Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Two-Hybrid System Techniques: 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.Protein Interaction Maps: Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Protein Interaction Domains and Motifs: 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.Protein Binding: 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.Proteins: 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, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Molecular Sequence Data: 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.Protein Structure, Tertiary: 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.Amino Acid Sequence: 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.Computational Biology: 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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Saccharomyces cerevisiae: 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.Computer Communication Networks: A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)Plasmodium falciparum: A species of protozoa that is the causal agent of falciparum malaria (MALARIA, FALCIPARUM). It is most prevalent in the tropics and subtropics.Malaria: 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, Falciparum: 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.Protozoan Proteins: Proteins found in any species of protozoan.Antigens, Protozoan: Any part or derivative of any protozoan that elicits immunity; malaria (Plasmodium) and trypanosome antigens are presently the most frequently encountered.District of Columbia: 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.Plasmodium: 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, Digital: Libraries in which a major proportion of the resources are available in machine-readable format, rather than on paper or MICROFORM.Membrane Proteins: 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.Rhodopsin: 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.Transducin: 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.-.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Libraries: 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)Library Automation: 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.Drug Industry: 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.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Drosophila Proteins: 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.Drosophila: 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.Biological Ontologies: Structured vocabularies describing concepts from the fields of biology and relationships between concepts.Vocabulary, Controlled: 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)National Center for Health Statistics (U.S.): 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Internet: 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.Dengue Virus: 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.Dengue: 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.Aedes: 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.Insects: 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)Neglected Diseases: 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).Tropical Medicine: The branch of medicine concerned with diseases, mainly of parasitic origin, common in tropical and subtropical regions.Severe 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.Xeroderma Pigmentosum Group A Protein: 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.DNA Repair: 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.Xeroderma Pigmentosum: 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.Endonucleases: 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.-.Magnetic Resonance Spectroscopy: 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).DNA Damage: 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.Ultraviolet Rays: 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)

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.
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 ...
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) ...
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 ...
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 ...
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
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.
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 (2005). "Towards a proteome-scale map of the human protein-protein interaction network.". Nature. 437 (7062): 1173-8. PMID 16189514. doi:10.1038/nature04209. ...
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 ...
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
Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. Numerous IDPs have close relationships with human diseases such as tumor, Parkinson disease, Alzheimer disease, diabetes, and so on. These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. Most of them in the disease datasets have more interactants and hence the size of the disease-associated IDPs interaction network is simultaneously increased. For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 interaction network; α-synuclein, an intrinsically disordered protein involved in Parkinson diseases, is also a hub of the protein network. The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore, novel strategies for drug discovery based on
The use of λ repressor fusions to study protein-protein interactions in E. coli was first described by Hu and others (1). Since then, the repressor system has been employed by several laboratories to...
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Nuria Sánchez-Puig is the author of this article in the Journal of Visualized Experiments: Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions
There are many characteristics of a protein-protein interaction that are important. Obviously, it is important to know which proteins are interacting. In many experiments and computational studies, the focus is on interactions between two different proteins. However, you can have one protein interacting with other copies of itself (oligomerization), or three or more different proteins interacting. The stoichiometry of the interaction is also important - that is, how many of each protein involved are present in a given reaction. Some protein interactions are stronger than others, because they bind together more tightly. The strength of binding is known as affinity. Proteins will only bind each other spontaneously if it is energetically favorable. Energy changes during binding are another important aspect of protein interactions. Many of the computational tools that predict interactions are based on the energy of interactions.. In recent years there has been a strong focus on predicting protein ...
Background Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial...
Background There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region. Methodology A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules. Results The water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be
To understand tissue morphogenesis and disease pathogenesis, ultimately we must understand what happens at the cellular and molecular levels. To do this, we use a number of techniques. To identify new protein-protein interactions important for establishing the machinery through which junctions carry out structural and signaling functions, we use in vitro biochemistry and a variety of protein interaction screens, including recently emerging Bio-ID proteomic approaches that allow for mapping nearest neighbors in cells and tissues in situ. How these protein interactions are regulated by post-translational modifications, including phosphorylation and protein methylation is also being uncovered through the use of mass spectrometry approaches.. To look at the importance of these protein interactions in cells, state-of-the-art optical imaging techniques are being employed. Fluorescently-tagged wild type and mutant desmosome and adherens junction molecules are tracked during intercellular junction ...
