Protein interaction mapping. Medical search

Methods for determining interaction between PROTEINS.

Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.

Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.

Any method used for determining the location of and relative distances between genes on a chromosome.

Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.

The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.

Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

A 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)

Protein interaction mapping is a research approach used to identify and characterize the physical interactions between different proteins within a cell or organism. This process often involves the use of high-throughput experimental techniques, such as yeast two-hybrid screening, mass spectrometry-based approaches, or protein fragment complementation assays, to detect and quantify the binding affinities of protein pairs. The resulting data is then used to construct a protein interaction network, which can provide insights into functional relationships between proteins, help elucidate cellular pathways, and inform our understanding of biological processes in health and disease.

A two-hybrid system technique is a type of genetic screening method used in molecular biology to identify protein-protein interactions within an organism, most commonly baker's yeast (Saccharomyces cerevisiae) or Escherichia coli. The name "two-hybrid" refers to the fact that two separate proteins are being examined for their ability to interact with each other.

The technique is based on the modular nature of transcription factors, which typically consist of two distinct domains: a DNA-binding domain (DBD) and an activation domain (AD). In a two-hybrid system, one protein of interest is fused to the DBD, while the second protein of interest is fused to the AD. If the two proteins interact, the DBD and AD are brought in close proximity, allowing for transcriptional activation of a reporter gene that is linked to a specific promoter sequence recognized by the DBD.

The main components of a two-hybrid system include:

1. Bait protein (fused to the DNA-binding domain)
2. Prey protein (fused to the activation domain)
3. Reporter gene (transcribed upon interaction between bait and prey proteins)
4. Promoter sequence (recognized by the DBD when brought in proximity due to interaction)

The two-hybrid system technique has several advantages, including:

1. Ability to screen large libraries of potential interacting partners
2. High sensitivity for detecting weak or transient interactions
3. Applicability to various organisms and protein types
4. Potential for high-throughput analysis

However, there are also limitations to the technique, such as false positives (interactions that do not occur in vivo) and false negatives (lack of detection of true interactions). Additionally, the fusion proteins may not always fold or localize correctly, leading to potential artifacts. Despite these limitations, two-hybrid system techniques remain a valuable tool for studying protein-protein interactions and have contributed significantly to our understanding of various cellular processes.

Protein interaction maps are graphical representations that illustrate the physical interactions and functional relationships between different proteins in a cell or organism. These maps can be generated through various experimental techniques such as yeast two-hybrid screens, affinity purification mass spectrometry (AP-MS), and co-immunoprecipitation (Co-IP) followed by mass spectrometry. The resulting data is then visualized as a network where nodes represent proteins and edges represent the interactions between them. Protein interaction maps can provide valuable insights into cellular processes, signal transduction pathways, and disease mechanisms, and are widely used in systems biology and network medicine research.

Chromosome mapping, also known as physical mapping, is the process of determining the location and order of specific genes or genetic markers on a chromosome. This is typically done by using various laboratory techniques to identify landmarks along the chromosome, such as restriction enzyme cutting sites or patterns of DNA sequence repeats. The resulting map provides important information about the organization and structure of the genome, and can be used for a variety of purposes, including identifying the location of genes associated with genetic diseases, studying evolutionary relationships between organisms, and developing genetic markers for use in breeding or forensic applications.

Protein interaction domains and motifs refer to specific regions or sequences within proteins that are involved in mediating interactions between two or more proteins. These elements can be classified into two main categories: domains and motifs.

Domains are structurally conserved regions of a protein that can fold independently and perform specific functions, such as binding to other molecules like DNA, RNA, or other proteins. They typically range from 25 to 500 amino acids in length and can be found in multiple copies within a single protein or shared among different proteins.

Motifs, on the other hand, are shorter sequences of 3-10 amino acids that mediate more localized interactions with other molecules. Unlike domains, motifs may not have well-defined structures and can be found in various contexts within a protein.

Together, these protein interaction domains and motifs play crucial roles in many biological processes, including signal transduction, gene regulation, enzyme function, and protein complex formation. Understanding the specificity and dynamics of these interactions is essential for elucidating cellular functions and developing therapeutic strategies.

Protein binding, in the context of medical and biological sciences, refers to the interaction between a protein and another molecule (known as the ligand) that results in a stable complex. This process is often reversible and can be influenced by various factors such as pH, temperature, and concentration of the involved molecules.

In clinical chemistry, protein binding is particularly important when it comes to drugs, as many of them bind to proteins (especially albumin) in the bloodstream. The degree of protein binding can affect a drug's distribution, metabolism, and excretion, which in turn influence its therapeutic effectiveness and potential side effects.

Protein-bound drugs may be less available for interaction with their target tissues, as only the unbound or "free" fraction of the drug is active. Therefore, understanding protein binding can help optimize dosing regimens and minimize adverse reactions.

Proteins are complex, large molecules that play critical roles in the body's functions. They are made up of amino acids, which are organic compounds that are the building blocks of proteins. Proteins are required for the structure, function, and regulation of the body's tissues and organs. They are essential for the growth, repair, and maintenance of body tissues, and they play a crucial role in many biological processes, including metabolism, immune response, and cellular signaling. Proteins can be classified into different types based on their structure and function, such as enzymes, hormones, antibodies, and structural proteins. They are found in various foods, especially animal-derived products like meat, dairy, and eggs, as well as plant-based sources like beans, nuts, and grains.

A protein database is a type of biological database that contains information about proteins and their structures, functions, sequences, and interactions with other molecules. These databases can include experimentally determined data, such as protein sequences derived from DNA sequencing or mass spectrometry, as well as predicted data based on computational methods.

Some examples of protein databases include:

1. UniProtKB: a comprehensive protein database that provides information about protein sequences, functions, and structures, as well as literature references and links to other resources.
2. PDB (Protein Data Bank): a database of three-dimensional protein structures determined by experimental methods such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy.
3. BLAST (Basic Local Alignment Search Tool): a web-based tool that allows users to compare a query protein sequence against a protein database to identify similar sequences and potential functional relationships.
4. InterPro: a database of protein families, domains, and functional sites that provides information about protein function based on sequence analysis and other data.
5. STRING (Search Tool for the Retrieval of Interacting Genes/Proteins): a database of known and predicted protein-protein interactions, including physical and functional associations.

Protein databases are essential tools in proteomics research, enabling researchers to study protein function, evolution, and interaction networks on a large scale.

Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.

Tertiary protein structure refers to the three-dimensional arrangement of all the elements (polypeptide chains) of a single protein molecule. It is the highest level of structural organization and results from interactions between various side chains (R groups) of the amino acids that make up the protein. These interactions, which include hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bridges, give the protein its unique shape and stability, which in turn determines its function. The tertiary structure of a protein can be stabilized by various factors such as temperature, pH, and the presence of certain ions. Any changes in these factors can lead to denaturation, where the protein loses its tertiary structure and thus its function.

An amino acid sequence is the specific order of amino acids in a protein or peptide molecule, formed by the linking of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid through a peptide bond. The sequence is determined by the genetic code and is unique to each type of protein or peptide. It plays a crucial role in determining the three-dimensional structure and function of proteins.

