)
  • Leo James' group from the LMB's PNAC Division, in collaboration with scientists at the Austrian Academy of Sciences and University of Basel, have established the first comprehensive overview of cellular proteins interacting with the LCMV polymerase. (cam.ac.uk)
  • To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. (sciencemag.org)
  • Quantitative β-galactosidase liquid assay was used to confirm the interactions between MAPK and MKK in yeast. (bl.uk)
  • A complementation assay was designed for testing structure/function relationships in cellulose synthase (CESA) proteins. (osti.gov)
  • The components of the assay include (1) construction of test vectors that drive expression of epitope-tagged PpCESA5 carrying engineered mutations, (2) transformation of a ppcesa5 knockout line that fails to produce gametophores with test and control vectors, (3) scoring the stable transformants for gametophore production, (4) statistical analysis comparing complementation rates for test vectors to positive and negative control vectors, and (5) analysis of transgenic protein expression by Western blotting. (osti.gov)
  • In conclusion, compared with existing methods for in vivo testing of protein function, this complementation assay provides a rapid method for investigating protein structure/function relationships in plants. (osti.gov)
  • A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions. (nih.gov)
  • A total of 22 high-confidence interactions, which essentially involved the viral nonstructural protein nsP2, were identified and further validated in protein complementation assay (PCA). (pasteur.fr)
  • Studying the full protein repertoire at the scale of a whole organism is the current challenge of proteomics. (innovations-report.com)
  • Proteomics is the study of proteins and their functions. (nih.gov)
  • The researchers analyzed the functions of known proteins involved in the interactions to reveal such clusters. (hhmi.org)
  • [¹] Roughly speaking, a Protein structure space map is the result of scoring how well known proteins match, structurally. (wikibooks.org)
  • The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. (psu.edu)
  • The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. (embopress.org)
  • We find that two alternative MAPKK's, the osmoresponse MAPKK Pbs2 and the hypotonic response MAPKK Mkk2, can be forced to functionally replace the mating MAPKK Ste7, but only if the proper ensemble of recruitment interactions are overlaid on their catalytic domains. (escholarship.org)
  • We have also found at least 18 new plausible interactions among functionally related proteins. (vcu.edu)
  • Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. (cshl.edu)
  • These direct physical interactions between transcription factors or cofactors and the chromosome can be detected by chromatin immunoprecipitation (ChIP) ( 1 ). (sciencemag.org)
  • Researchers have produced a detailed map that outlines thousands of physical interactions that take place between proteins found in the deadly malaria parasite, Plasmodium falciparum. (hhmi.org)
  • Another important distinction to identify protein-protein interactions is the way they have been determined, since there are techniques that measure direct physical interactions between protein pairs, named "binary" methods, while there are other techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, named "co-complex" methods. (wikipedia.org)
  • The scientists also used a method for ensuring specific production of the target malaria protein fragment in the yeast, as well as highly automated machinery for performing the large-scale assays. (hhmi.org)
  • From these assays, the scientists identified 2,846 protein-protein interactions, most of which included a protein whose function had not yet been identified, said Fields. (hhmi.org)
  • The overall false-negative rate ranges from 75% for worm to 90% for fly, which arises from a roughly 50% false-negative rate due to statistical undersampling and a 55% to 85% false-negative rate due to proteins that appear to be systematically lost from the assays. (nih.gov)
  • Here we show that GASP-1 interacts with US28 in vitro and set out to map the interaction sites of US28 and GASP-1 by using in vitro translation binding assays. (biomedcentral.com)
  • In vitro studies confirmed the ability of the purified proteins to interact and revealed a zinc dependence of the interaction. (mcponline.org)
  • The in vitro interaction between Delta and Omega depends on ATP but does not require the presence of specific DNA segments (the centromere) recognized by Omega. (microbiologyresearch.org)
  • Parmi les inhibiteurs de la traduction des protéines, l'effet antiviral le plus important a été observé in vitro avec la zotatitfine, actuellement en essais cliniques contre le cancer, et la ternatine-4/plitidepsine, approuvée par la FDA dans le traitement du myélome multiple. (asiliconvalleyinsider.com)