Protein-protein interactions (PPIs) play a critical role in all cellular processes, ranging from cellular division to apoptosis. Elucidating and analyzing PPIs is thus essential to understanding the underlying mechanisms in biology. Indeed, this has been a major focus of research in recent years, providing a wealth of experimental data about protein associations [1-9]. Current PPI networks have been constructed using a number of techniques, such as yeast-two-hybrid (Y2H), co-immunopurification or coaffinity purification, followed by mass spectroscopy and curation of published low-throughput experiments [10-16]. Despite this tremendous push, the current coverage of PPIs is still rather poor (for example, , 10% of interactions in humans) [17]. Additionally, despite considerable improvements in high-throughput (HTP) techniques, they are still prone to spurious errors and systematic biases, yielding a significant number of false-positives and false-negatives [18-21]. This limitation impedes our ...
Institut National de la Sante et de la Recherche Medicale U124-IRCL, Lille, France. The BTB/POZ domain defines a newly characterized protein-protein interaction interface. It is highly conserved throughout metazoan evolution and generally found at the NH2 terminus of either actin-binding or, more commonly, nuclear DNA-binding proteins. By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher order macromolecular complexes involved in ring canal formation or chromatin folding ...
Xin Guo Introducing... the DOMain-oriented Alignment of Interaction Networks (DOMAIN). Previous paradigms include the node-then-edge-alignment paradigm and direct-edge-alignment paradigm. In the latter, interactions are more likely to be conserved. Many studies have suggested that direct PPIs can be mediated by interactions of their domains. Their method follows the direct-edge-alignment paradigm. In the method: try to…
Protein-protein interactions, or PPIs, constitute a basic unit of our understanding of protein function. Though substantial effort has been made to organize PPI knowledge into structured databases, maintenance of these resources requires careful manual curation. Even then, many PPIs remain uncurated within unstructured text data. Extracting PPIs from experimental research supports assembly of PPI networks and highlights relationships crucial to elucidating protein functions. Isolating specific protein-protein relationships from numerous documents is technically demanding by both manual and automated means. Recent advances in the design of these methods have leveraged emerging computational developments and have demonstrated impressive results on test datasets. In this review, we discuss recent developments in PPI extraction from unstructured biomedical text. We explore the historical context of these developments, recent strategies for integrating and comparing PPI data, and their application to ...
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the TRAF5 protein, and the other against the TRAF3 protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0413) - Products - Abnova
This protein protein interaction antibody pair set comes with two antibodies to detect the protein-protein interaction, one against the CDC20 protein, and the other against the BUB1B protein for use in in situ Proximity Ligation Assay. See Publication Reference below. (DI0076) - 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.
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 ...
"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". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... 1999). "Decreased brain protein levels of cytochrome oxidase subunits in Alzheimer's disease and in hereditary spinocerebellar ... Sirchia R, Luparello C (2007). "Mid-region parathyroid hormone-related protein (PTHrP) and gene expression of MDA-MB231 breast ... q21 by FISH and radiation hybrid mapping". Cytogenet Cell Genet. 83 (3-4): 226-7. doi:10.1159/000015185. PMID 10072584.. ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ... Phosphorylated TFEB is then retained in the cytosol by interaction with 14-3-3 proteins.[18][20][19] These kinases are tuned to ... "A helix-loop-helix protein related to the immunoglobulin E box-binding proteins". Molecular and Cellular Biology. 10 (8): 4384- ... Transcription factor EB is a protein that in humans is encoded by the TFEB gene.[5][6] ...
"Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... Dermicidin, also known as proteolysis-inducing factor (PIF), is a protein that in humans is encoded by the DCD gene.[3][4] It ... protein binding. • hydrolase activity. • RNA binding. Cellular component. • extracellular exosome. • extracellular matrix. • ... Dermicidin is a secreted protein that is subsequently processed into mature peptides of distinct biological activities. The C- ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... This protein-related article is a stub. You can help Wikipedia by expanding it.. *v ... "Process outgrowth of oligodendrocytes is promoted by interaction of fyn kinase with the cytoskeletal protein tau". The Journal ... "Process outgrowth of oligodendrocytes is promoted by interaction of fyn kinase with the cytoskeletal protein tau". The Journal ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... This protein-related article is a stub. You can help Wikipedia by expanding it. *v ... RefSeq (protein). NP_001153800. NP_001153801. NP_115674. NP_001153800.1. NP_001153801.1. ... Synaptotagmin-3 is a protein that in humans is encoded by the SYT3 gene.[5][6] ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... Zinc finger protein Aiolos also known as Ikaros family zinc finger protein 3 is a protein that in humans is encoded by the ... protein binding. • protein heterodimerization activity. • nucleic acid binding. • transcription regulatory region DNA binding. ... This gene encodes a member of the Ikaros family of zinc-finger proteins. Three members of this protein family (Ikaros, Aiolos ...
2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ... protein binding. • extracellular matrix constituent conferring elasticity. • identical protein binding. • integrin binding ... Elastin microfibril interfacer 1 (EMILIN-1) is a protein that in humans is encoded by the EMILIN1 gene.[5] It is the best ... 2000). "Elastic fiber proteins in the glomerular mesangium in vivo and in cell culture". Kidney Int. 58 (4): 1588-602. doi: ...
2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ... Protein SSX4 is a protein that in humans is encoded by the SSX4 gene.[5] ... This protein-related article is a stub. You can help Wikipedia by expanding it.. *v ... These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral and ...
2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ... protein binding. • single-stranded RNA binding. • RNA binding. • double-stranded RNA binding. • hydrolase activity. • ATP ... Since LGP2 lacks CARD domains, its effect on downstream antiviral signaling is likely due to interaction with dsRNA viral ... The protein encoded by the gene DHX58 is known as LGP2 (Laboratory of Genetics and Physiology 2).[5][7][8] ...
2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ... The protein encoded by this gene is a member of the keratin gene family. As a type II hair keratin, it is a basic protein which ... Keratin, type II cuticular Hb1 is a protein that in humans is encoded by the KRT81 gene.[5][6][7] ... protein binding. • structural molecule activity. Cellular component. • intermediate filament. • keratin filament. • Q14325730. ...
de 2001). «Mapping of the interaction domain of the protein kinase CKII beta subunit with target proteins». Mol. Cells (Korea ( ... de 1999). «Interactions of protein kinase CK2beta subunit within the holoenzyme and with other proteins». Mol. Cell. Biochem. ( ... de 2002). «Interactions between protein kinase CK2 and Pin1. Evidence for phosphorylation-dependent interactions». J. Biol. ... de 1998). «Characterization of protein interaction among subunits of protein kinase CKII in vivo and in vitro». Mol. Cells ( ...
Ewing R. M., Chu P., Elisma F. et al. Large-scale mapping of human protein-protein interactions by mass spectrometry (англ.) ... Protein structure and conformations of the pure (Na+ +K+)-ATPase (англ.) // Biochim. Biophys. Acta (англ.)русск. : journal. - ... protein stabilization. • ion transport. • cellular potassium ion homeostasis. • potassium ion transport. • membrane ... protein localization to plasma membrane. • leukocyte migration. • positive regulation of potassium ion transmembrane ...
Several attempts have been made to map Protein-protein interactions among phage and their host. For instance, bacteriophage ... Synthesis of proteins and nucleic acid[edit]. Within minutes, bacterial ribosomes start translating viral mRNA into protein. ... "The protein interaction network of bacteriophage lambda with its host, Escherichia coli". J. Virol. 87 (23): 12745-55. doi: ... but these studies suggest that there are most likely several key interactions and many indirect interactions whose role remains ...