Computational biology is a branch of biology that uses mathematical and computational methods to study biological data, models, and processes. It involves the development and application of algorithms, statistical models, and computational approaches to analyze and interpret large-scale molecular and phenotypic data from genomics, transcriptomics, proteomics, metabolomics, and other high-throughput technologies. The goal is to gain insights into biological systems and processes, develop predictive models, and inform experimental design and hypothesis testing in the life sciences. Computational biology encompasses a wide range of disciplines, including bioinformatics, systems biology, computational genomics, network biology, and mathematical modeling of biological systems.

An algorithm is not a medical term, but rather a concept from computer science and mathematics. In the context of medicine, algorithms are often used to describe step-by-step procedures for diagnosing or managing medical conditions. These procedures typically involve a series of rules or decision points that help healthcare professionals make informed decisions about patient care.

For example, an algorithm for diagnosing a particular type of heart disease might involve taking a patient's medical history, performing a physical exam, ordering certain diagnostic tests, and interpreting the results in a specific way. By following this algorithm, healthcare professionals can ensure that they are using a consistent and evidence-based approach to making a diagnosis.

Algorithms can also be used to guide treatment decisions. For instance, an algorithm for managing diabetes might involve setting target blood sugar levels, recommending certain medications or lifestyle changes based on the patient's individual needs, and monitoring the patient's response to treatment over time.

Overall, algorithms are valuable tools in medicine because they help standardize clinical decision-making and ensure that patients receive high-quality care based on the latest scientific evidence.

In the context of medical and biological sciences, a "binding site" refers to a specific location on a protein, molecule, or cell where another molecule can attach or bind. This binding interaction can lead to various functional changes in the original protein or molecule. The other molecule that binds to the binding site is often referred to as a ligand, which can be a small molecule, ion, or even another protein.

The binding between a ligand and its target binding site can be specific and selective, meaning that only certain ligands can bind to particular binding sites with high affinity. This specificity plays a crucial role in various biological processes, such as signal transduction, enzyme catalysis, or drug action.

In the case of drug development, understanding the location and properties of binding sites on target proteins is essential for designing drugs that can selectively bind to these sites and modulate protein function. This knowledge can help create more effective and safer therapeutic options for various diseases.

Many technologies have been reported to map interactions and these have been systematically applied in yeast. To date, the ... number of reported yeast protein interactions that have been truly validated by at leas … ... The mapping of protein-protein interactions is key to understanding biological processes. ... The mapping of human protein interaction networks is even more complicated. Thus, it is unreasonable to try to map the human ...

https://pubmed.ncbi.nlm.nih.gov/15163370/

... of Texas MD Anderson Cancer Center in Houston identified 437 human proteins as the high-confidence interacting proteins - with ... Researchers develop detailed map of protein-protein interactions between SARS-CoV-2 and the host. *Download PDF Copy ... Researchers develop detailed map of protein-protein interactions between SARS-CoV-2 and the host. News-Medical. 22 September ... Researchers develop detailed map of protein-protein interactions between SARS-CoV-2 and the host. News-Medical, viewed 22 ...

https://www.news-medical.net/news/20210105/Researchers-develop-detailed-map-of-protein-protein-interactions-between-SARS-CoV-2-and-the-host.aspx

... an accessory factor whose interaction with RAG1 is critical for catalytic function. How RAG2 activates RAG1 is not understood. ... Keywords: Amino Acid; Biosensor; DNA Cleavage; DNA Recombination; Protein Structure; Protein-Protein Interaction; RAG1; RAG2; V ... Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2 J Biol Chem. 2015 ... Two adjacent acidic amino acids in this region (Asp-546 and Glu-547) are important for both the RAG1-RAG2 interaction and ...

https://pubmed.ncbi.nlm.nih.gov/25745109/

Protein. Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus. … the results of the ... systematic identification of protein−protein interactions for the hospital-acquired strain MRSA-252. Using a high-throughput ...

https://www.pacificimmunology.com/post-citation/mapping-the-protein-interaction-network-in-methicillin-resistant-staphylococcus-aureus/

Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. In: Journal of Biological ... Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. Journal of Biological ... Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking. / Ishmael, Faoud; Alley, ... Ishmael, F., Alley, S. C., & Benkovic, S. (2001). Identification and Mapping of Protein-Protein Interactions between gp32 and ...

https://pure.psu.edu/en/publications/identification-and-mapping-of-protein-protein-interactions-betwee

EPFL have developed a technique that can be a game-changer for genetics by making the characterisation of DNA-binding proteins ... The new technique called SMiLE-seq (semiautomated protein-dnA interaction characterisation technology, selective microfluidics- ... nor is it biased toward stronger affinity protein-DNA interactions as current methods might be. ... Germany boosts protein transition with €38m. Germany is set to follow countries such as the Denmark, the UK and the Netherlands ...

https://european-biotechnology.com/up-to-date/latest-news/news/new-technology-speeds-up-mapping-of-dna-protein-interaction.html

Sánchez Claros C, Tramontano A (2012) Detecting Mutually Exclusive Interactions in Protein-Protein Interaction Maps. PLoS ONE 7 ... Comprehensive protein interaction maps can complement genetic and biochemical experiments and allow the formulation of new ... BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns. ... Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through ...

https://repository.kaust.edu.sa/handle/10754/596839

Imaging the mobility of heterochromatin protein HP1α (ref. 4) in cell nuclei we could provide high-resolution diffusion maps ... To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions ... 3 measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue ... that performs fluorescence correlation spectroscopy at each pixel of an image to provide spatially resolved maps of protein ...

https://www.nature.com/articles/nbt.1928?error=cookies_not_supported&code=28f83a00-fc99-471b-9d87-effbd0192828

On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions. ... On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions. ...

https://experts.umn.edu/en/publications/on-silico-peptide-microarrays-for-high-resolution-mapping-of-anti/fingerprints/

It contains 2,922,202 unique protein-protein interactions (PPI) linked by 23,060 human proteins, making it the most ... The database of Human Annotated and Predicted Protein Interactions (HAPPI) version 2.0 is a major update to the original HAPPI ... These PPIs contain both physical/direct interactions and high-quality functional/indirect interactions. Compared with the HAPPI ... allowing them to retrieve human PPIs and available annotation information on the interaction type, interaction quality, ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3512-1/figures/4

Molecular interactions in cell membranes, particularly lipid-protein interactions in their hydrophobic core, are difficult to ... Our new article 1 present the proof of concept of a generalized approach for NMR studies of lipid-protein interactions that ... For instance, H/F substitution alters the charge distribution in the acyl chain, Also, interaction with membrane proteins may ... A generalized approach for NMR studies of lipid-protein interactions. Biochemistry • Chemistry • Molecular biology ...

https://mappingignorance.org/2018/09/19/a-generalized-approach-for-nmr-studies-of-lipid-protein-interactions/

