Protein interactions. Medical search. Frequent questions

8, 2020 Like wrenches made of Legos, SWI/SNF chromatin remodeling complexes tighten or loosen DNA in our cells to control how genes are turned on and made into proteins. (sciencedaily.com)
We have also made available our software through different web servers, such as pyDockWeb for protein-protein docking, pyDockSAXS for the structural prediction of protein complexes using Small-Angle X-ray Scattering (SAXS) data in collaboration with Pau Bernadó (CBS, Montpellier), or OPRA for the identification of RNA-binding residues in proteins. (bsc.es)
More efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. (bsc.es)
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)
In fact, a large number of proteins need to form protein complexes or oligomers to carry out their functions. (jove.com)
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. (jove.com)
Hydroxyl Radical Footprinting of Protein-DNA Complexes Indu Jagannathan and Jeffrey J. Hayes 6. (nhbs.com)
Ethylation Interference Footprinting of DNA-Protein Complexes Iain W. Manfield and Peter G. Stockley 10. (nhbs.com)
Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates within Model Chromatin Complexes David R. Chafin and Jeffrey J. Hayes 11. (nhbs.com)
Structural complexes between proteins and their substrates can be studied in the gas-phase to determine equilibrium dissociation constants. (biosyn.com)
then, a specific antibody immunoprecipitates protein-associated RNA-DNA complexes. (epigenie.com)
Indeed, the identification of Kcnq1ot1, which targets Polycomb complexes to repressed genomic domains, and the significant overlap of ncRNAs isolated via a conventional technique suggest that RedChIP represents the way forward for studies of RNA-protein-DNA interactions in live cells. (epigenie.com)
The ARID1A gene provides instructions for making a protein that forms one piece (subunit) of several different SWI/SNF protein complexes. (medlineplus.gov)
S487, 478 variants in 56 protein complexes. (lu.se)
S4191, 4191 single variants in 265 protein complexes, M1707, 1707 multiple variants in 120 protein complexes. (lu.se)
Jemimah S, Sekijima M, Gromiha M, ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification, Bioinformatics;36(6):1725-1730. (lu.se)

Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
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)
Computer programs can predict PPIs based on similar interactions found in other proteins by comparing protein sequences and three-dimensional structures. (jove.com)
The core experimental aim of the project is to develop a new single-molecule spectroscopic method, dynamic single-molecule Metal Induced Energy Transfer (or dynamic smMIET), which will be suited to study the conformational dynamics of intrinsically disordered peptides (sequences of FG-repeat proteins from the nuclear pore), and of small folding protein motifs, in particular helix-turn-helix (HTH) and WW-domain motifs. (uni-goettingen.de)
Natural proteins fold thus, not necessarily only because their structures are well-suited for folding, but because their sequences optimize packing and fit their structures well. (ncbs.res.in)
Additionally, in protein design, where sequences are designed for natural and new non-natural structures, tens of sequences still need to be tested before success is achieved. (ncbs.res.in)
Both these issues may be caused by the specific scaffolds used in design, i.e., some protein scaffolds may be more tolerant to packing perturbations and varied sequences. (ncbs.res.in)
Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. (nhbs.com)

Genetic interaction analysis,in which two mutations have a combined effect not exhibited by either mutation alone, is a powerful and widespread tool for establishing functional linkages between genes. (nih.gov)
The researchers have mapped altered protein-protein interactions resulting from mutations in major cancer-associated genes such as BRAF, AKT1, SPOP and SMAD4. (emory.edu)
The researchers extended this study and mapped altered protein-protein interactions resulting from mutations in other cancer-associated genes such as P53, PTEN and EGFR, and have made the data available to the cancer research community. (emory.edu)
We investigate the functional relevance of de novo missense variants, specifically whether they are likely to disrupt protein interactions, and nominate novel genes in risk for ASD through integrated genomic, transcriptomic, and proteomic analyses. (springer.com)
For genes encoding the disrupted interactions, we evaluate their expression patterns across developing brains and within specific cell types, using both bulk and inferred cell-type-specific brain transcriptomes. (springer.com)
Finally, we integrate protein interactions and cell-type-specific co-expression networks together with published association data to implicate novel genes in ASD risk in a cell-type-specific manner. (springer.com)
Genes encoding disrupted complementary interactors tend to be risk genes, and an interaction network built from these proteins is enriched for ASD proteins. (springer.com)
Consistent with other studies, genes identified by disrupted protein interactions are expressed early in development and in excitatory and inhibitory neuronal lineages. (springer.com)
Using the newly released and larger ASC dataset, we confirm these observations and take them in several new directions: (1) By defining a set of genes encoding these disrupted protein interactors in ASD subjects and another for their siblings, we evaluate their expression patterns in developing brain from fetal to early postnatal development and within general cell types of brain tissue. (springer.com)
The researchers hope that the identification of new autism genes will pave the way for studies of protein function that may help better understand the mechanics of autism at the cellular level. (sfari.org)
Gage's team conducted screens in cells from mice and rats to see which genes were being transcribed into proteins in precursor cells, immature neurons and astrocytes. (neurosciencenews.com)
Interestingly, Nup153 levels are also known to be high in cells with elevated levels of a mobile protein called Sox2, a transcription factor that floats around the nucleus and binds to genes and turns them on or off. (neurosciencenews.com)
Understanding the interactions between our environment and our genes and how they affect health outcomes offers a multitude of potential opportunities in public health. (cdc.gov)

