Important interactions protein residues. Medical search. Frequent questions

Non-covalent interactions involving π systems are pivotal to biological events such as protein-ligand recognition. (wikipedia.org)
Theoretical calculation of protein-protein and protein-ligand binding free energies is a grand challenge in computational biology. (utoronto.ca)
In this talk we develop an efficient approach (Interaction Entropy) to computing quantitative residue-specific contributions to protein-protein and protein-ligand binding free energies. (utoronto.ca)
Studies for an extensive set of realistic protein-protein interaction systems and for specific protein-ligand binding systems showed that by including the entropic contribution, the computed residue-specific binding free energies are in better agreement with the corresponding experimental data. (utoronto.ca)
1. Duan, L.L., X. Liu, and J.Z.H. Zhang, Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy. (utoronto.ca)
Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies, J. Chem. (utoronto.ca)
In silico investigation was carried out by protein-ligand docking using AutoDock Vina software. (omicsonline.org)
Binding energies were calculated for each ligand and the amino acids involved in the interaction of these ligands with the rCAL homology model were identified. (omicsonline.org)
To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: site identification by ligand competitive saturation) that intrinsically considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. (nih.gov)
The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. (nih.gov)
The physiological role of FABP's within the cell remains unclear but a targeting role for the protein would provide an attractive mechanism for ligand (fatty acid) transfer to membrane sites for further metabolism and requires an interaction between the FABP and the membrane. (soton.ac.uk)
This interaction was investigated in more detail in order to identify the parameters that affect binding and ligand release. (soton.ac.uk)
The ligand release that was observed with anionic vesicles was sensitive to the ionic strength of the assay conditions and the anionic charge density of the phospholipid at the interface, indicating that non-specific electrostatic interactions play an important role in the process. (soton.ac.uk)
The most likely explanation for ligand release is that interaction of LFABF with an anionic membrane interface induces a rapid conformational change, reducing the affinity of DAUDA for the protein. (soton.ac.uk)
The nature of this interaction involves both electrostatic and non-polar interactions as maximal release of LFABP from phospholipid vesicles with recovery of ligand binding cannot be achieved with high salt and requires the presence of a non-anionic detergent. (soton.ac.uk)
Analysis of phosphorylation-dependent interactions downstream of VEGFR-1 in mammalian cells, which is generally hindered by the lack of ligand-induced receptor phosphorylation, was enabled by the development of chimeric receptors. (figshare.com)
X-ray crystallography of human PPAR isoforms has revealed important residues responsible for ligand binding, heterodimerisation and co-factor interactions. (sigmaaldrich.com)
A greater understanding of the mechanism of transcriptional regulation by nuclear receptors has lead to the identification of multiple accessory proteins that bind to the nuclear receptors in a ligand-dependent manner. (sigmaaldrich.com)
Flexible flaps enclose the active site and provide important ligand binding interactions. (proteopedia.org)
We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
We also ran QM/MM simulations on casein-kinase 2 (CK2), where the ligand and a few surrounding residues were treated at the QM level, and the rest of the system at the MM level. (lu.se)
Furthermore, it is important and challenging to accurately model the large entropic contribution to ligand-binding free energies. (lu.se)
This entropy largely stems from the fluctuation of the protein and ligand. (lu.se)
Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)

CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. (rcsb.org)
Membrane proteins, such as those operating transport through the membrane in a controlled way, are prone to show interesting topological properties related to their function. (nature.com)
More efficient identification of correct docking poses, especially in difficult cases such as weak interactions, multi-protein complexes or membrane proteins. (bsc.es)
Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. (cipsm.de)
Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. (cipsm.de)
In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. (cipsm.de)
Thisimplies that BIN1 rather bundles actin than decorates single filaments.Third, we explored a strategy to purify an aggregation prone BAR protein.Aggregation is a property common in Peripheral Membrane Proteins. (kth.se)
Membrane proteins are translated by ribosomes and predominantly inserted into the membrane by the SecYEG-translocon. (uni-marburg.de)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