  • We found that subcellular distribution of the p57kip2 protein changed during differentiation of rat, mouse, and human oligodendroglial cells both in vivo and in vitro . (jneurosci.org)
  • MITOMI- A Microdluidic Platform for In vitro Characterization of Transcription Factor - DNA Interaction Sylvie Rockel, Marcel Geertz, and Sebastian J. Maerkl 7. (indigo.ca)
  • 15 of these interactions were further tested, and all were confirmed by co-immunoprecipitation and/or in vitro co-purification. (biomedcentral.com)
  • Of 19 experimentally validated interactions between DENV and humans extracted from the literature, this method was able to predict nearly half (9). (nih.gov)
  • Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. (embopress.org)
  • Figure 4: Additional biases among the experimentally identified proteins. (nature.com)
  • Genetic analysis of an experimentally validated, predicted interaction between ARR1 and PYL1 uncovered cross talk between ABA and cytokinin signaling in the control of root growth. (plantphysiol.org)
  • Abnormal collections of the tau protein accumulate and form tangles (seen in blue) within neurons, harming synaptic communication between nerve cells. (ucsd.edu)
  • Aranda S, Rutishauser D, Ernfors P (2014) Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells. (springer.com)
  • In experiments with mice, a team of scientists from the United States, Sweden and Japan has discovered that having a double dose of one protein is sufficient to change the normal balance of cells within the lining of the colon, thereby doubling the risk that a cancer-causing genetic mutation will trigger a tumor there. (news-medical.net)
  • Recent advances in science and computing have enabled 3D structures of proteins to be accurately predicted for a subset of small, simple proteins using nothing more than their amino acid sequence. (wikibooks.org)
  • Many prediction methods used to predict three-dimensional protein structure are the same as those used to predict how proteins of known structures will interact (click here) . (wikibooks.org)
  • However, other data types (e.g. protein alignments, ab initio prediction programs, trans-splice leader sites, poly-A signals and addition sites, SAGE and TEC-RED transcript tags, mass-spectroscopic peptides, and conserved protein domains) are useful in refining the structures, especially where expression is low and so transcripts are not sufficiently available. (wikipedia.org)
  • Finally, we detected an interaction between one of the MAP kinases, Kss1p, and a presumptive target, the transcription factor Ste12p. (nih.gov)
  • A map of the interactions involving cyclin-dependent kinases (Cdks). (biomedcentral.com)
  • Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. (embopress.org)
  • The disordered part of the human proteome contains a large number of short linear motif occurrences that can bind to MAP kinases. (embopress.org)
  • Within this thesis, I explore the relative contributions of modular interaction domains and motifs versus catalytic specificity in defining a kinases' identity. (escholarship.org)
  • Therefore, it is possible that a dysregulation in dopaminergic signaling may be brought about through alterations in proteins that serve to regulate signaling through dopamine and other receptors. (jneurosci.org)
  • Receptor phosphorylation serves to uncouple receptors from G-protein activation and promote arrestin binding and internalization ( Krupnick and Benovic, 1998 ). (jneurosci.org)
  • A candidate protein for sorting many G protein-coupled receptors to lysosomes is the G protein-coupled receptor-associated protein-1 (GASP-1). (biomedcentral.com)
  • Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. (edu.sa)
  • The researchers also identified a group of interacting proteins that the malaria parasite exports into the host cell. (hhmi.org)
  • As an offshoot of this, protein-protein alignments can be done according to structural features as well as amino acid sequence, suggesting the function of uncharacterized proteins with no known relatives and thus providing insight into the way they will interact with other proteins in a system. (wikibooks.org)
  • We predict over 4,000 interactions between DENV and humans, as well as 176 interactions between DENV and A. aegypti. (nih.gov)
  • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. (springer.com)
  • Umeyama, T & Ito, T 2018, ' DMS-seq for In Vivo Genome-Wide Mapping of Protein-DNA Interactions and Nucleosome Centers ', Current Protocols in Molecular Biology , vol. 123, no. 1, e60. (elsevier.com)
  • By protein sequence homology search using human and yeast polyadenylation factors, we identified 28 proteins that may be components of Arabidopsis polyadenylation machinery. (biomedcentral.com)