The research, performed by Vivien Nagy, a visiting graduate student, André Hoelz, a research associate, and colleagues in Rockefeller University's Laboratory of Cell Biology, uncovered the molecular structure of three interacting proteins that form the centerpiece of the Nup84 complex - an important structural component of the nuclear pore complex. (sciencedaily.com)
Previous X-ray structural studies at ambient temperature described several different protein domains including a large cavity in each subunit of the dimeric protein. (rcsb.org)
The main focus of our research is the development and optimization for High-Performing-Computing (HPC) of computational methodology for the structural and energetic characterization of protein interactions at molecular level. (bsc.es)
We aim to develop and optimize computational algorithms for characterizing and understanding protein-protein interactions, which remains one of the most important challenges in Structural Biology. (bsc.es)
At present it offers more information about protein-protein interaction dynamics than can be obtained with conventional structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. (the-scientist.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)
Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. (cshlpress.com)
hi, I try to purify a protein from yeast to assay some structural studies. (bio.net)
This includes selective binding of proteins, structural change after binding and the functional implications. (lu.se)

The team's analyses highlighted a host of interactions between SARS-CoV-2-encoded and human proteins, dubbed the SARS-CoV-2 interactome (HuSCI), prompting more detailed analyses and genetic knockdown experiments with gene-edited viruses and ACE2 receptor-expressing lung cell lines. (genomeweb.com)
The team's results suggested that proteins encoded by SARS-CoV-2 may be particularly prone to interacting with human proteins that contain genetic alterations previously implicated in individuals' risk of severe COVID-19 or "long COVID" cases that persist over long periods of time. (genomeweb.com)
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)
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)
We first use a maximum parsimony- based approach to infer the ages of human proteins. (princeton.edu)
However, not much is known about the general characteristic features of the human proteins interacting with viral proteins (referred to as hVIPs) as well as the motifs and domains utilized by human - virus protein - protein interactions (referred to as Hu-Vir PPIs). (bvsalud.org)
These aforementioned findings suggest that conformational flexibility , spatial diversity, abundance and slow evolution are the characteristic features of the human proteins targeted by viral proteins . (bvsalud.org)
Hu-Vir PPIs are mostly mediated via domain-motif interactions (DMIs) where viral proteins employ motifs that mimic host ELMs to bind to domains in human proteins . (bvsalud.org)

The physical shape of the interfaces determines the way two proteins interact. (jove.com)
Co-immunoprecipitation of proteins and yeast two-hybrid screening are widely used to provide evidence on whether two proteins interact in vitro . (jove.com)
In the first part of this thesis, we introduce a metric, functional insularity, to measure the degree to which proteins physically interact with functionally related proteins. (princeton.edu)
In addition, we nd that proteins tend to physically interact mainly with other proteins of similar age. (princeton.edu)
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)
Researchers also check their results by verifying whether the two proteins in question, such as BRAF and KEAP1, actually interact in relevant cancer cells using other biochemical and cellular tests. (emory.edu)
They have assembled a collection of proteins known to be implicated in these pathways and then screened a library of all human brain proteins to find other proteins that interact with those in the collection. (sfari.org)

Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
Identification of protein-protein interactions (PPIs) is important for understanding how proteins work together in a coordinated fashion in a cell to perform cellular functions. (nature.com)
PPIs are essential for individual protein functions, forming various cellular pathways, and are also involved in the development of diseases. (nature.com)
Other representative plant species cover even less protein involved in known PPIs. (nature.com)
Although protein-protein interactions (PPIs) are promising targets, drugging them is one of the key challenges in drug discovery 19 . (nature.com)