Cadherins form protein complexes with cytoplasmic proteins (catenins) that convert the specific, homophilic-binding capacity of the extracellular domain into stable cell adhesion. (embl.de)
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)
Transcriptional repression complexes play important roles in both repressing gene transcription and in "resetting" genes after rounds of active transcription. (esrf.fr)
The conserved "core" of the SMRT/NCoR repression complexes (called repression domain 1 or RD1) recruits HDAC3, TBL1 (and/or its homologue TBLR1) as well as a protein called GPS2 (also known as AMF1). (esrf.fr)
The MD simulations and MM-PBSA studies showed reasonable stability of protein-drug complexes and sustainability of key interactions between the drugs with their respective targets throughout the course of MD simulations. (ias.ac.in)
While the study has provided a detailed account of the chosen protein-drug complexes, it has explored the nature of seven important targets of SARSCoV-2 by evaluating the protein-drug complexation process in great detail. (ias.ac.in)

Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
Recent structural determination of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addition of stabilizing antibodies and small molecules that facilitate crystallization in cubic phase monoolein mixtures. (rcsb.org)
Indeed mutations in the grooves abolished interaction with both SMRT and GPS2. (esrf.fr)
Mutations in this motif in both proteins abolished recruitment to TBL1. (esrf.fr)
However, we observed that mutations at these residues often substantially reduce the degree of protein production. (aps.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)
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)
Scope includes mutations and abnormal protein expression. (cancerindex.org)

The results of these studies suggested that α-helix II, in particular, residue K31 of LFABP are involved in interactions with the anionic phospholipid interface. (soton.ac.uk)

The protease of adenovirus serotype 2 requires cysteine residues for both activation and catalysis. (microbiologyresearch.org)
Critical cysteine residues of Keap1 in suppression of Nrf2 basal activity and arsenic-sensing by regulating the ubiquitination-proteasomal degradation of Nrf2 protein. (cdc.gov)
Our findings support the notion that arsenic binds to different sets of Keap1 cysteine residues to regulate divergent functions in Nrf2 signaling. (cdc.gov)

Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)
Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. (nature.com)
The Laguerre space partition is the basis underlying all the implemented topological analysis methods: inter-atomic, inter-residue or inter-molecular contacts, connected components of the bulk or of the surface, optimal paths, porosity, genus of the surface, stratification. (nature.com)
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 used constant pH molecular dynamics simulations, NMR spectroscopy, and thermodynamic double mutant cycles to probe the structure and energetics of the interaction between the charged residues. (lu.se)
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)
A deeper knowledge of how this molecular evolution happened will broaden our understanding of present day protein-protein interactions and might aid the design of drugs that can mimick proteins. (elifesciences.org)
The long term goal of our research is to elucidate the molecular mechanisms by which proteins are targeted to specific and distinct compartments. (stanford.edu)
We also identify a molecular switch in the top of TM7 important for keeping CCR7 in an inactive conformation (Tyr312), as introduction of the chemokine receptor-conserved Glu (or Ala) induces high constitutive activity. (ku.dk)
Recombinant human Midkine is a 13.4 kDa protein containing 123 amino acid residues including five intra-molecular disulfide bonds. (reliatech.de)
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)
Next, we extend the cell model to all-atom molecular dynamics (MD) simulations, which account for explicit solvent solvatation and internal protein flexibility, and show that protein concentration dependent osmotic pressures can be obtained by confining counter-ions in a virtual spherical subspace defining the protein number density. (lu.se)
Protein structures are invaluable for biochemical studies and for mechanical or molecular mechanics calculations have become the understanding of how proteins work. (lu.se)
One of the key molecular events in skin sensitization is protein haptenation, i.e. the chemical modification of self-skin protein(s) thus forming macromolecular immunogens. (cdc.gov)
The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)

Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
The association of potential effector proteins with the VEGFRs were assessed in both yeast and mammalian cells, and the identity of the interacting residues was probed using site-directed mutagenesis and peptide competition experiments. (figshare.com)
Employing site-directed mutagenesis we identify residues in this pocket of selective CCL21 importance. (ku.dk)