  • These interactions organize into three distinct hubs involving the Arabidopsis polyadenylation factors. (biomedcentral.com)
  • Notably, the obtained binary data allow us to extract more complex interaction networks, including the one that may explain a currently unsolved mechanism for the connection between distinct steps of vesicular transport. (pnas.org)
  • These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). (embopress.org)
  • A new map of human cortex combines data from multiple imaging modalities and comprises 180 distinct regions. (the-scientist.com)
  • The classic workaround to correlate 1 H with the better resolved 13 C frequencies is impractical for lipids where the required 13 C isotope enrichment is costly, may not resolve all overlap problems, and provides no distinct molecular marker from a likewise 13 C labelled protein to single out inter- from intramolecular NOE signals. (mappingignorance.org)
  • The zinc finger region of GATA-2 is required for binding to PLZF and FAZF, but distinct interfaces on the PLZF and FAZF molecules mediate the interaction, suggesting that GATA-2 activity is controlled by these 2 homologous proteins through distinct mechanisms. (bloodjournal.org)
  • Figure 2: Count of distinct protein identifications as a function of overall high-quality peptide identifications and results of several Monte Carlo simulations. (nature.com)
  • Distinct protein subunits interact in hetero-oligomers, which are essential to control several cellular functions. (wikipedia.org)
  • We propose that short MAPK‐binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles. (embopress.org)
  • These simple protein‐protein recruitment sites represent a major resource for ancient signaling enzymes to acquire new regulatory roles. (embopress.org)
  • Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. (edu.sa)
  • To address these aspects, we applied two complementary, untargeted approaches-split-ubiquitin yeast 2-hybrid and co-immunoprecipitation screens-to identify proteins interacting with CYP83A1 and CYP83B1, two homologous enzymes specific for aliphatic and indole glucosinolate biosynthesis, respectively. (frontiersin.org)
  • This technique provides a straightforward, general approach to mapping protein interactions without mutagenesis. (elsevier.com)
  • Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. (psu.edu)
  • Our approach is based on structural similarity between DENV and host proteins and incorporates knowledge from the literature to further support a subset of the predictions. (nih.gov)
  • Additional predictions suggest specific interactions between virus and host proteins relevant to interferon signaling, transcriptional regulation, stress, and the unfolded protein response. (nih.gov)
  • Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component. (pasteur.fr)
  • This technology combines chromatin immunoprecipitation (ChIP), using antibodies specific to a protein of interest and high throughput sequencing. (france-genomique.org)
  • High-throughput SPR technique is an ideal solution that enables scientists to map protein binding sites and characterize the molecular basis of the interaction easily and affordably. (indianaheadlines.com)
  • Coupled with next generation sequencing, ChIP-seq experiments map protein-DNA interactions in a genome-wide fashion. (springer.com)
  • Here, we establish methods for massively parallel sequencing and analyses of RNase-accessible regions of human mitochondrial RNA and thereby identify specific regions within mitochondrial transcripts that are bound by proteins. (garvan.org.au)
  • Mapping protein-DNA interactions using ChIP-sequencing. (cam.ac.uk)
  • Chromatin ImmunoPrecipitation Sequencing is a methodology used to analyze the DNA-proteins interactions. (france-genomique.org)
  • As a result, his lab has hijacked brain parasites to deliver therapeutic proteins in the brain and collaborated with biblical scholars, ancient DNA and metagenomics experts to piece together Dead Sea Scrolls fragments by sequencing ancient DNA obtained from the animal skin the scrolls are made of. (mpg.de)
  • Deep sequencing of these fragments identifies protein-bound sites as peaks of protected fragments or troughs of cleavage sites. (elsevier.com)
  • DMS added to the culture medium readily enters the cell and methylates its DNA throughout the genome except for the regions bound by proteins, thereby obviating the need for nuclear isolation in genomic footprinting. (elsevier.com)
  • Therefore, DMS-seq provides a unique method for non-targeted profiling of in vivo protein-DNA interactions. (elsevier.com)
  • This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. (mdpi.com)