Another Salk professor and a coauthor on the paper, Martin Hetzer, previously found that proteins in the nuclear membrane influence gene expression in different kinds of cancer cells. (neurosciencenews.com)
In the precursors, they discovered high numbers of a protein called Nup153, which is part of a multiprotein complex that forms a gatekeeping pore in the nuclear membrane, controlling what goes in or out. (neurosciencenews.com)
Mechanisms of toxicity include inhibition of enzyme activity and protein synthesis, alterations in nucleic acid function, and changes in cell membrane permeability. (medscape.com)

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)
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)
Laboratory methods, such as affinity purification, mass spectrometry, and protein microarrays, can be used to identify new interactions. (jove.com)
We foresee that applying this strategy on a variety of domain families of different architecture will enable the development of general models that can predict the affinity of an interaction from the sequenece of the two partners. (irbbarcelona.org)
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)
We start this review by describing three techniques that can be used for this purpose: (i) affinity-tagged proteins (ii) the two-hybrid system and (iii) some quantitative proteomic techniques that can be used in combination with, e.g., affinity chromatography and coimmunoprecipitation for screening of protein-protein interactions. (lu.se)
Li M, Petukh M, Alexov E, Panchenko A, Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity,J Chem Theory Comput:1770-1780. (lu.se)
Zhang C, Zheng W, Zhang Y, BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts, J Mol Biol. (lu.se)
Huang X, Zheng W, Pearce R, Zhang Y, Huang X, Zheng W, Pearce R, Zhang Y, SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function, Bioinformatics;36(8):2429-2437. (lu.se)
Wang M, Cang Z, Wei G, A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation, Nat Mach Intell):116-123. (lu.se)

Glycosylation, i.e., the addition of glycans (a generic name for monosaccharides and oligosaccharides) to a protein, is one of the major post-translational modification of proteins contributing to the enormous biological complexity of life. (wikipedia.org)
A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. (nature.com)
To achieve high biological specificity, protein kinases and phosphatases often recognize their targets through interactions that occur outside of the active site. (nih.gov)
Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. (nature.com)
Many biological processes depend on protein-protein interactions. (jove.com)
Protein-protein interaction (PPI) networks enable the transmission of biological in- formation throughout cells, allowing cells to respond to environmental stimuli. (princeton.edu)
In sum, this thesis advances our understanding of PPI networks by showing that the dual requirements of modularity and connectivity are balanced using \connector" proteins and "module" proteins, which have distinct biological traits, and by un- covering differences between young and old proteins that suggest that proteins gain functions and integrate into networks over time. (princeton.edu)
Our study not only revealed an elegant example of biological regulation but also provides a new approach for developing pH-dependent protein devices and biomaterials for biotechnological application," said Feng. (phys.org)
MOTIVATION Viruses , from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. (bvsalud.org)
We study the interaction between proteins in biological fluids as well as single proteins to nanomaterials of different kinds. (lu.se)

However, we observed that mutations at these residues often substantially reduce the degree of protein production. (aps.org)
Overall, this method can be used to identify protein scaffolds that are more amenable to whole protein design as well as to identify protein regions which are sensitive to perturbations and where further mutations should be avoided during protein engineering. (ncbs.res.in)
Scientists at Emory University led by Winship Cancer Institute researcher Haian Fu, PhD , have revealed widespread distortions of a cell's protein interaction machinery resulting from cancer-causing mutations. (emory.edu)
Rodrigues C, Pires D, Ascher D, mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions, Nucleic Acids Res;49(W1):W417-W424. (lu.se)
Rodrigues C, Myung Y, Pires D, Ascher D, mCSM-PPI2: predicting the effects of mutations on protein-protein interactions, Nucleic Acids Res. (lu.se)

In other cases, different proteins or polypeptides come together to form a functional unit. (jove.com)
We find that functional and topological network modules con- tain proteins with a range of insularity values, including low-insularity proteins that might may function as \interfaces" to other modules. (princeton.edu)
The model proposes the cap's interactions, with eIF4E, eIF4G, PABP, and the poly(A) tail and that the disruption of these interactions leads to functional effects. (biosyn.com)
This type of switching between two functional sites has not been noted for any interaction between proteins previously. (phys.org)
Protein interaction networks represent the backbone of the cell's functional organization. (irbbarcelona.org)