Mutagenesis established that only Glu-313 is important, contributing approximately 5-10-fold to rate acceleration of fXa and fXIa inhibition. (rcsb.org)
Here we want to investigate the interaction between the CheA and receptor protein by using mutagenesis and phosphorylation assay. (ucsb.edu)
On the basis of the X-ray crystallographic 3D structure, an approach including site-directed and random mutagenesis is taken to determine functional important residues and regions. (lu.se)

π-metal interactions can also be involved directly with the function of ligands on the catalyst. (wikipedia.org)
To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivities, and to predict noncovalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. (nih.gov)
The binding of extracellular matrix ligands to integrins triggers autophosphorylation at Tyr-397, and activation of FAK through phosphorylation of Tyr residues (Tyr-576 and Tyr577) in the kinase domain activation loop. (fishersci.com)
In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)

In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. (cipsm.de)
The interface between the core and terminal domains is composed primarily of small hydrophobic residues. (proteopedia.org)
PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
corresponding to different fractions of hydrophobic residues. (lu.se)
For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)

The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. (rcsb.org)
The FepA membrane protein is surrounded by a lipid bilayer separating the extracellular medium and the periplasm. (nature.com)
Cadherins depend on calcium for their function: calcium ions bind to specific residues in each cadherin repeat to ensure its proper folding, to confer rigidity upon the extracellular domain and is essential for cadherin adhesive function and for protection against protease digestion. (embl.de)
This entry represents the extracellular repeated domains found in cadherins and related proteins. (embl.de)
This is mediated by the secretion of extracellular proteins and other biological molecules. (uni-marburg.de)
The protein RemA is central to this process, as it activates the secretion of these extracellular components. (uni-marburg.de)

Just like in an electrostatic interaction where a region of negative charge interacts with a positive charge, the electron-rich π system can interact with a metal (cationic or neutral), an anion, another molecule and even another π system. (wikipedia.org)
Electrostatic forces are important for protein folding and are favored targets of protein engineering. (lu.se)
We find good agreement between experiments and simulations and use the simulations to rationalize our observations and to provide a detailed mechanistic understanding of the electrostatic interactions. (lu.se)
To obtain information about BIN1's interaction with themembrane in near native environments, we used artificial lipid systems suchas liposomes and lipids nanotubes.First, we have shown that electrostatic interactions are more important forBIN1 when binding to membranes with low curvature. (kth.se)
The formation ofinvaginations (or tubules) is regulated by the composition of negativecharged lipids in membrane bilayer or electrostatic residues on the BARdomain. (kth.se)

The role of adenovirus structural proteins in the regulation of adenovirus infection. (microbiologyresearch.org)
gag gene codes for structural proteins which forms the 'body' of the viral particle, among other proteins. (proteopedia.org)
Cells depend on their DNA for coding information to make various classes of proteins that include enzymes, certain hormones, transport proteins, and structural proteins that support life. (cdc.gov)

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)
PB2 genes (viral ribonucleoproteins [RNPs]) and are most- encoded protein sequences have not been extensively ly located in the functional domains related to RNP-RNP reported. (cdc.gov)
Protein functional properties are determined to a large extent by a protein s physicochemical and structural properties ( Diniz and Martin, 1997 ). (scialert.net)
HIV-1 Protease acts as 'chemical scissors' to cleave the polyproteins into functional constituent proteins. (proteopedia.org)
Currently, alignment-based methods are routinely used for functional characterization of novel protein sequences. (uni-goettingen.de)
functional proteins. (lu.se)

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)

Abstract: Among the five retroviral genera with Class I viral fusion proteins (lentiviruses and the alpha-, beta-, gamma-, and deltaretroviruses) are found either of two mechanisms of Env subunit association - covalent association mediated by disulfide bonding between cysteines, or noncovalent interactions among various residues at the SU/TM interface. (tufts.edu)

Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
Accurate prediction of critical residues along with their specific and quantitative contributions to protein-protein binding free energy is extremely helpful to reveal binding mechanisms and identify drug-like molecules that alter protein-protein interactions. (utoronto.ca)
But the competition, called Critical Assessment of Protein Structure Prediction (CASP), went decades without a solution. (bigthink.com)
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)
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)

The number of available protein structures still lags far behind the number of known protein sequences. (nih.gov)
We applied support vector machines to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. (nih.gov)
We subse- the mechanism of influenza viral infection and replication quently used 15,785 protein sequences from the National in different host species. (cdc.gov)
It uses evolutionarily related sequences, multiple sequence alignment (MSA), and a representation of amino acid residue pairs to refine this graph. (bigthink.com)
Examination of the GPS2 and SMRT sequences adjacent to the coiled-coil identified a common a-helical sequence motif that could mediate interaction with TBL1. (esrf.fr)
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)
Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)

Midkine (MK) and its functionally-related protein Pleiotrophin are heparin-binding neurotrophic factors that signal through the same receptor, known as anaplastic lymphoma kinase (ALK). (reliatech.de)
By means of biochemical methods, crucial residues of RemA responsible for DNA interaction could be functionally investigated. (uni-marburg.de)
This complex domain structure results in a functionally diverse protein. (tocris.com)

In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. (nature.com)
They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
This makes it important to predict which residues participate in protein-protein interactions using only sequence information. (nih.gov)
In addition, we found evidence to indicate that conformation as well as sequence was important for good hexon binding in our assays. (microbiologyresearch.org)
Patterns of sequence conservation are widely used in studies of proteins. (aps.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)
PAS domains form a diverse superfamily of signaling proteins defined by a weak but characteristic pattern of sequence conservation. (aps.org)
The lack of covalent bonding in the Env proteins of these two genera correlates with the lack of a particular cysteine in the TM ectodomain, as well as a couple of other TM sequence features that allow easy distinction between the two TM types--lack of an immunosuppressive domain (ISD) and a longer membrane proximal external region (MPER). (tufts.edu)
However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. (cipsm.de)
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)
Furthermore, using sequence analysis of human genomic DNA, researchers concluded that the amino acids important for catalysis by COX-1 are conserved and are equally important for catalysis by COX-2. (medscape.com)

The most common strong alternative and complement to experimental methods to methods to obtain protein structures are X-ray crystallography obtain insight in biochemical processes. (lu.se)

The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
We are interested in the substrate - enzyme interaction, and especially in the interactions that are likely to direct the specificity of the enzyme. (lu.se)

Within a protein, pairs of amino acids can interact in numerous ways, and these particular interactions determine the final shape of the protein. (bigthink.com)
Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues and thus may offer a more effective therapeutic approach. (nih.gov)
The structure revealed that the two proteins interact through a tight antiparallel coiled-coil ( Figure 102a ). (esrf.fr)
The antiparallel nature of the coiled-coil positions the regions that interact with TBL1 at the same end of the complex suitable for simultaneous interaction with TBL1 immediately suggesting an arrangement for the ternary complex. (esrf.fr)
Yet, these proteins play important roles in many processes that require the protein to interact with a number of other proteins. (elifesciences.org)
Coactivator proteins such as SRC1 and CBP/p300 are recruited by agonist bound receptors and promote initiation of transcription by remodelling the chromatin structure while coactivators such as the PPAR binding protein (PBP) and TRAP220 interact directly with the transcriptional machinery. (sigmaaldrich.com)
Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected based on the docking score, ability to interact with four or more targets and having a reasonably good number of interactions with key residues in the targets. (ias.ac.in)
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)

The 9 most strongly PAS-conserved residues are located at structurally inconspicuous positions that remain largely unstudied. (aps.org)
Part 3: Membrane protein biogenesis is regulated by a structurally unique, co-translational state of FtsY. (uni-marburg.de)

These regions are highly conserved amongst mastadenovirus pVI proteins. (microbiologyresearch.org)