  • To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. (mdpi.com)
  • Schmid, M. Determination and Quantification of Molecular Interactions in Protein Films: A Review. (mdpi.com)
  • 2014. "Determination and Quantification of Molecular Interactions in Protein Films: A Review. (mdpi.com)
  • Molecular interactions in cell membranes, particularly lipid-protein interactions in their hydrophobic core, are difficult to analyse and remain poorly characterised despite high relevance in physiological and pathological processes. (mappingignorance.org)
  • Structural rearrangements in membranes and embedded proteins, and the way molecular interactions contribute to their function are unresolved questions in biophysical chemistry. (mappingignorance.org)
  • It is hoped that the research leads to a better understanding of how chronic viral infections start and the complex molecular interactions between viruses and their hosts. (cam.ac.uk)
  • Although these proteins appear to be recruited to the division site in a hierarchical order, the molecular interactions underlying the assembly of the cell division machinery remain mostly unspecified. (asm.org)
  • We used this library to map the periphery of the binding site on the core enzyme (α 2 ββ') of Escherichia coli RNA polymerase. (elsevier.com)
  • Traviglia, SL, Datwyler, SA & Meares, CF 1999, ' Mapping protein-protein interactions with a library of tethered cutting reagents: The binding site of σ 70 on Escherichia coli RNA polymerase ', Biochemistry , vol. 38, no. 14, pp. 4259-4265. (elsevier.com)
  • Formation of the Escherichia coli division septum is catalyzed by a number of essential proteins (named Fts) that assemble into a ring-like structure at the future division site. (asm.org)
  • And the protein interaction data can be important in yielding new hypotheses and new insights about how the organism works. (hhmi.org)
  • This 'simple' model organism allows them to study a 'reference set' of proteins that includes most of those known to be involved in human cancer. (innovations-report.com)
  • A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases. (cshl.edu)
  • Overall, 43 interactions between EBV proteins and 173 interactions between EBV and human proteins were identified. (pnas.org)
  • The goal of this study was to investigate interactions among EBV proteins and between EBV and human proteins in an unbiased manner. (pnas.org)
  • therefore, a more detailed mapping of their interactions with core herpesvirus proteins, other gamma-specific proteins, and human proteins is important for understanding their assembly into the tegument and their role in infection. (pnas.org)
  • Researchers identified non-coding regions of the human genome that control the development and function of four brain cell types and mapped genetic risk variants for psychiatric diseases. (ucsd.edu)
  • Could it be that the complexity of a human being comes from the proteins? (innovations-report.com)
  • Citation Query Towards a proteome-scale map of the human protein-protein interaction network. (psu.edu)
  • This interaction map revealed two factors involved in Mtb pathogenesis-the secreted Mtb protein, LpqN, and its binding partner, the human ubiquitin ligase CBL. (altmetric.com)
  • Collectively, these findings illustrate the utility of this Mtb-human PPI map for developing a deeper understanding of the intricate interactions between Mtb and its host. (altmetric.com)
  • To identify proteins involved in mediating D2 receptor signaling, we used the C terminus of the D2 receptor as bait to screen a human brain cDNA library. (jneurosci.org)
  • Understanding such interactions will improve our understanding of how the human body works and what can go wrong to cause disease. (nih.gov)
  • Its global scientific objectives are to reveal the "solar system" of the human liver proteome, expression profiles, modification profiles, a protein linkage (protein-protein interaction) map, and a proteome localization map, and to define an ORFeome, physiome, and pathome. (mcponline.org)
  • As the first initiative on human tissues/organs, HLPP aims to 1) generate an integrative approach leading to a comprehensive protein atlas of the liver, 2) expand the liver proteome to its physiome and pathome to dramatically accelerate the development of diagnostics and therapeutics toward liver diseases, and 3) develop standard operating procedures (SOPs) for other HUPO initiatives. (mcponline.org)
  • Those human liver transcriptomes provide considerable resources not only for the integration (data-based) of transcriptome data with corresponding proteome data but also for scaling protein identification (data-based) and protein linkage map (cDNA-based) during liver proteome analysis. (mcponline.org)
  • Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). (asiliconvalleyinsider.com)