Although the role of modular protein-protein interaction domains in kinase and phosphatase signaling has been well characterized, it is becoming clear that many kinases and phosphatases utilize docking interactions - recognition of a short peptide motif in target partners by a groove on the catalytic domain that is separate from the active site. (nih.gov)
In a study published in Nature Cancer , a research team at The Hospital for Sick Children (SickKids) showcased a new potential treatment approach for glioblastoma called a designer peptide, which targets a protein-protein interaction in the glioblastoma cells. (innovations-report.com)
By uncovering the role of a previously unknown protein-protein interaction in glioblastoma, we were able to develop a designer peptide which possesses robust therapeutic efficacy in treating all major types of glioblastoma in preclinical models," says Dr. Xi Huang , a Senior Scientist in the Developmental & Stem Cell Biology program . (innovations-report.com)
The development of the designer peptide began when Huang and first author Dr. Weifan Dong discovered that two proteins called EAG2 and Kvβ2, both highly present in glioblastoma cells, were interacting where cancerous cells meet with healthy brain tissue. (innovations-report.com)
The designer peptide prevents the protein-protein interaction from occurring, slowing growth and deterring the cancer from spreading into surrounding cells. (innovations-report.com)
Using this YaxAB nanopore, we demonstrate label-free, single-molecule detection of interactions between the anticancer Bcl-xL protein and small-molecule drugs as well as the Bak-BH3 peptide. (nature.com)
SmMIET is based on the distance-dependent quenching of the fluorescence emission of fluorescent molecules by metallic or semi-metallic thin films, and it requires labeling of the peptide/protein of interest by only one dye, in contrast to single-molecule Förster Resonance Energy Transfer, which requires labeling with a donor and an acceptor dye label. (uni-goettingen.de)
The proposed objectives were design and synthesis of photo-cross-linking peptide-based probes specific for PTMs and validation of the methodology using purified proteins, cell lysates and representative cancer cell lines. (europa.eu)
Consistent with the project proposal, synthesis of peptide probes carrying various synthesised unnatural amino acids, photo cross-linkers and bio-orthogonal moieties were optimised and the probes were successfully applied in protein labelling experiments. (europa.eu)
Following extensive optimisations at the chemical synthesis stages, peptide probe libraries were generated to target key PTMs such as protein arginine methylation and protein lysine side-chain succinylation in histone- and non-histone proteins. (europa.eu)
After several rounds of extensive labelling validation experiments, a probe derived from peptide sequence of the mitochondrial protein glutamate dehydrogenase (GDH) was found to be one of the best, and has served as a prototype system for the further research developments in the project. (europa.eu)
The mechanism of this antigen presentation involves the formation of a so-called MHC-I peptide-loading complex (PLC) where several proteins are involved. (lu.se)
One of these proteins, which help to stabilize, facilitate and edit the peptide-loading complex, is Tapasin, a chaperone transmembrane protein. (lu.se)

The aim of the project is to investigate protein-protein interactions between the molecular chaperone DNAJB6 and aggregation-prone peptides and proteins which cause severe neurodegenerative protein aggregation diseases. (lu.se)

The interactions of a protein surface with water, that is, its hydrophobicity dictates the interactions of the protein with ligands, other proteins, and extended interfaces. (confex.com)

This value is two to three orders of magnitude higher than previously measured 2D K d values for interacting leukocyte surface proteins. (lu.se)
values for interacting leukocyte surface proteins. (lu.se)
We have obtained some preliminary data that suggest a group of NTHi surface proteins are capable of binding to CRL. (lu.se)
Currently, our focus is to determine whether the interaction between NTHi surface proteins and CRL can trigger an immune response, as this information will be valuable in identifying potential vaccine candidates. (lu.se)

Researchers have also shown that one member of the three-protein structure interacts promiscuously with two nucleoporins as do other proteins in the nuclear pore, supporting a model of a flexible complex that can rearrange itself into different formations. (sciencedaily.com)
They also describe competing interactions within the Nup84 complex and discuss the possibility of binding promiscuity as a common feature in the nuclear pore complex. (sciencedaily.com)
Nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) were used to describe the distinct features of this interaction. (phys.org)

This interface is observed frequently in proteins that contain leucine zipper domains such as eukaryotic transcription factors. (jove.com)
To adress the sequence-function relationship`in protein-protein interactions, we conducted a deep mutational scanning of the entire human basic leucine zipper (bZIP) interaction network. (irbbarcelona.org)

Whereas most fluorescent labels require genetic modification of target proteins, I-SO attaches covalently to the protein of interest and changes its fluorescence during a binding event. (the-scientist.com)