... protein catalysts) in important metabolic pathways of existing land plants. Characterising protein-protein interaction networks ... Untangling the protein-protein interaction networks behind plant metabolic adaptation to land. Much as fish evolved into land ... However, little is known about the proteins in these pathways and their interactions in complex protein networks. With the ... Charting the evolution of protein-protein interaction networks shaping plant metabolic adaptation to land. ...

https://cordis.europa.eu/project/id/101065828

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 ...

https://en.wikipedia.org/wiki/Kethoxal

1. Yeast Protein Interaction Network. 2. Experimental music notation. 3. Seven Bridges of Königsberg. 4. Financial Network ... Mapping The Blogosphere mvblogosphere La Blogosphere Politique Mapping the Italian Blogosphere Visualization of Blogspace ... Mapping The Blogosphere mvblogosphere La Blogosphere Politique Mapping the Italian Blogosphere Visualization of Blogspace ... 1. map. 2. facebook. 3. timeline. 4. architecture. 5. music 6. time. 7. twitter. 8. network. 9. tree. 10. internet. ...

http://www.visualcomplexity.com/vc/index.cfm?trend=Blogosphere

1. Yeast Protein Interaction Network. 2. Seven Bridges of Königsberg. 3. Experimental music notation. 4. Neurovis. 5. Financial ... 1. map. 2. facebook. 3. timeline. 4. architecture. 5. music 6. time. 7. twitter. 8. network. 9. tree. 10. internet. ... 1. NYC Subway Map Redesign. 2. Windows vs Linux Server. 3. I Wish.... 4. Data visualisation of a social network. 5. Oil Money. ... 7. Web Trend Map v3.0. 8. Musicovery. 9. Neuronal Network. 10. Visualizing the Processing Flickr group. ...

http://visualcomplexity.com/vc/index.cfm?method=Radial%20Centralized%20Networks

... miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. starBase v2.0 now ... starBase v2.0: decoding miRNA-ncRNA, miRNA-ceRNA and protein-RNA interaction maps from large-scale CLIP-Seq data. Christoph , ... starBase v2.0: decoding miRNA-ncRNA, miRNA-ceRNA and protein-RNA interaction maps from large-scale CLIP-Seq data. ... 9,000 miRNA-circRNA interactions, (6)~10,000 ceRNA pairs, (7)~300,000 protein-RNA interactions, (8) two tools for functional ...

https://mirnablog.com/starbase-v2-0-decoding-mirna-ncrna-mirna-cerna-and-protein-rna-interaction-maps-from-large-scale-clip-seq-data/

The tool may be useful for protein engineering and drug design. ... A new technology that uses a proteins structure to predict the ... inner wiring that controls the proteins function and dynamics is now available for scientists to utilize. ... New Tool Enables Mapping of Protein Interaction Networks at Scale. Aug. 3, 2021 Bioengineers have developed a technology ... capable of revealing the protein-protein interactions (PPI) among thousands of proteins in a cell, in a single experiment. The ...

https://www.sciencedaily.com/releases/2020/09/200903095628.htm

A powerful platform for protein-protein interaction and protein phosphorylation studies in situ is created by combining Abnovas ... Antibody Pair for Protein Protein Interaction by Abnova - A powerful platform for protein-protein interaction and protein ... Lec 110 - Fly Paper: Mapping the Protein .... 03:05 , 3737 views Watch VIDEO. 10671 views ... This revolutionary combination enables unprecedented specificity and sensitivity of protein detection and quantification for ...

https://www.dnatube.com/video/4340/Antibody-Pair-for-Protein-Protein-Interaction

Mapping of domains responsible for nucleocapsid protein-phosphoprotein interaction of Henipaviruses. J Gen Virol. 2004;85:1675- ... Patch JR, Han Z, McCarthy SE, Yan L, Wang LF, Harty RN, The YPLGVG sequence of the Nipah virus matrix protein is required for ... Mutagenesis of the nucleocapsid protein of Nipah virus involved in capsid assembly. J Gen Virol. 2009;90:392-7. DOIPubMedGoogle ... Mutation of YMYL in the Nipah virus matrix protein abrogates budding and alters subcellular localization. J Virol. 2006;80: ...

https://wwwnc.cdc.gov/eid/article/18/2/11-1492-f2.htm

Protein Interaction Mapping. Watson GW, Wickramasekara S, Fang Y, Maier CS, Williams DE, Dashwood RH, Perez VI, Ho E. 2016. ... MRE11 Homologue Protein. Palomera-Sanchez Z, Watson GW, Wong CP, Beaver LM, Williams DE, Dashwood RH, Ho E. 2017. The ... Neoplasm Proteins. Palomera-Sanchez Z, Watson GW, Wong CP, Beaver LM, Williams DE, Dashwood RH, Ho E. 2017. The phytochemical 3 ...

https://lpi.oregonstate.edu/biblio?f%5Bauthor%5D=3156&o=asc&page=4&s=keyword

Next articleNew Technology Provides Protein Interaction Mapping a Proper Boost. Sophia Ktori ... "This work gives us unprecedented insight into mitochondrias life cycle and how they are recycled by key proteins that, when ... In most cells, damaged mitochondria are decomposed in a process known as mitophagy, which is initiated by two proteins, PINK1 ... Mutations in these same proteins also cause hereditary forms of Parkinsons disease. While the role of PINK1 and Parkin in ...

https://www.genengnews.com/news/genes-mutated-in-parkinsons-disease-linked-to-mitochondrial-recycling-in-neurons/

RNA-binding proteins (RBPs) are implicated in many biological functions. Here the authors expand the human and yeast RNA ... and many intensively studied proteins surprisingly emerge as RBPs (termed enigmRBPs), including almost all glycolytic enzymes ... and suggesting new roles of RNA as modulators of protein function. ... RNA-binding proteins (RBPs) exert a broad range of biological functions. To explore the scope of RBPs across eukaryotic ...

https://www.nature.com/articles/ncomms10127?error=cookies_not_supported&code=c5091869-768e-4980-abc7-a18a86bad28d

Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein ... Protein engineering, model predictions and designer proteins to characterize and reengineer protein interactions controlling ... Over the past several years, we have engineered a range of proteins with new functions, including protein-protein interactions ... A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. ...

https://pharmacy.ucsf.edu/tanja-kortemme

Mapping cell structure across scales by fusing protein images and interactions. Trey Ideker, UC San Diego School of Medicine, ... Interpretable prediction of molecular phenotypes in cancer with dense, high-resolution cell and tissue maps. Andrew H. Beck, ...

https://www.aacr.org/meeting/artificial-intelligence-2021/program-2/

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. Available at ... Considerations for Drug Interactions on QTc in Exploratory COVID-19 (Coronavirus Disease 2019) Treatment. Circulation. 2020 Apr ... Omicron spike protein is vulnerable to reduction. bioRxiv. 2023 Jan 06. [Full Text]. ... C-reactive protein 75 mg/L or greater) ...