  • A further challenge in genomes large or small is to map factor-binding sites with high positional resolution. (sciencemag.org)
  • Loading of the helicase onto gp32 (the T4 single strand binding protein)-coated single-stranded DNA requires gp59 to remove gp32 and replace it with gp41. (elsevier.com)
  • Since Cys-166 lies in the DNA binding core domain of gp32, this interaction may affect the association of gp32 with DNA. (elsevier.com)
  • ChIP enables the mapping of all DNA binding sites of a protein of interest at the genome level. (france-genomique.org)
  • One of the primary rRNA binding proteins. (string-db.org)
  • One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. (string-db.org)
  • The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins. (frontiersin.org)
  • In the current report, we demonstrate a comprehensive study of interactions between RBP and lncRNAs at a transcriptome scale through extensive analysis of the crosslinking and immunoprecipitation (CLIP) experimental datasets available for 70 RNA binding proteins. (frontiersin.org)
  • Profacgen, a cutting-edge life science company pioneering protein services that accelerate pharmaceutical development, announces the launch of Protein Binding Site Mapping Service . (indianaheadlines.com)
  • Surface plasmon resonance (SPR) spectroscopy is a rapidly developing technique for the study of binding events involving proteins, which are the major molecular targets for validated drugs and for current drug discovery. (indianaheadlines.com)
  • Profacgen employs SPR techniques to identify binding sites involved in protein-protein interactions. (indianaheadlines.com)
  • Its protein binding site mapping service is highly customizable, which suits their customers' specific research goals. (indianaheadlines.com)
  • To know more information about Protein Binding Site Mapping Service in Profacgen, please visit https://www.profacgen.com/protein-binding-site-mapping.htm . (indianaheadlines.com)
  • it also influences the distribution of drugs via the synthesis of their binding proteins. (mcponline.org)
  • By interpolating PROMIS with the list of predicted protein-metabolite interactions, we provided experimental validation for 225 binding events. (edu.sa)
  • 13 and actin binding proteins, including IQGAP 17 and α-actinin 4. (asnjournals.org)
  • Experimental evidence suggests that the inhibitory role of p57kip2 depends on specific interactions with binding proteins such as LIMK-1, CDK2, Mash1, and Hes5 either by controlling their site of action or their activity. (jneurosci.org)
  • Convenient Determination of Protein-Binding DNA Sequences using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein Min-Jeong Kim, Pil Joong Chung, Tae-Ho Lee, Tae-Hoon Kim, Baek Hie Nahm, and Yeon-Ki Kim 5. (indigo.ca)
  • ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. (uniprot.org)
  • These interactions between proteins are dependent on highly specific binding between proteins to ensure efficient electron transfer. (wikipedia.org)
  • In the case of the mitochondrial P450 systems, the specific residues involved in the binding of the electron transfer protein adrenodoxin to its reductase were identified as two basic Arg residues on the surface of the reductase and two acidic Asp residues on the adrenodoxin. (wikipedia.org)
  • We conclude that we could not find all the known interactions because they require chaperones, post-translational modifications, or multiple proteins for their interactions. (vcu.edu)
  • Are they self-assembled, or are scaffolding proteins and chaperones involved? (frontiersin.org)
  • GATA factors comprise a family of transcriptional regulatory proteins characterized by the ability to bind a common conserved DNA sequence (W GATA R) by virtue of evolutionarily conserved C4 zinc finger domains. (bloodjournal.org)
  • 15 Functions of the wild-type PLZF protein are not fully understood, though it has been implicated in apoptosis, growth suppression, differentiation, 16 17 and transcriptional repression. (bloodjournal.org)
  • Genome-wide Dissection of Post-transcriptional and Post-translational Interactions Mukesh Bansal and Andrea Califano 9. (indigo.ca)
  • Specifically, a group of protein interactors involved in cell death and the hypersensitive response provides a potential link between the glucosinolate defense compounds and defense against biotrophic pathogens, mediated by protein-protein interactions. (frontiersin.org)
  • The inserted malaria protein fragments were also engineered to be expressed together with either of two components of a regulatory protein. (hhmi.org)
  • We applied the approach to map the interface of the catalytic domain of the DNA methyltransferase Dnmt3a with its regulatory factor Dnmt3L. (cf.ac.uk)
  • Search proteins in UniProtKB for this molecule. (uniprot.org)