HIV-1 protease cleaves an human immunodeficiency virus (HIV) precursor proteins, such as cleaving the env protein , glycoprotein (GP) 160 , into gp41 and gp120 . (proteopedia.org)
In other words, HIV-1 protease is responsible for maturation of the virion by cleaving proteins into their mature form. (proteopedia.org)
Pol gene on the other hand codes for three essential enzymes which are Reverse Transcriptase (RT), Integrase (IN) and Protease (PR), among other proteins. (proteopedia.org)

The signaling complex which is composed of a transmembrane receptor, histidine protein kinase CheA and adaptor protein CheW plays an important role in chemotaxis signaling pathway. (ucsb.edu)
Cadherins are a group of transmembrane proteins that serve as the major adhesion molecules located within adherens junctions. (embl.de)

The protein encoded by this gene belongs to the pyridine nucleotide-disulfide oxidoreductase family, and is a member of the thioredoxin (Trx) system. (cancerindex.org)

In addition, the observed dependence of some of these effects on a specific tyrosine residue within VEGFR-2 suggested that the chimeric receptors couple to downstream effectors in a manner analogous to that of the full-length receptors. (figshare.com)
The nuclear receptor corepressor (N-CoR) or silencing mediator of retinoid and thyroid receptors (SMRT) proteins bind and mediate repression of transcription by the unliganded receptors. (sigmaaldrich.com)

Disrupted protein interactions identify gene sets involved in risk for ASD. (springer.com)
This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. (thebiogrid.org)
This work provided the first evidence for a postulate, based on the long standing gene-for-gene hypothesis that direct and specific protein interactions occurred between flax resistance and flax rust avirulence proteins. (science.org.au)
What does this gene/protein do? (cancerindex.org)
What pathways are this gene/protein implicaed in? (cancerindex.org)
env gene codes for viral envelop proteins. (proteopedia.org)

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)
Dodds' innovative discoveries provide a foundation for the rational design of synthetic rust resistance genes to protect the world's most important food crops from rust diseases. (science.org.au)
We found that the acidic domain of MZF-1 and the heparin-binding domain of Elk-1 facilitate the heterodimeric interaction between the two genes before the complex formation binds to the PKCα promoter. (oncotarget.com)
Analyzing 5′-upstream non-protein-encoding regions of the human mitochondrial function-associated genes, we speculate that mitochondrial functions could be recovered or improved at a transcriptional level. (intechopen.com)

Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation , histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. (frontiersin.org)
They are large "platform" or "hub" proteins (c.2500 amino acids) that assemble a complex containing a number of histone deacetylase enzymes. (esrf.fr)
Hence the tetrameric nature of the TBL1 suggests that the protein may serve as a scaffold for a multivalent chromatin-targeted repression machine that contains multiple co-repressor proteins and histone deacetylase enzymes. (esrf.fr)
The studied enzymes have several important applications in the food/feed and pulp/paper industries. (lu.se)

Changes in the redox state of cells affect proteins, lipids, and nucleic acids in different ways. (hindawi.com)

The field of protein-analysis is a major research area for bioinformatics. (uni-goettingen.de)

Recent reports demonstrate that the expression of protein kinase C alpha (PKCα) in triple-negative breast cancer (TNBC) correlates with decreased survival outcomes. (oncotarget.com)
In addition, phosphorylation of other Tyr residues (Tyr-925, and Tyr-861) creates binding sites for SH2 domains of intracellular signaling molecules such as Src, PI3 kinase, and Grb2. (fishersci.com)
It was first identified as an inhibitor of the GTPase activity of GTP-bound Cdc42, but it also promotes cell survival via the phosphorylation of several effector proteins, such as the androgen receptor (AR) and protein kinase B (Akt) . (tocris.com)
The kinase activity of Ack1 is regulated via the post-translational modification of several tyrosine residues. (tocris.com)
In addition to a catalytic kinase domain, Ack1 contains seven other domains, which are important for substrate recognition, regulation of enzymatic activity, cellular localization and protein-protein interactions. (tocris.com)
Members of the Ack family are unique in that they are the only tyrosine kinases to have a CRIB domain, for interaction with Cdc42, and an SH3 domain C-terminal to the kinase domain. (tocris.com)