https://emedicine.medscape.com/article/2500114-guidelines

DamID and pA-DamID: methods for the mapping of in vivo protein-genome interactions. ... 4D Nucleome: DamID-seq and pA-DamID-seq maps of nuclear lamina interactions. • GEO: A variety of whole-genome datasets (DamID, ... m6A-tracer: a derivative of DamID, to visualize DNA that has contacted a protein of interest in living cells. ... SuRE: a massively parallel reporter assay to map and measure the activity of regulatory elements in entire mammalian genomes. ...

https://www.nki.nl/research/research-groups/bas-van-steensel/our-technologies/

... combinatorial phage libraries against recombinant MMADHC allowed mapping of putative sites of interaction on each protein. ... Protein-protein interactions for early intracellular vitamin B12 metabolism in mammals. Vitamin B12, or cobalamin, is a water- ... Protein interaction analyses were extended by our recombinant production of the lysosomal membrane proteins LMBD1 and ABCD4. ... the objective of this thesis was to characterize the protein-protein interactions that coordinate this process. ...

https://www.mcgill.ca/microimm/james-w-coulton

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020. [Google Scholar] [CrossRef] ... Up-regulation of IL-6 and TNF-alpha induced by SARS-coronavirus spike protein in murine macrophages via NF-kappaB pathway. ... Three-Dimensional Interactions Analysis of the Anticancer Target c-Src Kinase with Its Inhibitors ... Von Langen, J.; Fritzemeier, K.H.; Diekmann, S.; Hillisch, A. Molecular basis of the interaction specificity between the human ...

https://www.mdpi.com/2072-6694/12/8/2325

Explore the role of protein-protein interactions in cancer at the Chemical Biology Program at Dana-Farber. Our research is ... Several labs in our program are driven by major interests in mapping, understanding, and targeting protein-protein interactions ... Protein-protein interactions (PPIs) mediate many of the cellular processes that are misfiring in cancer and other diseases. Yet ... The Kim Lab is developing innovative chemical methodologies for mapping and investigating PPIs. ...

https://www.dana-farber.org/research/integrative-research/chemical-biology/protein-protein-interactions

In short, from a total of 437 high-confidence interacting proteins that bind to one or more SARS-CoV-2 genes, the researchers have identified several gene products, M protein, NSP6, ORF3a, ORF6 and ORF7b that interacted with host cell membrane proteins and complexes. (news-medical.net)
For import of iron-siderophore complexes, seven proteins in the cell envelope of Escherichia coli are essential. (mcgill.ca)
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. (thebiogrid.org)
however, even knowledge of the stoichiometry, affinity and lifetime of every protein-protein interaction would not reveal the functional relationships between and within such complexes. (thebiogrid.org)
For some proteins it is known that they often bind to each other to form protein complexes. (unil.ch)
It won't work if you want to co-immunoprecipitate them or apply any proteomic biochemical method because you will have to use detergents, and then you destroy all the protein complexes. (genomeweb.com)
Unlike immunofluorescence microscopy approaches, which provide correlative information about proteins sharing cellular space, co-IP can confirm direct often high-affinity physical interactions between two proteins or protein complexes of equal or better affinity. (aacrjournals.org)
Protein complexes, which are formed as a result of these interactions, consist of two or more components that associate along specific pathways - protein association pathways. (lu.se)

By conducting a state-of-the-art interactome study between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host cells, researchers from the University of Texas MD Anderson Cancer Center in Houston identified 437 human proteins as the high-confidence interacting proteins - with substantial implications for understanding coronavirus disease 2019 (COVID-19) pathology and potential treatments. (news-medical.net)
As these may unveil promising drug targets, the analysis of host-virus interactome (i.e., a complete set of molecular interactions in a particular cell) is direly needed and have actually been reported recently. (news-medical.net)
For that purpose, we have two well-established strategies for studying protein-protein interactome on our disposal - affinity purification and a proximity labeling-based strategy, which is followed by mass spectrometry analysis. (news-medical.net)
The identified proteins were filtered with the use of Significance Analysis of INTeractome (abbreviated as SAINTexpress). (news-medical.net)
We show that this conserved RNA interactome harbours many proteins without previously assigned roles in RNA biology (enigmRBPs), including surprisingly many metabolic enzymes. (nature.com)
Proteins shown in red (FDR 0.01) represent the mRNA interactome. (nature.com)
c ) Overlap of mRNA interactome proteins in yeast and HuH-7. (nature.com)
d ) Validation of the yeast mRNA interactome using western blotting of input samples and eluate after interactome capture with specific antibodies (ADH1, alcohol dehydrogenase 1, PUB1) or against TAP-tagged proteins (PGK1, phosphoglycerate kinase 1, TDH1, triose phosphate dehydrogenase, TRX2, thioredoxine 2, SHE2, Swi5p-dependent HO Expression 2). (nature.com)
Yet, PPIs are notoriously difficult to target with small molecules, which necessitates the development of fundamentally different strategies to target and interrogate PPIs and map the cellular interactome, including those PPIs that involve intrinsically disordered proteomes (IDPs). (dana-farber.org)
At the Chemical Biology Program, we are developing new chemistry-based methodologies for targeting PPIs, such as stapled peptides, fragment-based strategies (FBDD), and complex natural product-based molecules, as well as pursuing biologically compatible reactions for mapping the cellular interactome. (dana-farber.org)
Mapping this network of interactions, or "interactome," has been slow going in the past because the number of interactions that could be tested at once was limited. (salk.edu)
The interactome of a cell, like a map of social networks, lets scientists see who's working with who in the world of proteins. (salk.edu)
Researchers from the University of Toronto have created a map of the protein interactions of 19 members of the ATP-binding cassette transporter class in a species of yeast, combining this data with previously-reported ABC transporter interactions into a comprehensive "interactome. (genomeweb.com)
The group went on in its recent study to investigate two potentially interesting associations revealed in the yeast ABC transporter interactome map: physical interactions of ABC transporters with one another and the interaction of these molecules with members of the zinc transport system. (genomeweb.com)

