Interactions with proteins. 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)
Proteins usually bind together to form complexes, which play an important role in cellular activities. (ict.ac.cn)
Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. (ict.ac.cn)
We present a novel framework (CPL) that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. (ict.ac.cn)
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)

Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.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)
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)
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)
analyzed the amino acid sequences of two specific intrinsically disordered proteins from different organisms to reconstruct the versions of the proteins that were likely found in their common ancestors 450-600 million years ago. (elifesciences.org)
Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. (nhbs.com)

Finally, in light of some recent findings, we speculate on the possibility of a new regulatory code for intrinsically disordered proteins and the potential biophysical and functional advantages that disorder might provide. (nih.gov)
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. (elifesciences.org)
Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. (elifesciences.org)
However, a group of proteins called 'intrinsically disordered proteins' are flexible in their shape and lack a stable three-dimensional structure. (elifesciences.org)

The technology, among other applications, can be used in combination with CompoZr® Zinc Finger Nuclease-mediated gene editing to track knocked-out or knocked-in genes and with MISSION® RNA interference technologies to track protein expression following gene knockdown. (genengnews.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)
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)
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 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)
We first use a maximum parsimony- based approach to infer the ages of human proteins. (princeton.edu)
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)
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)

In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. (nature.com)
It intends to bridge statistical and bioinformatic characterization of representative protein-DNA systems with biophysical and biochemical approaches. (biophysics.org)
We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. (elifesciences.org)
The ancestral proteins were then 'resurrected' by recreating them in test tubes and their characteristics and properties analyzed with experimental and computational biophysical methods. (elifesciences.org)

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)
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 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)
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)
Yet, these proteins play important roles in many processes that require the protein to interact with a number of other proteins. (elifesciences.org)
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)

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)

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)

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)

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)

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)
This suggests that an originally weak and dynamic interaction is relatively quickly turned into a tighter one by random mutations and natural selection. (elifesciences.org)
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)

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)

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)

More specifically, we present recent work on the molecular bases of transient peptide-mediated interactions and the role that post-translational modifications and disordered regions might play. (nih.gov)
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)

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)

A PPI network provides crucial information on how biological pathways are structured and coordinated from individual protein functions. (nature.com)
The ability to visualize these protein-protein interactions in unmodified cells under endogenous expression and at very low levels is a fundamental advance that allows greater insight into basic biology, pathways, spatial phenomena, and potential therapeutic targets in those pathways," said Josef Zihlmann, vice president at Sigma Life Science. (genengnews.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)
MOTIVATION Viruses , from the human protein-protein interaction network perspective, target hubs, bottlenecks and interconnected nodes enriched in certain biological pathways. (bvsalud.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)

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)
In other cases, different proteins or polypeptides come together to form a functional unit. (jove.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)

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)
The synchronization and regulation of these biological functions is indeed critical and is usually carried out by complex networks of transient protein interactions. (nih.gov)
To achieve high biological specificity, protein kinases and phosphatases often recognize their targets through interactions that occur outside of the active site. (nih.gov)
Sigma® Life Science, Sigma-Aldrich's biological products and services business, signed an agreement to distribute worldwide Olink Bioscience's Duolink® In Situ products, which present a new method for imaging and measuring protein-protein interactions in unmodified cells. (genengnews.com)
Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. (nature.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)
Many biological processes depend on protein-protein interactions. (jove.com)
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)

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)

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)
Various computational and biochemical methods are used to study protein interfaces. (jove.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)

According to the company, the PLA® technology allows Olink's Duolink In Situ products to quickly image the locations of single protein-protein interactions regardless of strength, measure protein expression levels, and identify relative changes in post-translational modification events. (genengnews.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)
The specific order of amino acids in a protein determines its shape and structure, which in turn controls what the protein can do. (elifesciences.org)
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)
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)

Lectins is a generic name for proteins with carbohydrate-recognizing domains (CRD). (wikipedia.org)
PAS domains form a diverse superfamily of signaling proteins defined by a weak but characteristic pattern of sequence conservation. (aps.org)
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 then determine various function-related traits for each age group, such as protein-protein interaction count, expression ubiquity, and number of unique domains. (princeton.edu)
We find that young proteins in human have fewer protein-protein interactions, have fewer unique domains, are expressed in fewer tissues, and are less likely to be essential than older proteins. (princeton.edu)

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

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)
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)
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)
The CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. (ict.ac.cn)
Methods for accurately and efficiently characterizing the context-dependent hydrophobicity of protein surfaces will presented. (confex.com)
A large number of methods have been developed over the years to study protein-protein interactions. (lu.se)

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)
Fluorescent detection probes bind the several hundred-fold amplified DNA at high density, allowing visualization of single protein-protein interactions inside an intact cell using a standard fluorescence microscope. (genengnews.com)
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)

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)

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)
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)

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)

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

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)

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)
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)