The chemical intuition suggests that the glycan-binding sites may be enriched in polar amino acid residues that form non-covalent interactions, such as hydrogen bonds, with polar carbohydrates. (wikipedia.org)
Among others, we have developed software for prediction of protein-protein complex structure by docking simulations, identification of binding sites on protein surfaces, or prediction of hot-spot residues from energy calculations. (bsc.es)
Obtaining a comprehensive understanding of the factors that drive the conservation of residues at specific positions in a protein is an important challenge in understanding protein structure, function, and evolution. (aps.org)
Further analysis revealed conserved residues that affect protein stability and in vivo protein production, indicating that both effects drive evolutionary conservation in PYP, but through two largely distinct sets of residues. (aps.org)

DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)

These gatekeepers have proved largely inscrutable to researchers over the years, despite their conspicuously large size (they are made of 30 different proteins, or nucleoporins), but bit by bit, scientists are learning how these machines work. (sciencedaily.com)

It intends to bridge statistical and bioinformatic characterization of representative protein-DNA systems with biophysical and biochemical approaches. (biophysics.org)
Mass spectrometry combined with X-ray crystallography allows the characterization of cap protein interactions. (biosyn.com)

NEW YORK - Studies by two independent research teams have spelled out interactions between SARS-CoV-2 viral proteins and proteins from human host cells during COVID-19 infections, revealing protein-protein interaction networks with clues to disease biology and potential treatment strategies. (genomeweb.com)
For the first of these studies, published in Nature Biotechnology on Monday, an international team led by investigators at the Pasteur Institute, Dana-Farber Cancer Institute, the University of Toronto, and the German Research Center for Environmental Health turned to yeast-two-hybrid experiments and other assays to examine interactions between more than two dozen viral open reading frames (ORFs) and almost 17,500 human ORFs. (genomeweb.com)
Among the specific contacts examined was an interaction between the viral protein NSP14 and a human transcription network under the control of NF-kappa-B, along with other interactions that impact human immune activity. (genomeweb.com)
Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets," the study's authors wrote, noting that genetic or small molecule inhibitor-based knockdown of interacting host proteins, such as the ubiquitin-specific peptidase 25 enzyme, seemed to dial down SARS-CoV-2 replication in cell line experiments. (genomeweb.com)
Even so, the authors noted, their results suggest that alterations affecting protein-coding portions of the SARS-CoV-2 genome - including changes linked to known SARS-CoV-2 variants - can lead to changes in interactions and network patterns associated with the viral proteins. (genomeweb.com)
Although it is currently unknown whether the respective interactions promote viral replication or facilitate immune recognition," they explained, "the observed changes demonstrate the plasticity of the contactome and, together with recent reports of increased replication of the Delta strain, strongly suggest that this dimension of viral evolution should also be monitored to assess the risk posed by emerging variants. (genomeweb.com)
Our study has revealed that hVIPs are mostly disordered proteins , whereas viral proteins are mostly ordered proteins . (bvsalud.org)
Protein disorder in viral proteins and hVIPs varies from one subcellular location to another. (bvsalud.org)
In any given viral- human PPI pair, at least one of the two proteins is structurally disordered suggesting that disorder associated conformational flexibility as one of the characteristic features of virus -host interaction. (bvsalud.org)

One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. (cshlpress.com)

The therapeutic efficacy of drugs is mediated by physical interaction with their cognate targets (mainly proteins). (nature.com)
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)
Xiulei Mo, PhD, Qiankun Niu, PhD, and Andrey Ivanov, PhD, are co-first authors of a new paper that identifies prevalent mutation-enhanced protein-protein interactions in cancer, revealing potential tumor-selective drug targets. (emory.edu)

We are continuously validating our docking methods in CAPRI , a world-wide community experiment that aims to evaluate the current state of protein-protein docking prediction. (bsc.es)
New methods for protein-RNA and protein-DNA binding. (bsc.es)
Interestingly, only seven proteins overlapped between these two methods. (news-medical.net)
Various computational and biochemical methods are used to study protein interfaces. (jove.com)
To gain a better understanding of possible DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between DNA and proteins. (ku.edu)
Monte Carlo methods were used to simulate proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the DNA. (ku.edu)
Methods for accurately and efficiently characterizing the context-dependent hydrophobicity of protein surfaces will presented. (confex.com)
As present knowledge of interaction partners of many PTMs are very limited, highly innovative chemical biology methods have been developed and applied in this project in order to describe for the first time the global interactome profiling of important PTMs in human cancer cell lines. (europa.eu)
Furthermore, since the project relates to application of chemical methods in the profiling of fundamentally important posttranslational protein modifications, its findings are expected to immediately aid the research of biochemists and biologists, and ultimately society as a whole will benefit. (europa.eu)
A large number of methods have been developed over the years to study protein-protein interactions. (lu.se)
Deepened knowledge on the biophysical chemistry of proteins with emphasis on properties rather than methods. (lu.se)