When the interactomes of NSP1 and N protein (i.e., two key SARS-CoV-2 proteins) were compared with other human coronaviruses , host pathways manipulations and divergent protein-protein interactions responsible for differences in disease pathology were uncovered. (news-medical.net)
The water-to-land transition was likely accompanied by the emergence and/or expansion of protein families that supported novel plant metabolic pathways. (europa.eu)
However, little is known about the proteins in these pathways and their interactions in complex protein networks. (europa.eu)
With the support of the Marie Skłodowska-Curie Actions programme, the EPPIMAL project will take a closer look at key enzymes (protein catalysts) in important metabolic pathways of existing land plants. (europa.eu)
Characterising protein-protein interaction networks will shed light on the evolution of plant metabolic pathways and potentially reveal overlooked proteins. (europa.eu)
This has been for instance the case for the pathways generating phenylpropanoids, specialized molecules serving as anti-UV and precursors to structural polymers, and the hormones abscisic acid (ABA) and strigolactones (SL) that help plant coordinate stress responses and interaction with microorganisms. (europa.eu)
While these three plant metabolic pathways are almost fully elucidated, little is known about (i) the organization of involved proteins in interacting networks and (ii) the evolutionary relevance of protein-protein interaction (PPI) networks for the emergence and function of metabolic pathways. (europa.eu)
The project shall disclose the conservation or expansion of PPI networks in the course of land plant evolution and potentially identify overlooked protein involved in investigated metabolic pathways. (europa.eu)
Altogether, EPPIMAL will bring original information on the evolution of protein networks shaping three iconic land plant metabolic pathways that supported plant adaptation to land. (europa.eu)
Wang and Dokholyan hypothesized that the physical forces from interactions between the atoms that make up the amino acids would allow them to predict allosteric pathways and sites in proteins. (sciencedaily.com)
Ohm was designed to account for the interactions between atoms and identifies areas of density in proteins to predict allosteric pathways and sites in proteins. (sciencedaily.com)
Ohm identifies regions and pathways of atomic density that allow it to predict allosteric sites in proteins. (sciencedaily.com)
Researchers around the world can use Ohm to predict allosteric sites and pathways in their protein of interest," Wang said. (sciencedaily.com)
This helps them figure out the roles of different proteins and piece together the different players in molecular pathways and processes. (salk.edu)
protein-protein interaction, canonical pathways etc. (unil.ch)
Kegg pathways include: cytokine-cytokine receptor interaction, Jak- STAT signaling pathway, MAPK signaling pathway, and hematopoietic cell lineage. (cdc.gov)

2020). A molecular map of lung neuroendocrine neoplasms. (who.int)
2020). Protein-altering germline mutations implicate novel genes related to lung cancer development. (who.int)

PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)

Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling. (nature.com)
Slaughter, B.D., Schwartz, J.W. & Li, R. Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging. (nature.com)
We aim to study the coupling between LTCC and β adrenergic receptors in different cardiomyocyte microdomains, the distinct involvement of PKA and CAMKII (Ca2+/calmodulin-dependent protein kinase II) and explore how this functional complex is disrupted in heart failure.Methods:Global signaling between LTCCs and β adrenergic receptors was assessed with whole-cell current recordings and western blot analysis. (imperial.ac.uk)
These 211 genes were interrogated with DAVID to find GO terms which included cytokine production, MAP kinase phosphatase activity, and cytokine binding. (cdc.gov)

We used affinity purification- mass spectrometry (AP-MS) to compare flavivirus -host interactions for two viruses (DENV and ZIKV ) in two hosts ( human and mosquito ). (bvsalud.org)
There are numerous methods for the discovery of unknown associated protein networks, with purification of the bait (the protein of interest) followed by mass spectrometry as a common theme. (aacrjournals.org)

The transmembrane domain prediction also indicated that these viral gene products contain at least one transmembrane domain in their protein sequences - with the exception of ORF6, which is actually a short protein with only 61 amino acids. (news-medical.net)
Each protein is built using sequences of 20 different amino acids. (sciencedaily.com)

We also introduce here the Estrella server that embodies this strategy, is designed for users interested in validating specific hypotheses about the functional role of a protein-protein interaction and it also allows access to pre-computed data for seven organisms. (edu.sa)
STRING 8--a global view on proteins and their functional interactions in 630 organisms. (edu.sa)
Defining the functional relationships between proteins is critical for understanding virtually all aspects of cell biology. (thebiogrid.org)
Interestingly, local stimulation of β1AR did not elicit any change in the Po of LTCCs, indicating a lack of proximal functional interaction between the two, but we confirmed a general activation of LTCC via β1AR. (imperial.ac.uk)
The goal of our laboratory is to develop, scale up, and broadly disseminate molecular technologies for mapping cells and functional circuits. (stanford.edu)
Overall, the study yielded a map covering 537 unique binary interactions across 366 proteins, the study authors wrote, which they annotated with functional classifications to create a standard map, as well as a map showing protein conservation in humans and known disease associations. (genomeweb.com)

Systems-level analysis of how flaviviruses hijack cellular processes through virus -host protein - protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. (bvsalud.org)
RNA-binding proteins (RBPs) mediate pivotal cellular functions such as RNA transport, degradation or translation and represent key effectors of post-transcriptional gene regulation. (nature.com)
Protein-protein interactions (PPIs) mediate many of the cellular processes that are misfiring in cancer and other diseases. (dana-farber.org)
At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)
Beyond the single cell, we also strive to map cellular ensembles, such as brain tissue. (stanford.edu)
We develop tools that can be used to construct cell and tissue atlases, and map the cellular circuits that give rise to function and behavior. (stanford.edu)
A new mapping method let researchers discover new links (gray lines) between two groups of plant proteins (yellow and blue) that have a common structure (the BBX domain), suggesting many different combinations of interactions, rather than a few, are involved in coordinating cellular programs like flowering time and circadian rhythm. (salk.edu)
If a newly discovered protein interacts with lots of other proteins involved in cellular metabolism, for instance, researchers can deduce that's a likely role for the new protein and potentially target it for treatments related to metabolic dysfunction. (salk.edu)
The group hopes the map, published online this week in Nature Chemical Biology , will be a resource for future applied research, providing insight into these molecules' roles in a variety of cellular processes with implications for drug development and other clinical areas. (genomeweb.com)
Stagljar and his colleagues previously developed a method, called a membrane yeast two-hybrid, or MYTH assay to allow them to study interactions of full-length membrane proteins in their natural cellular environment. (genomeweb.com)
One half of a split ubiquitin molecule is attached to an ABC transporter (or another cellular protein of interest) and the other half to its potential interaction targets. (genomeweb.com)
This involves purification of a specific protein from the pool of cellular proteins, followed by Western blotting of a suspected interacting protein ( 1 ). (aacrjournals.org)

Prof Malmström has a particular focus on developing new proteomics techniques to investigate protein interactions between hosts and pathogen and to investigate systemic proteome changes during sepsis. (lu.se)
Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. (lu.se)

In this study, the researchers applied the two aforementioned strategies: tandem affinity purification with the SFB ( S-protein , FLAG epitope, and streptavidin-binding peptide) tag, as well as proximity labeling by using a second-generation biotin ligase, BioID2. (news-medical.net)
Moreover, 314 high-confidence interacting proteins were identified from tandem affinity purification experiments, while 130 of them with the use of BioID2 strategy. (news-medical.net)
Here, we used biolayer interferometry and pulldown assays to identify regions of RAG1 necessary for interaction with RAG2 and to measure the RAG1-RAG2 binding affinity (KD ∼0.4 μM) (where RAG1 and RAG2 are recombination activating genes 1 or 2). (nih.gov)
According to the authors, SMiLE-seq is not limited by either the length of the DNA target sequence, nor is it biased toward stronger affinity protein-DNA interactions as current methods might be. (european-biotechnology.com)
Kinetic analyses using surface plasmon resonance (SPR) confirmed a sub-micromolar affinity for the MMACHC-MMADHC interaction. (mcgill.ca)
Whereas binding was undetectable in solution, the affinity of the CD4/pMHC II interaction could be measured in 2D using CD4- and adhesion molecule-functionalized, supported lipid bilayers, yielding a 2 D Kd of ∼5,000 molecules/μm 2 . (lu.se)