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

Mitochondrial dysfunction is putatively central to glioblastoma (GBM) pathophysiology but there has been no systematic analysis in GBM of the proteins which are integral to mitochondrial function. (gla.ac.uk)
Alterations in proteins in mitochondrial enriched fractions from patients with GBM were defined with label-free liquid chromatography mass spectrometry. (gla.ac.uk)
256 mitochondrially-associated proteins were identified in mitochondrial enriched fractions and 117 of these mitochondrial proteins were markedly (fold-change ≥2) and significantly altered in GBM (p ≤ 0.05). (gla.ac.uk)

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)

You put [a] domain with the dye hanging on it into a live cell, and it will respond to the endogenous protein, so you don't have to overexpress endogenous material, [or] modify the endogenous material to see what's going on," Hahn explains. (the-scientist.com)
The biosensor really adds to the field, says Mark Philips, professor at New York University School of Medicine, because it enables the observation of endogenous signaling proteins. (the-scientist.com)

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)

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)
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)
Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. (nhbs.com)

Yet, not all protein interfaces involve closely-matching surfaces. (jove.com)
Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. (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 spike protein is a trimeric structure, with each subunit containing 22 N-glycosylation sites, making it an attractive target for vaccine search. (wikipedia.org)
The long funnel-shaped structure and nanofluidic characteristics of the YaxAB nanopore enable the electro-osmotic trapping of diverse folded proteins and high-resolution monitoring of PDIs. (nature.com)
PPI networks can be represented as graphs, and graph analysis techniques have been ap- plied in order to determine the topological roles played by individual proteins in PPI network structure. (princeton.edu)
The 16 non-structure proteins (NSPs) are cleaved products of the large polyprotein open reading frame (ORF)1ab or ORF1a. (news-medical.net)
In conclusion, the physical structure and chemical properties of the interacting parts determine the type of interface between two proteins. (jove.com)

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)
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)
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)
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)
With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. (ict.ac.cn)
Protein-protein interaction analysis highlighted a reduction in multiple proteins coupled to energy metabolism (in particular respiratory chain proteins, including 23 complex-I proteins). (gla.ac.uk)
After the addition of anti-Tg antibodies labeled with ruthenium complex and streptavidin-coated microparticles, the immunocomplex produced becomes bound to the solid phase via interaction of biotin and streptavidin. (cdc.gov)
The entire complex becomes bound to the solid phase via interaction of biotin and streptavidin. (cdc.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)

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

Excited by their findings, Huang's team began investigating this specific interaction as a potential target for glioblastoma treatment. (innovations-report.com)
They determined that EAG2-Kvβ2 interaction is required for neurons to communicate with glioblastoma cells, facilitating tumour growth, invasion and chemoresistance. (innovations-report.com)

Protein conformation fluctuation dynamics is a stochastic process," says lead investigator H. Peter Lu, a staff scientist at PNNL. (the-scientist.com)

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 Duolink In Situ products work in tandem with Sigma Life Science's antibody portfolio and will allow researchers to target the precise protein of interest and enable analyses and imaging. (genengnews.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)
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)

However, it is not clear how such interactions emerge and evolve on a molecular level. (elifesciences.org)
The findings shed light on fundamental principles of how new protein-protein interactions emerge and evolve on a molecular level. (elifesciences.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)

Changes in pH have previously been shown to result in "on-off" switches within protein functions, many of which occur naturally and are essential for life processes. (phys.org)

A next step for the future will be to investigate how other protein-protein interactions have evolved and to identify general underlying patterns. (elifesciences.org)

Among them, ABT-737 is well-known as a potent small-molecule inhibitor of the Bak-BH3/Bcl-xL interaction 24 . (nature.com)
Collectively, these findings furnish proof of concept for the usefulness of small molecule probes designed to dysregulate bacterial iron homeostasis by targeting a protein-protein interaction pivotal for iron storage in the bacterial cell. (rcsb.org)

Complexes12

Sequences9

Intrinsically disordered proteins4

Genes13

Human proteins8

Biophysical4

Interact8

PPIs5

Membrane2

Motifs1

Affinity7

Ligands1

Surface proteins4

Mutations4

Structural7

Peptides1

Peptide14

Nuclear3

Leucine zipper2

Target proteins1

Pathways5

Residues4

Several proteins1

Different proteins2

Viral9

Biological9

Folding2

Computational4

Post-Translational1

Amino6

Domains5

Aggregation1

Methods10

Bind4

Specificity5

Functional3

Weak interactions1

Covalently1

Targets3

Fluorescence2

Cognate1

Mitochondrial3

Molecules4

Intracellular2

Endogenous2

Living organisms1

Sequence4

Surfaces3

Structure5

Complex9

Genetic1

Gene expression1

Glioblastoma2

Dynamics1

Researchers5

Molecular level2

Glycosylation1

Antigens1

Occur1

Patterns1

Small molecule2