  • We have launched a systematic identification of mutually interacting protein pairs in the budding yeast Saccharomyces cerevisiae . (pnas.org)
  • The polyadenylation process requires two components, the cis -elements on the mRNA and a group of protein factors that recognize the cis -elements and produce the poly(A) tail. (biomedcentral.com)
  • This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. (string-db.org)
  • One of the early assembly proteins it binds 23S rRNA. (string-db.org)
  • This protein binds to the 23S rRNA, and is important in its secondary structure. (string-db.org)
  • Model calculations indicate that the conjugates in this library should be capable of cutting nearby sites on the backbone of almost any protein or nucleic acid to which σ 70 binds. (elsevier.com)
  • section indicates at which position the protein binds a given metal ion. (uniprot.org)
  • In many metabolic reactions, a protein that acts as an electron carrier binds to an enzyme that acts its reductase. (wikipedia.org)
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein. (uniprot.org)
  • Suchanek said she managed to get Theile's photo-amino acids to incorporate into a number of different proteins the first time that she tried. (genomeweb.com)
  • Deciphering these interactions is an essential step in understanding the role(s) of these different proteins in the cytokinesis process. (asm.org)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • According to its official speaker, the customer only need to send the company the target protein sequence and analyte protein sample(s) and they'll perform all the necessary procedures from library preparation to data analysis. (indianaheadlines.com)
  • There are a number of features of proteins integral to their function and interaction with other proteins that are not determined by amino acid sequence alone. (wikibooks.org)
  • This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. (string-db.org)
  • Our analysis suggests that density of interaction sites for these proteins was significantly higher for specific sub-classes of lncRNAs when compared to protein-coding transcripts. (frontiersin.org)
  • The hierarchical appearance of the Fts proteins at the septum site suggests potential protein-protein interactions between the E. coli division proteins. (asm.org)
  • Researchers at the Max Planck Institute have developed a new method for observing protein-protein interactions by incorporating specially synthesized photo-reactive amino acids into proteins. (genomeweb.com)
  • The trick to the new method is that two modified, photo-reactive amino acids - photo-leucine and photo-methionine - irreversibly cross-link to other nearby proteins when exposed to ultraviolet light. (genomeweb.com)
  • The Max-Planck Society has submitted a patent application that covers the amino acids and their use in detection of protein-protein interactions, he said. (genomeweb.com)
  • When you introduce this unnatural amino acid into an active site, where there was an important methionine or leucine, that could screw up the function of the enzyme, and thereby the interaction of the protein with other proteins," he said. (genomeweb.com)
  • Suchanek said that one limitation of the new technique is that the modified amino acids are hydrophobic, and may not be suitable for observing interactions between non-hydrophobic proteins. (genomeweb.com)
  • Before putting the photo amino acids to use for the first time about two years ago, Suchanek was studying protein-protein interactions by doing co-immunoprecipitation reactions. (genomeweb.com)
  • The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. (mdpi.com)
  • Delta most probably interacts with Omega as a dimer since two amino acid substitutions in a conserved region between the A′ and B motifs abolish both the dimerization of Delta and its interaction with Omega. (microbiologyresearch.org)
  • Surface-exposed lysine amino groups and other reactive nucleophiles of the σ 70 protein were conjugated with the cutting reagent iron (S)-1-[p- (bromoacetamido)benzyl]ethylenediaminetetraacetate (FeBABE) via 2- iminothiolane (2IT) with low efficiency. (elsevier.com)
  • Protein-protein interactions are extremely dependent upon the three-dimensional structure of involved proteins, more-so than just their amino acid sequences. (wikibooks.org)
  • Analysis of yeast, worm, and fly data indicates that 25% to 45% of the reported interactions are likely false positives. (nih.gov)
  • Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. (springer.com)
  • The method is advantageous in that the cross-linking of proteins is covalent, and therefore stable for processing and analysis after linking, he said. (genomeweb.com)