The known membrane protein structures, derived mainly by crystallography, provide little insight into lipid-protein interactions as bound lipid molecules are rarely visible. (mappingignorance.org)
NMR spectroscopy, contrarily, does not require molecular order and lipid-protein contacts may be sampled at low resolution to gauge protein insertion into the lipid layer, e.g. by use of paramagnetic agents that perturb the NMR signals of nearby membrane protein atoms. (mappingignorance.org)
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)
Overall, membrane protein interactions are difficult to study because of their biochemical features," he said. (genomeweb.com)

Proteins' structures are heterogeneous, so energy will flow through them in regions where the atoms are more densely packed together. (sciencedaily.com)
Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. (ucsf.edu)
For a subset of interactions essential for the virus life cycle, the authors determined the cryo-electron microscopy structures and mined patient data to understand how targeting host factors may be relevant to clinical outcomes. (cdc.gov)
Protein structures are invaluable for biochemical studies and for mechanical or molecular mechanics calculations have become the understanding of how proteins work. (lu.se)
The most common strong alternative and complement to experimental methods to methods to obtain protein structures are X-ray crystallography obtain insight in biochemical processes. (lu.se)

Loading of the helicase onto gp32 (the T4 single strand binding protein)-coated single-stranded DNA requires gp59 to remove gp32 and replace it with gp41. (psu.edu)
Since Cys-166 lies in the DNA binding core domain of gp32, this interaction may affect the association of gp32 with DNA. (psu.edu)
Scientists at EPFL have developed a technique that can be a game-changer for genetics by making the characterisation of DNA-binding proteins much faster, more accurate, and efficient. (european-biotechnology.com)
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)
RNA-binding proteins (RBPs) exert a broad range of biological functions. (nature.com)
Only 60% of yeast and 73% of the human RBPs have functions assigned to RNA biology or structural motifs known to convey RNA binding, and many intensively studied proteins surprisingly emerge as RBPs (termed 'enigmRBPs'), including almost all glycolytic enzymes, pointing to emerging connections between gene regulation and metabolism. (nature.com)
One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
Pentapeptide insertion mutagenesis of the Hoxa1 protein: mapping of transcription activation and DNA-binding regulatory domains. (nih.gov)
However, when presented multivalently on magnetic beads, soluble CD4 bound pMHC II-expressing B cells, confirming that it is active and allowing mapping of the native coreceptor binding site on pMHC II. (lu.se)
The high mobility of hydration water ensures that all thermally activated processes at the protein-water interface, such as binding, recognition and catalysis, can proceed at high rates. (lu.se)
To make proteins, such as binding, recognition and catalysis, often progress, it is therefore helpful to adopt a sceptical atti- involve specific interactions with individual water mol- tude. (lu.se)

Interestingly, only seven proteins overlapped between these two methods. (news-medical.net)

He said that many drugs on the market, such as G Protein-Coupled Receptor (GPCR) drugs, may cause unintended side effects because they target proteins that are similar in structure to their intended target. (sciencedaily.com)
It concerns finding suitable drug candidates against the SARS-coV-2 virus using magnetic X-ray-based high-efficiency screening of appropriate substance libraries to find substances that act directly against two important target proteins that the virus has. (umu.se)

mechanics (QM), in particular the Schr ¨odinger equation, allow us different proteins, e.g. alcohol dehydrogenase, blue copper proteins, to calculate any measurable property of a defined set of atoms. (lu.se)

They then combined the MYTH screening results with previously reported ABC transporter physical interactions available through the BioGRID database. (genomeweb.com)

Genome annotation disclosed 29 SARS-CoV-2 gene products - including 16 non-structural proteins, 4 structural proteins and 9 accessory factors. (news-medical.net)
Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies. (edu.sa)
Structural rearrangements in membranes and embedded proteins, and the way molecular interactions contribute to their function are unresolved questions in biophysical chemistry. (mappingignorance.org)
SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
A general property of disordered proteins is their structural expansion that results in a high macromolecular flexibility. (lu.se)

abstract = "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. (psu.edu)

the objective of this thesis was to characterize the protein-protein interactions that coordinate this process. (mcgill.ca)

In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)

A genetic interaction is inferred when mutations in separate genes, each of which alone causes a minimal phenotype, result in a significant growth defect under a given condition when combined in the same cell. (thebiogrid.org)

Quantitative Western blotting allowed us to estimate that mouse thymocytes contain on average ∼1,800 monomers of RAG1 and ∼15,000 molecules of RAG2, implying that nuclear concentrations of RAG1 and RAG2 are below the KD value for their interaction, which could help limit off-target RAG activity. (nih.gov)
These are locations where proteins are particularly sensitive to relay certain changes in their structure and function as a result of external stimuli including other proteins, small molecules, water or ions. (sciencedaily.com)
Maps also chart the connectivity between these molecules, elucidating the circuits and signaling processes that give rise to function. (stanford.edu)
Recent oxygen-17 magnetic relaxation dispersion (MRD) experiments have shown that the vast majority of water molecules in the protein hydration layer suffer a mere twofold dynamic retardation compared with bulk water. (lu.se)

While the molecular nature of intracellular cobalamin metabolism in mammals remains poorly understood, the proteins MMACHC, MMADHC, LMBD1 and ABCD4 are implicated in its early uptake and processing. (mcgill.ca)

This revolutionary combination enables unprecedented specificity and sensitivity of protein detection and quantification for high performance immunofluorescence and immunohistochemistry applications. (dnatube.com)

In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
LA JOLLA-Salk scientists have developed a new high-throughput technique to determine which proteins in a cell interact with each other. (salk.edu)
If the proteins of interest interact inside the cell, a gene called Cre is activated. (salk.edu)
They revealed more than 8,000 interactions among those proteins tested, giving them new insight into which Arabidopsis transcription factors interact with each other. (salk.edu)
Igor Stagljar, the study's senior author, told ProteoMonitor this week that his team has been interested broadly in how integral membrane proteins interact at the genome-wide level. (genomeweb.com)
One contribution of 16 to a Discussion Meeting Issue `The molecular interact with a protein can, with little ambiguity, be classi- basis of life: is life possible without water? (lu.se)

Ultimately, specific lipid-protein contacts are revealed by intermolecular 1 H, 1 H nuclear Overhauser effect signals. (mappingignorance.org)
Orthogonal isotope filtering for 19 F (on the acyl chain) vs . 13 C or 15 N (on the protein) will then yield NMR spectra with only intermolecular lipid-protein signals and well-dispersed acyl chain 1 H frequencies. (mappingignorance.org)
Recently we have shown that a coarse-grained model based on the primitive model, that has been used for modelling polyelectrolytes for over 30 years, works well for a range of IDPs where electrostatics governs the intra- and intermolecular interactions [1]. (lu.se)

Cross-linking studies between gp32 and gp59 reveal an interaction between Cys-166 of gp32 and Cys-42 of gp59. (psu.edu)
Imaging the mobility of heterochromatin protein HP1α (ref. 4 ) in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. (nature.com)