While RNA-DNA proximity ligation techniques map genome-wide ncRNA interactions , they don´t describe the proteins involved. (epigenie.com)
We then describe some public protein-protein interaction databases that can be searched to identify previously reported interactions for a given bait protein. (lu.se)

This reduces interactions between partially folded proteins, misfolding, and aggregation, and makes the proteins tractable in biotechnological applications. (ncbs.res.in)

4E-binding proteins (4E-BPs) block the interaction of eIF4E with eIF4G to negatively regulate the formation of the eIF4F complex. (biosyn.com)
Salk Institute scientists have discovered that an interaction between two key proteins helps regulate and maintain the cells that produce neurons. (neurosciencenews.com)

Although antibodies exhibit nanomolar affinities toward protein antigens, the specificity against glycans is very limited. (wikipedia.org)
Their architecture relies on the specificity of these interactions. (irbbarcelona.org)
Understanding how the sequence of a protein determines the specificity of its interaction profile thus represents an important step towards a model of the genotype-phenotype map. (irbbarcelona.org)
This interaction domain family, composed of 54 members in humans, has served as a model system for the study of protein interaction specificity. (irbbarcelona.org)
While the general rules of bZIP specificity are relatively well known, it remains impossible to predict interaction partners accurately. (irbbarcelona.org)

In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. (nature.com)

Further analyses reveal that hVIPs are (i) slowly evolving proteins , (ii) associated with high centrality scores in human -PPI network, (iii) involved in multiple pathways, (iv) enriched in eukaryotic linear motifs (ELMs) associated with protein modification, degradation and regulatory processes, (v) associated with high number of splice variants and (vi) expressed abundantly across multiple tissues . (bvsalud.org)

Intramolecular glycan-protein (protein-glycan) interactions occur between glycans and proteins that they are covalently attached to. (wikipedia.org)

Glycan-Protein interactions represent a class of biomolecular interactions that occur between free or protein-bound glycans and their cognate binding partners. (wikipedia.org)

4,800 such genetic interaction data. (nih.gov)
We demonstrate that by combining these data with information on protein-protein, prote in-DNA or metabolic networks, it is possible to uncover physical mechanisms behind many of the observed genetic effects. (nih.gov)
Using a probabilistic model, we found that 1,922 genetic interactions are significantly associated with either between- or within-pathway explanations encoded in the physical networks, covering approximately 40% of known genetic interactions. (nih.gov)
These models predict new functions for 343 proteins and suggest that between-pathway explanations are better than within-pathway explanations at interpreting genetic interactions identified in systematic screens. (nih.gov)
This study provides a road map for how genetic and physical interactions can be integrated to reveal pathway organization and function. (nih.gov)
This event brings together people with interest and expertise in quantitative studies of protein-nucleic acid interactions and dynamics in genetic and epigenetic regulation. (biophysics.org)
We found some articles related to environmental interactions with inherited genotype and others on environmental exposures that damage genetic material and initiate molecular pathways of pathogenesis. (cdc.gov)

For another paper appearing in Nature Biotechnology , researchers at the Cleveland Clinic, Cornell University, and elsewhere reported on findings from their own yeast-two-hybrid- and mass spectrometry-based interactome analyses, which unearthed more than 700 apparent ties between SARS-CoV-2 proteins and human host proteins. (genomeweb.com)
The researchers found that the two proteins fluctuated between bound and loosely associated states, in support of the so-called fly-casting mechanism of protein-protein interaction. (the-scientist.com)
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)
In a case study, researchers show how a common mutation in the gene BRAF - V600E, found in most melanomas, as well as lung and colon cancers - triggers a new interaction between the BRAF-encoded protein and a redox regulator protein KEAP1. (emory.edu)
The researchers detect altered interactions by harnessing engineered proteins, originally derived from jellyfish and a deep-sea shrimp. (emory.edu)

A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein-DNA interactions. (cshlpress.com)
Here, we report a computational method for assessing the response of protein structures to packing perturbations. (ncbs.res.in)
A computational algorithm was integrated to expose mutation-enabled interactions. (emory.edu)

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)

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)

Proposed by Peter Wolynes at the University of California, San Diego, 2 this theory states that weak interactions between relatively unstructured proteins initiate protein-protein binding. (the-scientist.com)
PAS domains form a diverse superfamily of signaling proteins defined by a weak but characteristic pattern of sequence conservation. (aps.org)
Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. (jove.com)

In 'DNA-Protein Interactions: Principles and Protocols, Third Edition', this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. (nhbs.com)