  • It's a method for proteomic analysis, whereas the other methods, such as fluorescence, are used for observing interactions. (genomeweb.com)
  • Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network. (nih.gov)
  • Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism. (edu.sa)
  • Large-scale analysis of the yeast proteome by multidimensional protein identification technology. (nature.com)
  • A deletion mapping analysis carried out with two of these proteins, FtsQ and FtsI, revealed that different regions of the polypeptides are involved in their associations with their partners. (asm.org)
  • Some EBV-specific proteins are important in latent B lymphocyte infection, lymphoproliferative disease, Burkitt lymphoma, Hodgkin disease, and nasopharyngeal carcinoma. (pnas.org)
  • The function of other EBV-specific and most gamma-specific herpesvirus proteins is less clearly understood (reviewed in refs. (pnas.org)
  • For example, recent studies of mature EBV virions revealed they contain many gamma-specific proteins in the tegument ( 5 ). (pnas.org)
  • Furthermore, although much is known about the role of some EBV-specific protein interactions with lymphocyte proteins in cell growth and survival, the effects are well delineated for relatively few proteins (reviewed in refs. (pnas.org)
  • Exploration of these complex protein networks requires specific methodologies as well as powerful bioinformatic tools to analyze them. (innovations-report.com)
  • Dengue virus manipulates cellular processes to its advantage through specific interactions with the host's protein interaction network. (nih.gov)
  • Furthermore, the negative controls for BiFC (spilt GFP with no fusions partners) gave strong fluorescence, indicative of non-specific interaction between the split GFP. (bl.uk)
  • There are other chemical-crosslinking methods available for "freezing" protein interactions in time, but they involve the use of large molecules such as paraformaldehyde or DSS, which cross-link to a much wider, less-specific range of proteins, said Monika Suchanek, the first author of the new study, which appears in the April issue of Nature Methods . (genomeweb.com)
  • Usually [with co-immunoprecipitation], there was a pretty high background, so I was not sure if the interaction was specific," said Suchanek. (genomeweb.com)
  • Ultimately, specific lipid-protein contacts are revealed by intermolecular 1 H, 1 H nuclear Overhauser effect signals. (mappingignorance.org)
  • We have conducted a protein interaction study of components within a specific sub-compartment of a eukaryotic flagellum. (ox.ac.uk)
  • Formation of the segrosome, a nucleoprotein complex crucial for proper functioning of plasmid partition systems, involves interactions between specific partition proteins (ParA-like and ParB-like), ATP and specific DNA sequences (the centromeric sites). (microbiologyresearch.org)
  • interactions with its partner ParA and its target parS and specific effects on bacterial growth. (microbiologyresearch.org)
  • Because proteins function through coordinated interaction, it is important to characterize the nature of these relationships. (plantphysiol.org)
  • And some of these proteins may turn out to be useful vaccine targets. (hhmi.org)
  • The interaction networks presented here provide a set of hypothesis for further experimental investigation into the DENV life cycle as well as potential therapeutic targets. (nih.gov)
  • All this information enables the creation of large protein interaction networks - similar to metabolic or genetic/epigenetic networks - that empower the current knowledge on biochemical cascades and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. (wikipedia.org)
  • However, these recruitment interactions cannot be used in a "plug and play" method to alter any kinase's specificity. (escholarship.org)
  • You could increase the number of washes to increase specificity, but then you would risk losing some of the interaction partners. (genomeweb.com)
  • These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. (uniprot.org)
  • More recent work on the phylogeny of the reductase has shown that these residues involved in protein-protein interactions have been conserved throughout the evolution of this enzyme. (wikipedia.org)
  • Chromatin immunoprecipitation (ChIP) is the most widely used method to analyze protein-DNA interactions in vivo. (springer.com)
  • CovalX's MALDI technology used to analyze the proteins, page 5, item 2.12. (covalx.com)
  • Using MALDI-TOF MS coupled with a high-mass detector to directly analyze intact proteins in thyroid tissues. (covalx.com)
  • All previously found and new interactions are combined into structural and network models of phage lambda. (vcu.edu)
  • the prediction is then based on the structural similarity of the two protein models to the template complex. (plantphysiol.org)