We found that TRIM13 mRNA and protein expression was reduced in NSCLC tissues and cell lines in comparison to paired non-cancerous tissues and a human normal bronchial epithelial cell line, respectively. (cancerindex.org)
At the ribosome, the processed mRNA is translated to produce proteins from amino acid units. (cdc.gov)
The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

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)

Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)

Anion-π interactions: interaction of anion with π system Cation-π interactions: interaction of a cation with a π system C-H-π interactions: interaction of C-H with π system: These interactions are well studied using experimental as well as computational techniques. (wikipedia.org)
There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
In this study, we used several computational interactions that are important for viral replication. (cdc.gov)
Zhang, J.Z.H., Interaction Entropy for Computational Alanine Scanning. (utoronto.ca)
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)
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)

The approach provides explicit contribution of the entropic loss in binding free energy of individual residues directly from fluctuation of the interaction energy in MD simulation. (utoronto.ca)

We mapped the regions in the three proteins required for interaction and demonstrated that the amino-terminal domain of TBL1 (TBL1-NTD) is able to bind both GPS2 and SMRT forming a ternary complex. (esrf.fr)
The amino terminal domain of TBL1, that mediates interaction with both SMRT and GPS2, crystallised in three different forms that diffracted to between 2.2 Å and 5 Å resolution. (esrf.fr)
In addition to the amino-terminal tetramerisation domain, TBL1 contains a C-terminal WD40 domain that could potentially bind to histone tails and to intact nucleosomes, since such domains have been observed in this role in other proteins. (esrf.fr)

Aromatic-aromatic interactions (π stacking): involves interactions of aromatic molecules with each other. (wikipedia.org)
HMGB1 is an abundant protein, 10 6 molecules per cell [ 7 ], which has been postulated as a redox sensor [ 8 ]. (hindawi.com)

Temperature sensitivity of processing of viral proteins. (microbiologyresearch.org)

Other widely known reactions based on π-metal catalysis interactions are: Heck reaction Hiyama coupling Kumada coupling Negishi coupling Petasis reaction Sonogashira coupling Suzuki reaction. (wikipedia.org)
Another π metal interaction directly involved with catalysis involves π stacking. (wikipedia.org)

Our study uses classical algorithms such as space partitions and Dijkstra paths search 9 , applied in an original and novel way by taking into account the full representation of a membrane protein including the solvent and the lipid bilayer (Fig. 1 ). (nature.com)
This domain includes a mostly solvent exposed loop (residue 33-43) preceding the beta hairpin containing the flaps (residue 44-63). (proteopedia.org)

The serpin ZPI is a protein Z (PZ)-dependent specific inhibitor of membrane-associated factor Xa (fXa) despite having an unfavorable P1 Tyr. (rcsb.org)
P1 tyrosine thus ensures that reaction with fXa or most other arginine-specific proteinases is insignificant unless PZ binds and localizes ZPI and fXa on the membrane, where the combined effects of Gla-Gla interaction, template bridging, and interaction of fXa with Glu-313 overcome the unfavorability of P1 Tyr and ensure a high rate of reaction as an inhibitor. (rcsb.org)
Position-specific entropy profiles created from scan- comparison of human versus avian influenza A viruses ning 306 human and 95 avian influenza A viral genomes would show the evolutionary similarities and differences showed that 228 of 4,591 amino acid residues yielded sig- between them and thus provide information for studying nificant differences between these 2 viruses. (cdc.gov)
Scientists have long been puzzled by how specific chains of amino acids go on to form three-dimensional proteins. (bigthink.com)
He resolved the crystal structure of the avirulence protein and identified polymorphic surface residues as the keys for specific recognition. (science.org.au)
More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. (biorxiv.org)
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)
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)
Often, an interaction that is specific for a group of organisms has evolved a long time ago and not changed since. (elifesciences.org)
In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)
However, protein shape anisotropy and the surface charge distribution are ignored in the original cell model, as are specific ion-residue and ion-ion interactions. (lu.se)
We also show the possibility of using specific interaction parameters for the protein-ion and ion-ion interactions, which would provide a more accurate description of osmotic pressures of protein solutions. (lu.se)