It is thought to be related in amino acid sequence to segments of apolipoprotein B and the microsomal transfer protein responsible for the assembly of low-density lipoproteins. (rcsb.org)
Protein families, and more recently also protein superfamilies, are characterized by a shared three-dimensional structure and patterns of conservation of amino acid sequence. (aps.org)
However, covalent disulfide bonds between cysteine amino acids on each protein surface may also play a role to keep them together. (jove.com)
However, the hydrophobicity of a complex, heterogeneous protein surface depends, not only on the chemistry of the underlying amino acids, but also on the precise chemical pattern and topographical context presented by the protein surface. (confex.com)
Using our established deepPCA system, we measured the effect of all single amino acid substitutions in all 54 members, on the interaction with all 54 wild-type members. (irbbarcelona.org)

The cavity was free of any visible electron density for lipid molecules at room temperature, suggesting that only dynamic interactions exist with the protein. (rcsb.org)
Scientists at the Pacific Northwest National Laboratory in Richland, Wash., have used an established technique to observe real-time interactions between single protein molecules for the first time. (the-scientist.com)
Proteins-large, complex molecules-catalyze virtually all of the chemical reactions that take place in the body. (salk.edu)
Within the cellulosome cellular structure, the protein molecules dockerin and cohesin were the focus of this study. (phys.org)

In the responsive immune system major histocompatibility complex class I (MHC I) proteins plays a key role in the recognition of intracellular pathogens (virus and cancer). (lu.se)
Four strategies for validation of protein-protein interactions are presented: confocal microscopy for intracellular colocalization of proteins, coimmunoprecipitation, surface plasmon resonance (SPR) and spectroscopic studies. (lu.se)

Other aspects of how V600E warps cell metabolism have been studied, but this interaction was not previously known. (emory.edu)
1995. Copper and zinc metabolism in health and disease: Speciation and interactions. (cdc.gov)

Bioinformatics analysis of contact maps in PAS domains revealed conserved networks of interactions, where side chain identity is variable, but a cluster of inter-residue interactions is retained. (aps.org)

We examined these two proteins closely and found that when they interacted they created a potassium channel complex that is fundamental to the aggressive nature of the cancer," says Dong, a former PhD student and current post-doctoral fellow in the Huang Lab . (innovations-report.com)
Sometimes, two or more identical proteins form a complex, such as this kinesin dimer. (jove.com)
Here we discuss the challenges and implications emerging from a modular protein landscape for a better understanding of complex genotype-phenotype patterns. (rsc.org)
The RNA helicase eIF4A and the scaffold protein eukaryotic translation initiation factor 4G (eIF4G) and the capping protein eIF4E are part of the complex that loads the mRNAs onto the 40 S ribosomal subunit, together with eIF3. (biosyn.com)
Next, the team wants to explore how the interaction of the pore complex with other transcription factors affects neuronal function, which could yield insights into the underlying causes of certain neurological disorders. (neurosciencenews.com)
Now, "RedChIP" has us stampeding in anticipation towards the exploration of the complex interactions taking place between RNA, DNA, and proteins in the nucleus. (epigenie.com)

Patterns of sequence conservation are widely used in studies of proteins. (aps.org)
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)
Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. (nhbs.com)
This dataset of ~ 2M quantitative protein-protein interaction measurements will enable training a deep neural network that captures the sequence-function relationship in order to quantitatively predict interaction between bZIPs from sequence alone. (irbbarcelona.org)
Li M, Simonetti F, Goncearenco A, Panchenko A, MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions, Nucleic Acids Res. (lu.se)

Yet, not all protein interfaces involve closely-matching surfaces. (jove.com)
Further, how such estimates of protein hydrophobicity can be used to estimate interactions between two such protein surfaces will be discussed. (confex.com)

The drug mediates interactions between these receptors, growth factors, and proteins within that pathway to reduce new abnormal bone formation. (medscape.com)

Many single-domain proteins are not only stable and water-soluble, but they also populate few to no intermediates during folding. (ncbs.res.in)
We then benchmark this method using designed proteins and find that it can identify scaffolds whose folding gets disrupted upon perturbing packing, leading to the population of intermediates. (ncbs.res.in)

Nonetheless, the association signal primarily arises from de novo protein-truncating variants, as opposed to the more common missense variants. (springer.com)
Utilizing our previous interactome perturbation predictor, we identify a set of missense variants that are likely disruptive to protein-protein interactions. (springer.com)
Extending earlier work, we show that de novo missense variants that disrupt protein interactions are enriched in individuals with ASD, often affecting hub proteins and disrupting hub interactions. (springer.com)
The evidence, however, largely comes from protein-truncating variants (PTVs) as opposed to de novo missense (dnMis) variants. (springer.com)
The ARID1A gene variants involved in Coffin-Siris syndrome lead to an abnormally short, nonfunctional protein. (medlineplus.gov)
1102 single variants in 57 protein. (lu.se)