Roy P (2008). "Functional mapping of bluetongue virus proteins and their interactions with host proteins during virus ... In addition to the seven structural proteins, three non-structural (NS) proteins, NS1, NS2, NS3 (and a related NS3A) are ... The two remaining non-structural proteins, NS1 and NS2, are produced at high levels in the cytoplasm and are believed to be ... The two outer capsid proteins, VP2 and VP5, mediate attachment and penetration of BTV into the target cell. The virus makes ...
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 ...
Gopinath SCB (2009). "Mapping of RNA-protein interactions". Analytica Chimica Acta. 636 (2): 117-128. doi:10.1016/j.aca.2009.01 ... ISBN 0-935702-49-0. Yu E, Fabris D (2003). "Direct probing of RNA structures and RNA-Protein interactions in the HIV-1 ... Karaduman R, Fabrizio P, Hartmuth K, Urlaub H, Luhrmann R (2006). "RNA structure and RNA-protein interactions in purified yeast ... Nucleotides may be protected from DMS modification by base pairing, tertiary contacts, or protein-RNA interactions. This can be ...
"Protein-protein interaction panel using mouse full-length cDNAs". Genome Research. 11 (10): 1758-65. doi:10.1101/gr.180101. PMC ... "Cluster analysis of an extensive human breast cancer cell line protein expression map database". Proteomics. 2 (2): 212-23. doi ... "Molecular interaction between human tumor marker protein p150, the largest subunit of eIF3, and intermediate filament protein ... "A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling". Nature Biotechnology. 21 ...
"Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... The protein is a nucleocytoplasmic shuttling protein that accumulates in the nucleus upon heavy metal exposure and binds to ... Metal regulatory transcription factor 1 is a protein that in humans is encoded by the MTF1 gene.[5][6] ... protein binding. • histone acetyltransferase binding. • nucleic acid binding. • RNA polymerase II core promoter proximal region ...
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. · ...
Network compression as a quality measure for protein interaction networks.. Royer L, Reimann M, Stewart AF, Schroeder M.. PLoS ... Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.. Rat Genome Sequencing and Mapping ... Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting.. Zheng-Bradley X, Flicek P.. Hum Mutat. 2012 ... An integrated map of genetic variation from 1,092 human genomes. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks ...
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 ...
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 ...
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. ...
... 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 ...
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 ...
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. ...
  • 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)
  • 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)
  • Protein-protein interactions (PPIs) play essential roles in almost all cellular processes, including gene regulation, metabolic control, signal transduction, and cell communication. (indianaheadlines.com)
  • We cloned the fl3 gene and determined that it encodes a PLATZ (plant AT-rich sequence and zinc binding) protein. (plantcell.org)
  • 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)
  • Similarly, gene regulatory networks overlap substantially with protein interaction networks and signaling networks. (wikipedia.org)
  • From this model genetic interactions can be observed at multiple scales which will assist in the study of concepts such as gene conservation. (wikipedia.org)
  • After eliminating any vectors that self-activated the reporter gene, they then generated a draft map by screening individual baits with prey libraries. (alzforum.org)
  • Eukaryotic translation initiation factor 3 subunit A ( eIF3a ) is a protein that in humans is encoded by the EIF3A gene . (wikipedia.org)
  • 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)
  • In searching for interactions between proteins, the scientists used a technique known as the yeast two-hybrid assay, which Fields invented. (hhmi.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)
  • 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)
  • 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)
  • Quantitative β-galactosidase liquid assay was used to confirm the interactions between MAPK and MKK in yeast. (bl.uk)
  • 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)
  • 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)
  • Protein interaction partners can be identified at high-throughput in vivo using a yeast fitness assay based on the dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA). (jove.com)
  • Here, we describe a protocol for the yeast protein-fragment complementation assay (PCA), a powerful method to detect direct and proximal associations between proteins in living cells. (jove.com)
  • The high-throughput protocol presented here is performed using a robotic platform that parallelizes mating of bait and prey strains carrying complementary DHFR-fragment fusion proteins and the survival assay on MTX. (jove.com)