This graph is important for understanding the physical interactions within proteins, as well as their evolutionary history. (bigthink.com)
Cadherins are evolutionary related to the desmogleins which are component of intercellular desmosome junctions involved in the interaction of plaque proteins. (embl.de)
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)

Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. (frontiersin.org)

Here, we employed transmission electronmicroscopy and other biophysical methods to elucidate how BAR domainproteins steer processes at the membrane.In this work we studied the BAR protein bridging integrator 1 (BIN1), whichhas an established role in cancer, Alzheimer's disease and skeletalmyopathies. (kth.se)

Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. (nih.gov)

Modeling of the ternary Michaelis complex implicated ZPI residues Glu-313 and Glu-383 in fXa binding. (rcsb.org)
SMRT, GPS2 and TBL1 form a ternary complex in a three-way interaction. (esrf.fr)

FAK's ability to bind numerous structural and signaling proteins via a variety of interactions is important for FAK activation level, and for FAK interaction with a variety of substrates localized to sites of cell adhesion. (fishersci.com)
Here we define the precise Rab29 binding region of the LRRK2 Armadillo domain between residues 360-450 and show that this domain, termed 'Site #1', can also bind additional LRRK2 substrates, Rab8A and Rab10. (stanford.edu)

Moreover, we identify a distinct, N-terminal, higher affinity interaction interface between LRRK2 phosphorylated Rab8 and Rab10 termed 'Site #2', that can retain LRRK2 on membranes in cells to catalyze multiple, subsequent phosphorylation events. (stanford.edu)

In chemistry, π-effects or π-interactions are a type of non-covalent interaction that involves π systems. (wikipedia.org)

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
A global genetic interaction network maps a wiring diagram of cellular function. (thebiogrid.org)
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. (elifesciences.org)
PPARs play an important role in many cellular functions including lipid metabolism, cell proliferation, differentiation, adipogenesis and inflammatory signalling. (sigmaaldrich.com)
Cell membranes need to change their shapes during many cellular processeslike protein trafficking, cytokinesis and membrane homeostasis. (kth.se)
Specialized cell structures called ribosomes are the cellular organelles that actually synthesize the proteins (RNA transcription). (cdc.gov)

Vascular endothelial growth factor (VEGF) is an essential angiogenic factor for formation of the embryonic vasculature, and also has important roles in pathological conditions such as diabetic retinopthy, rheumatoid arthritis and cancer. (figshare.com)
The study demonstrates important roles of C273 and C288 in the suppression of Nrf2 by Keap1 under basal conditions and critical function of C151 in arsenic sensing and responsiveness. (cdc.gov)

Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane. (cipsm.de)

Connecting all disrupted pairs of proteins, we construct an "ASD disrupted network. (springer.com)
In other words, AlphaFold learned that particular amino acid configurations-say, distances between pairs, angles between chemical bonds-signaled that the protein would likely take a particular shape. (bigthink.com)
We have designed a purposely simple system to investigate this problem by systematically introducing individual and pairs of charged and titratable residues in a protein otherwise free of such residues. (lu.se)
Additionally, the interaction between pairs of residues was found to be highly context dependent, with some pairs having no apparent preferential interaction, while other pairs would engage in coupled titration forming a highly stabilized salt bridge. (lu.se)

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)

SMRT and NCoR are homologous corepressor proteins that are recruited to many repressive transcription factors. (esrf.fr)
Adjacent interaction regions in SMRT and GPS2 form a binary complex. (esrf.fr)
Fig. 102: a) NMR structure of the anti-parallel coiled-coil interaction between GPS2 (red) and SMRT (blue). (esrf.fr)
These grooves were suggestive of an interaction surface with the SMRT:GPS2 heterodimer. (esrf.fr)

Features important for intracellular G-protein activation and signal transduction are revealed. (rcsb.org)
Liver fatty acid binding protein (LFABP) belongs to a family of small (14kDa) intracellular lipid-binding proteins, which have a characteristic β-barrel structure. (soton.ac.uk)