Because my protein is a DNA binding protein, I think that I lost some proteins fixed on genomic DNA that are found in the pellet during the step of clarification just after breaking cells. (bio.net)
Overall, the authors see RedChIP as a straightforward and accurate means of identifying RNAs associated with genomic regions occupied by a protein of interest. (epigenie.com)

instead, they combined RNA-DNA proximity ligation ( Red-C ) with chromatin immunoprecipitation (ChIP) to create RedChIP, which identifies RNAs associated with a DNA-bound protein of interest. (epigenie.com)
Chromatin is the network of DNA and protein that packages DNA into chromosomes. (medlineplus.gov)

One reason why a mutation is tumorigenic is the altered network of protein-protein interactions," says lead author Haian Fu, PhD, leader of Winship's Discovery and Developmental Therapeutics Program and professor and chair of pharmacology and chemical biology at Emory University School of Medicine. (emory.edu)
The mutation may form a new epitope: a new interaction surface. (emory.edu)
They termed these new mutation-enhanced protein-protein interactions "neoPPIs. (emory.edu)

For instance, SARS-CoV-2, the causative agent of COVID-19, employs its extensively glycosylated spike (S) protein to bind to the ACE2 receptor, allowing it to enter host cells. (wikipedia.org)
For instance, many enzymes, such as protein kinase A here, form a cleft that can recognize and bind polypeptide loops of their binding partners. (jove.com)
To pinpoint single residue change-induced neoPPIs, the research team tested the ability of a mutated protein to bind a cancer-associated protein in comparison with its wild type counterpart. (emory.edu)

Scientists can detect when the two proteins come within 10 nanometers of each other in living cells, using a combination of bioluminescence and fluorescence (BRET or bioluminescence resonance energy transfer). (emory.edu)
The probes and control probes were subsequently evaluated by in-gel fluorescence scanning for protein labelling performance using purified proteins and the probes that showed the best labelling performance at this stage were chosen for further in-depth studies. (europa.eu)

The study of glycan-protein interactions provides insight into the mechanisms of cell-signaling and allows to create better-diagnosing tools for many diseases, including cancer. (wikipedia.org)

The spike protein is a trimeric structure, with each subunit containing 22 N-glycosylation sites, making it an attractive target for vaccine search. (wikipedia.org)
In contrast to template-driven protein biosynthesis, the "language" of glycosylation is still unknown, making glycobiology a hot topic of current research given their prevalence in living organisms. (wikipedia.org)
Indeed, there are no known types of cancer that do not involve erratic patterns of protein glycosylation. (wikipedia.org)

The main task of the MHC-I proteins is to present antigens, which may impose a hazard to the cell. (lu.se)

We study their interactions to discover how they heal or how they harm. (salk.edu)
To study how proteins might be moving along the DNA, I studied the use of the uniform motion "n-step" model. (ku.edu)
A typical protein-protein interaction study usually starts with an initial screen for novel binding partners. (lu.se)
We aim to study low concentrations of nanoparticles down to single particles in biologically relevant concentrations of proteins. (lu.se)

Anatomy13

Organisms15

Diseases4

Chemicals and Drugs76

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Phenomena and Processes80

Disciplines and Occupations6

Technology, Industry, Agriculture1

Information Science28

Health Care4

Complexes16

Sequences8

Genes13

Structural9

Human proteins8

Interact7

PPIs5

Membrane3

Affinity11

Biological10

Mutations5

Functional5

Peptide13

Peptides1

Ligands1

Surface proteins4

Nuclear3

Leucine zipper2

Target proteins1

Residues4

Several proteins1

Different proteins1

Characterization2

Viral9

Gene expression1

Targets3

Methods11

Describe2

Aggregation1

Regulate2

Specificity5

Biophysical1

Motifs1

Covalently1

Cognate1

Genetic7

Researchers5

Computational3

Pathways1

Molecular Interactions1

Weak3

Genome-wide1

Amino5

Molecules4

Intracellular2

Metabolism2

Bioinformatics1

Complex6

Sequence5

Surfaces2

Receptors1

Folding2

Variants6

Genomic2

Chromatin2

Mutation3

Bind3

Fluorescence2

Diseases1

Glycosylation3

Antigens1

Study4