As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis. (springer.com)
Though the group did the mapping with ABC transporters from a yeast species - Saccharomyces cerevisiae - many of the proteins are homologous to disease-linked human ABC proteins. (genomeweb.com)

Thus, comparative flavivirus -host PPI mapping provides biological insights and, when coupled with in vivo models, can be used to unravel pathogenic mechanisms. (bvsalud.org)
Stagljar said that his team is interested in following up on some insights from the map that are promising for human pharmaceutical research. (genomeweb.com)

Conserved virus -host PPIs revealed that the flavivirus NS5 protein suppresses interferon stimulated genes by inhibiting recruitment of the transcription complex PAF1C and that chemical modulation of SEC61 inhibits DENV and ZIKV replication in human and mosquito cells . (bvsalud.org)
The Popeye domain containing (POPDC) genes encode sarcolemma-localized cAMP effector proteins. (imperial.ac.uk)
For example, the encoded protein represses the transcription of differentiation-specific genes during keratinocyte proliferation, but this repression is then overcome by differentiation signals. (nih.gov)
The genes for two proteins, each on their own circle of DNA, are added to the same cell. (salk.edu)
When turned on, Cre physically splices the two individual circles of DNA together, thus pairing the genes of interacting proteins together so the team can easily find them through sequencing. (salk.edu)
The team can generate a massive library of yeast cells-each containing different pairs of proteins by introducing random combinations of genes on circular DNA called plasmids. (salk.edu)
Therefore, if we have multiple loci all containing a gene that affects the trait and we know that each locus contains a gene whose protein product form a complex together, it is probable, that its these genes have an effect on the trait. (unil.ch)
Las redes funcionan para en última instancia especificar la expresión de conjuntos concretos de GENES para estados, momentos o lugares específicos. (bvsalud.org)

Ohm may be useful for biomedical researchers seeking to identify allosteric sites in proteins that play key roles in biological processes of certain diseases. (sciencedaily.com)

Molecular interactions in cell membranes, particularly lipid-protein interactions in their hydrophobic core, are difficult to analyse and remain poorly characterised despite high relevance in physiological and pathological processes. (mappingignorance.org)

The researchers have also built an interaction network by utilizing the 437 identified virus-host protein-protein interactions, which enabled all the complex analyses that they have pursued. (news-medical.net)
Higher resolution analyses of lipid-protein contacts require more range-limited, directed, and unambiguous NMR indicators. (mappingignorance.org)
We do not aim to provide an exhaustive analysis of all available techniques, but instead will highlight some of the most widely used methods for protein-protein assessment and will describe some recent advances in global protein-protein analyses that are enabling non-experts to identify interactomes of their favorite factor. (aacrjournals.org)

But finding all the interactions between, for instance, 1,000 proteins, would require 1000 separate experiments to screen once for each bait's interaction partners. (salk.edu)

Panning combinatorial phage libraries against recombinant MMADHC allowed mapping of putative sites of interaction on each protein. (mcgill.ca)
These tend to fall roughly into two categories: validation of putative or suspected interactions and identification of unknown associated proteins. (aacrjournals.org)

To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. (nature.com)
Expression of these proteins is spatially and temporally regulated during embryonic development. (nih.gov)

With this in mind, a research group led by Dr. Zhen Chen from the Department of Experimental Radiation Oncology at the University of Texas MD Anderson Cancer Center in Houston (USA) started with a quest for key human proteins that are implicated in the SARS-CoV-2 life cycle. (news-medical.net)
Create new proteins and devices with more advanced functions by experimental engineering. (ucsf.edu)
Our aim here is to critically examine central concepts in the description of protein hydration, and to assess the experimental basis for the current view of protein hydration, with the focus on dynamic aspects. (lu.se)
During this evolutionary process, the experimental basis of the current (multiple) views on proteins have adapted to and exploited the unique physi- protein hydration, with an emphasis on the dynamic cal properties of liquid water (Eisenberg & Kauzmann aspects. (lu.se)
Quasielastic incoherent neutron scattering (QENS) is a well-suited experimental method to study protein dynamics from the picosecond to several nanoseconds and in the Ångström length-scale. (lu.se)

methods for the mapping of in vivo protein-genome interactions. (nki.nl)
Briefly, MYTH adapts a previously developed split ubiquitin method as an in vivo sensor of protein-protein interactions. (genomeweb.com)

The computational analysis of the maps may help to focus on interesting cases and thereby to appropriately prioritize the validation experiments. (edu.sa)
I. Develop computational methods for modeling & design of proteins, in the program Rosetta ( www.rosettacommons.org ). (ucsf.edu)
Most recently, we have focused on application of computational protein design to endow cells with the ability to sense and respond to new molecular signals and orchestrate desired biological responses, one of the most fundamental capabilities of living systems (Glasgow*, Huang*, Mandell* et al. (ucsf.edu)

To date, the number of reported yeast protein interactions that have been truly validated by at least one other approach is low. (nih.gov)

The tool, developed by researchers at Penn State, may be useful for protein engineering and drug design. (sciencedaily.com)
Dokholyan, a member of the Penn State Cancer Institute, said that Ohm can analyze allosteric paths in any protein and that researchers can access the tool through a server on his lab's website. (sciencedaily.com)
The study is a collaboration between researchers at Gothenburg University and Umeå University, where the Umeå-based national SciLifeLab nodes Swedish NMR Centre and Chemical Biology Consortium Sweden are used together with Umeå University's own Protein Expertise Platform (PEP), where the target protein is produced. (umu.se)
The new approach, published June 26 in Nature Methods , lets researchers test millions of relationships between thousands of proteins in a single experiment. (salk.edu)
Until now, researchers have typically relied on standard high-throughput yeast two-hybrid (Y2H) assays to determine the interactions between proteins. (salk.edu)
When cells are positive for a protein interaction, the researchers can use genetic sequencing to figure out what the two proteins interacting are, using new high-throughput DNA sequencing technologies similar to those used for human genome sequencing. (salk.edu)
As such, approaches for rapid, unbiased identification of protein interactomes are becoming a standard tool in the researchers toolbox, rather than a technique that is only available to specialists. (aacrjournals.org)

An Epistatic MiniArray Profile (E-MAP) analysis was used to quantitatively score genetic interactions based on fitness defects estimated from the colony size of double versus single mutants. (thebiogrid.org)

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. (bvsalud.org)
Mapping the MOB proteins' proximity network reveals a unique interaction between human MOB3C and the RNase P complex. (iric.ca)
An Epstein-Barr virus protein interaction map reveals NLRP3 inflammasome evasion via MAVS UFMylation. (harvard.edu)

Significant insight into the function of proteins can be delineated by discovering and characterizing interacting proteins. (aacrjournals.org)