  • A particularly powerful method for the yeast system is the dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA), an assay that has been used in different contexts to study the yeast PIN in standard and perturbed conditions 11,22-26 . (jove.com)
  • The interactomes based on PPIs should be associated to the proteome of the corresponding species in order to provide a global view ("omic") of all the possible molecular interactions that a protein can present. (wikipedia.org)
  • This protocol allows to systematically test for thousands of protein-protein interactions (PPIs) involving bait proteins of interest and offers several advantages over other PPI detection assays, including the study of proteins expressed from their endogenous promoters without the need for modifying protein localization and for the assembly of complex reporter constructs. (jove.com)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. (biomedcentral.com)
  • Irradiation with UV-C light creates a covalent bond between proteins and RNAs that are in direct contact in vivo without requiring pre-incubation of cells with photoreactive ribonucleoside analogs. (biomedcentral.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)
  • REEP proteins were required for ER network formation in vitro, and REEP1 also bound microtubules and promoted ER alignment along the microtubule cytoskeleton in COS7 cells. (jci.org)
  • Here we have identified shank-interacting protein-like 1 (SIPL1) as a PTEN-NR in human tumor cell lines and human primary cervical cancer cells. (jci.org)
  • Advances in techniques for analysing single cells and tissues have inspired an international effort to create comprehensive reference maps of all human cells - the fundamental units of life - as a basis for both understanding human health and diagnosing, monitoring and treating disease. (elifesciences.org)
  • Hydroxyl radicals attack the ribose/deoxyribose ring and this results in breaking of the phosphate backbone, which is independent of secondary structure, as all backbone is accessible, but is instead resultant of protein or tertiary structure protection. (wikipedia.org)
  • When examining the gel produced by running the gels on a band the areas of various strength of protection where areas of stronger protection for hydroxyl radicals can be said to have tighter association with a protein, or if no protein associates with the nucleic acid it can be caused by the tertiary fold. (wikipedia.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)
  • 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)
  • 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)
  • In addition to these two most conserved residues, acidic residues within or flanking the core consensus sequence also contribute to Atg8 binding by electrostatic interactions with basic residues on Atg8. (elifesciences.org)
  • It can thus be used to probe the interactions involved with the secondary structure and other binding interactions of RNA and help with nucleic acid sequence analysis. (wikipedia.org)
  • And some of these proteins may turn out to be useful vaccine targets. (hhmi.org)
  • 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)
  • A great need exists for prediction of antibody response for the generation of antibodies toward protein targets. (nih.gov)
  • The data set presented here can be used for further studies to design new prediction tools for the generation of antibodies to specific protein targets. (nih.gov)
  • Crystal structures revealed that the Atg8-Hfl1 interaction is not mediated by the typical Atg8-family-interacting motif (AIM) that forms an intermolecular β-sheet with Atg8. (elifesciences.org)
  • The study demonstrates that a propensity scale might be useful for prediction of antibody response generated by immunization of recombinant protein fragments. (nih.gov)
  • the prediction is then based on the structural similarity of the two protein models to the template complex. (plantphysiol.org)
  • These technologies provide information on the direct association between pairs of proteins, which allows constructing binary networks. (jove.com)
  • Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. (plantphysiol.org)
  • 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)
  • The atlastin-1 GTPase interacts with spastin, a microtubule-severing ATPase, as well as with the DP1/Yop1p and reticulon families of ER-shaping proteins, and SPG3A caused by atlastin-1 mutations has been linked pathogenically to abnormal ER morphology. (jci.org)
  • 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)
  • Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network. (nih.gov)
  • While PTEN displays phosphatase activity for both protein and lipid substrates ( 1 ), accumulating evidence reveals that its lipid phosphatase activity, which dephosphorylates the 3ι-position phosphate from the inositol ring of phosphatidylinositol 3,4,5-triphosphate (PIP 3 ) ( 2 , 3 ), contributes to PTEN's tumor suppression activities. (jci.org)
  • 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)
  • 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)
  • Here, we show a comparative analysis based on 12,634 affinity-purified antibodies generated in a standardized manner against human recombinant protein fragments. (nih.gov)
  • Mapping membrane protein interactions in cell signaling systems. (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)