Prothrombin (factor II of the coagulation cascade) is a critical protein in hemostasis. (medscape.com)
Thus, while evolution indicates that these residues are critical, the mechanistic reason for their conservation remains unresolved. (aps.org)
and subsequent dissociation of the SU and TM subunits are important in ensuring that critical regions of Env are exposed for the briefest time possible during receptor binding and fusion, when retroviral Env proteins are vulnerable to neutralizing antibodies produced by the host organism. (tufts.edu)
It not only plays a critical role in clot formation but also activates the protein C anticoagulant system by binding to thrombomodulin on the endothelial surface, indirectly controlling its own production. (medscape.com)

Our experimental data on photoactive yellow protein argue against a role in allosteric switching or protein stability. (aps.org)
Characterization of the human ortholog of Mov34 reveals eight N-terminal residues important for MPN domain stability. (nih.gov)
The osmotic pressure of protein solutions is an important measure of intermolecular interactions and can be used to predict stability and phase separation. (lu.se)

This model, hereafter formation of three-dimensional protein structures. (lu.se)

PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)

Bin/Amphiphysin/Rvs (BAR) proteins are peripheralmembrane proteins (PMP) and play an important role in sculpturingmembranes and in the regulation of actin dynamics. (kth.se)
For metal- powerful methods to obtain and compare reaction and activation loproteins, a third method to obtain local information about the energies for suggested enzyme mechanisms and they can also provide atomic details about the protein dynamics. (lu.se)

Metal-π interactions play a major role in organometallics. (wikipedia.org)
They may play an important role in the sorting of different cell types during morphogenesis, histogenesis and regeneration. (embl.de)
The CusB protein is part of the CusCBA periplasmic Cu(I) efflux system in Gram-negative bacteria, and it was recently reported to play a key role in the functioning of the whole CusCBA system, in which conformational changes as well as the assembly/disassembly process control the opening of the transporter. (biorxiv.org)
Here, we combine in-vitro structural measurements, which used EPR spectroscopy and UV-Vis measurements, with cell experiments to explore the role of the various methionine residues in CusB. (biorxiv.org)
This review describes recent advances in the role of human HMGB proteins and other proteins interacting with them, in cancerous processes related to oxidative stress, with special reference to ovarian and prostate cancer. (hindawi.com)
MK plays an important regulatory role in epithelial-mesenchymal interactions during fetal development and in postnatal lung development. (reliatech.de)
Background: Hypoxia plays an important role in the lung metastasis of hepatocellular carcinoma (HCC). (bvsalud.org)
Abnormal angiogenesis plays an important role in pathogenesis of diabetic kidney disease (DKD). (medscape.com)

Anatomy10

Organisms11

Chemicals and Drugs109

Analytical, Diagnostic and Therapeutic Techniques and Equipment46

Phenomena and Processes78

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care4

Ligand24

Membrane proteins9

Complexes6

Mutations8

Suggested that1

Cysteine residues3

Molecular16

Site-directed mu3

Mutagenesis3

Ligands4

Hydrophobic5

Extracellular6

Electrostatic5

Structural proteins3

Functional6

Inter-residue1

Abstract1

Prediction5

Sequences8

Functionally3

Sequence13

Biochemical1

Specificity2

Interact8

Structurally2

Highly conserved1

Protease3

Transmembrane2

Disulfide1

Receptors2

Gene6

Genes8

Enzymes4

Affect proteins1

Bioinformatics1

Kinase6

MRNA4

Several proteins1

Accessory proteins1

Computational6

Fluctuation1

Amino-terminal3

Molecules2

Viral proteins1

Catalysis2

Solvent2

Specific12

Evolutionary3

Chromatin1

Biophysical methods1

Metrics1

Ternary2

Bind2

Affinity1

Chemistry1

Cellular6

Roles2

Weak1

Pairs4

DNAs1

SMRT4

Intracellular2

Critical4

Stability3

Structures1

Transcription1

Dynamics2

Role8