The system requires using a single known protein-known as the "bait"-to screen against a pool of "prey" proteins. (salk.edu)
This way, they're no longer limited to testing one "bait" protein at a time, but could test the interactions between all the proteins in a library at once. (salk.edu)

starBase is a database that can be used for decoding miRNA-mRNA, miRNA-ceRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. (mirnablog.com)
The neuroinflammatory response was further confirmed with elevated pSTAT3 protein by ELISA and elevated neuroinflammatory cytokines and chemokines mRNA (TNFalpha, IL6, CCL2, IL1beta, LIF, and OSM) by qPCR. (cdc.gov)

Here we describe a microscope based on light-sheet illumination 2 that allows massively parallel fluorescence correlation spectroscopy (FCS) 3 measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. (nature.com)

In recent years, advances have permitted the purification of endogenous proteins and methods for scaling down starting material. (aacrjournals.org)

by Abnova - A powerful platform for protein-protein interaction and protein phosphorylation studies in situ is created by combining Abnovas dual recognition, primary antibody pair with proximity ligation assay from Olink Bioscience. (dnatube.com)
We have also engineered proteins whose functions can be switched by phosphorylation or light. (ucsf.edu)

The mapping of human protein interaction networks is even more complicated. (nih.gov)
instead, interaction mapping in human cell lines should be focused along the lines of diseases or changes that can be associated with specific cells. (nih.gov)
In this paper, an approach for combining different 'omics' technologies to achieve efficient mapping and validation of protein interactions in human cell lines is presented. (nih.gov)
Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools. (edu.sa)
A genome-scale library of Gateway-adapted human ORF clones, the CCSB Human ORFeome Library (aka hORFeome V5.1) is ideal for transferring thousands of open reading frames into a variety of protein expression systems. (horizondiscovery.com)
Important for the map's potential usefulness in future clinically-oriented research, 50 percent of the interactions mapped involve a target with an identifiable human ortholog, about 40 percent of which are known to be associated with human disease. (genomeweb.com)

The RAG endonuclease consists of RAG1, which contains the active site for DNA cleavage, and RAG2, an accessory factor whose interaction with RAG1 is critical for catalytic function. (nih.gov)
Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)

the results of the systematic identification of protein−protein interactions for the hospital-acquired strain MRSA-252. (pacificimmunology.com)
The number of studies that have used protein interaction discovery approaches for identification of associated factors is overwhelming. (aacrjournals.org)

Dynamic mapping of proteome trafficking within and between living cells by TransitID. (stanford.edu)

According to Dokholyan, Ohm's ability to predict allosteric sites in proteins may be useful for developing targeted therapeutics for certain disease states. (sciencedaily.com)

The mapping of protein-protein interactions is key to understanding biological processes. (nih.gov)
Signaling at and between allosteric sites in proteins regulate many biological processes. (sciencedaily.com)
Our predictions generate hypotheses on protein conformations controlling biological processes - such as protein recognition, signal transduction, and enzyme active site gating - and are laying the foundation for our work reengineering and "reshaping" protein interfaces and active sites for new functions. (ucsf.edu)
Over the past several years, we have engineered a range of proteins with new functions, including protein-protein interactions that are specific enough to control complex biological processes in mammalian cells (Kapp*, Liu* et al. (ucsf.edu)

After cell lysis, polyadenylated RNAs were captured on oligo d(T) beads followed by stringent washes to remove non-crosslinked proteins. (nature.com)
The Coulton research group studies membrane proteins (MPs) that are required for transport of iron, an essential nutrient, across the bacterial cell envelope. (mcgill.ca)
If the two bind, the ubiquitin molecule reforms, triggering the yeast cell to signal the interaction by turning blue, Stagljar explained. (genomeweb.com)
We strive for a detailed understanding of the interactions between cells and nanostructures with respect to cell behavior, cell physiology and cell mechanics. (lu.se)
Our goal is to understand in detail the interactions between cells and nanostructures such as nanowires and nanotubes with respect to cell behavior, cell physiology and cell mechanics. (lu.se)
In order to deepen our understanding of the interactions between the cell membrane and nanostructures, we perform STED microscopy live imaging of the membrane of cells cultured on nanostructures. (lu.se)

Chemicals and Drugs1

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

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

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

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

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

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

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

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

No images available that match "protein interaction mapping"

Protein Interaction Mapping

Two-Hybrid System Techniques

Protein Interaction Maps

Chromosome Mapping

Protein Interaction Domains and Motifs

Protein Binding

Proteins

Databases, Protein

Molecular Sequence Data

Protein Structure, Tertiary

Amino Acid Sequence

Computational Biology

Algorithms

Binding Sites

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

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

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

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

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

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

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

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

Combining different 'omics' technologies to map and validate protein-protein interactions in humans

Researchers develop detailed map of protein-protein interactions between SARS-CoV-2 and the host

Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2

Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus

Identification and Mapping of Protein-Protein Interactions between gp32 and gp59 by Cross-linking<...

New technology speeds up mapping of DNA-protein interaction - European Biotechnology

Detecting mutually exclusive interactions in protein-protein interaction maps.

Quantitative fluorescence imaging of protein diffusion and interaction in living cells | Nature Biotechnology

On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions -...

HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions | BMC Genomics | Full Text

A generalized approach for NMR studies of lipid-protein interactions - Mapping Ignorance

Charting the evolution of protein-protein interaction networks shaping plant metabolic adaptation to land | EPPIMAL | Project |...

Kethoxal - Wikipedia

visualcomplexity.com | A visual exploration on mapping complex networks

visualcomplexity.com | A visual exploration on mapping complex networks

starBase v2.0: decoding miRNA-ncRNA, miRNA-ceRNA and protein-RNA interaction maps from large-scale CLIP-Seq data - miRNA Blog

New computational tool enables prediction of key functional sites in proteins based on structure | ScienceDaily

Antibody Pair for Protein Protein Interaction - DnaTube.com - Scientific Video and Animation Site

Figure 2 - Characterization of Nipah Virus from Outbreaks in Bangladesh, 2008-2010 - Volume 18, Number 2-February 2012 -...

Biblio | Page 5 | Linus Pauling Institute | Oregon State University

Genes Mutated in Parkinson's Disease Linked to Mitochondrial Recycling in Neurons

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs | Nature Communications

Tanja Kortemme, PhD · School of Pharmacy · UCSF

Program | Artificial Intelligence, Diagnosis, and Imaging | AACR Meetings

Coronavirus Disease 2019 (COVID-19) Guidelines: Guidelines Summary, CDC Evaluating and Testing Persons Under Investigation (PUI...

Our technologies | Netherlands Cancer Institute

James W Coulton | Microbiology & Immunology - McGill University

Cancers | Free Full-Text | Sex Hormones and Hormone Therapy during COVID-19 Pandemic: Implications for Patients with Cancer

Protein-Protein Interactions | Dana-Farber Cancer Institute

Complexes8

Interactome14

Pathways16

20202

Localization1

Kinase4

Mass spectrometry2

Sequences2

Functional6

Cellular12

Proteomics2

Affinity6

Membrane protein4

Structures5

Binding11

Seven proteins1

Target proteins2

Different proteins1

Physical Interactions1

Structural5

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Characterize1

Humans1

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Molecules4

Metabolism1

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Interact6

Intermolecular3