  • 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)
  • 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)
  • Nucleic acid NMR uses similar techniques as protein NMR, but has several differences. (wikipedia.org)
  • Probing with hydroxyl radicals shows the protection of structured nucleic acids by the proteins thought to be associated or folding on itself, where cleavage again results in a band formed through gel electrophoresis (after RT-PCR in the case of RNA) that is shorter than the full nucleic acid depending upon where it is cleaved. (wikipedia.org)
  • Could it be that the complexity of a human being comes from the proteins? (innovations-report.com)
  • 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)
  • A new map of human cortex combines data from multiple imaging modalities and comprises 180 distinct regions. (the-scientist.com)
  • In the human world, it may not always work like that, but how about the protein world, which is considerably smaller? (alzforum.org)
  • Establishing the same maps for the mouse or human would require more computing power and sophisticated industrialization to handle the large data sets generated. (alzforum.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)
  • Even metabolic networks can be considered as molecular interaction networks: metabolites, i.e. chemical compounds in a cell, are converted into each other by enzymes , which have to bind their substrates physically. (wikipedia.org)
  • A further challenge in genomes large or small is to map factor-binding sites with high positional resolution. (sciencemag.org)
  • Knowledge of protein interactions can help reveal that function, he said. (hhmi.org)
  • In brains affected by Alzheimer's disease, abnormal levels of the beta-amyloid protein clump together to form plaques (seen in brown) that collect between neurons and disrupt cell function. (ucsd.edu)
  • Structural rearrangements in membranes and embedded proteins, and the way molecular interactions contribute to their function are unresolved questions in biophysical chemistry. (mappingignorance.org)
  • Recently, we have provided evidence that promyelocytic leukemia protein (PML) has the capacity to physically associate with GATA-2 and to modify its function. (bloodjournal.org)
  • In the fl3 endosperm, the levels of many tRNAs and 5S rRNA that are transcribed by RNAPIII are significantly reduced, suggesting that the incorrectly folded fl3 protein may impair the function of RNAPIII. (plantcell.org)
  • Identifying the physical interaction partners of a given protein therefore provides rich information on the function and regulation of that protein 2,3 . (jove.com)
  • The researchers also identified a group of interacting proteins that the malaria parasite exports into the host cell. (hhmi.org)
  • Since then, significant efforts have been made to better understand the biology of this virus, but we still have poor knowledge of CHIKV interactions with host cell components at the molecular level. (pasteur.fr)
  • 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)
  • 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)
  • 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)
  • In the present study, we used a bacterial two-hybrid system based on interaction-mediated reconstitution of a cyclic AMP (cAMP) signaling cascade to unravel the molecular basis of septum assembly by analyzing the protein interaction network among E. coli cell division proteins. (asm.org)
  • Altogether, these data suggest that the cell division machinery assembly is driven by the cooperative association among the different Fts proteins to form a dynamic multiprotein structure at the septum site. (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)
  • Fluorescence microscopy studies using immunofluorescence or the green fluorescent protein (GFP) fused to the Fts proteins have revealed that assembly of the septum starts with the positioning of an FtsZ ring in the cell center. (asm.org)
  • Direct associations between E. coli cell division proteins have been demonstrated for FtsZ, FtsA, and ZipA. (asm.org)
  • Designer proteins, with their tailor-made functions in catalysis or molecular recognition, have revolutionized our way of investigating cell biology. (hindawi.com)
  • This special issue aims to plot new frontiers in engineering designer proteins and using them as tools to study cell biology. (hindawi.com)
  • Machine learning models of coordinated hippocampal ensemble activity during sharp wave ripple activity encode structure that mirrors the place cell map expressed during exploration, and enable a new paradigm for analyzing and understanding this offline activity. (elifesciences.org)
  • Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. (springer.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)
  • 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)
  • Both novices and experts will find this an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis. (wiley-vch.de)
  • With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts. (wiley-vch.de)
  • This analysis yielded a map of 4,780 unique interactions among 4,679 proteins. (alzforum.org)
  • Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, SHAPE, nucleotide analog interference mapping (NAIM), and in-line probing. (wikipedia.org)