• However, we observed that mutations at these residues often substantially reduce the degree of protein production. (aps.org)
  • Truncating RAD21 variants are shown above, and missense mutations and in-frame deletions are shown below the protein representation. (springer.com)
  • Several of these mutations lead to misfolding or toxic gain of function in the SOD1 protein. (mathtube.org)
  • Expression of TRAF6 variants with mutations in this region in cultured cells demonstrated that TRAF6 residue T475 facilitates interaction with different SOD1 mutants. (mathtube.org)
  • f Driver activity assay, by MTT assay, of FaDu cells that ectopically expressed somatic mutations from pan-cancers9C11, and recognized hotspot mutation cluster regions (arbitrarily defined in this study as mutation sites with 5 mutations) at Rabbit Polyclonal to GCVK_HHV6Z amino acid residues E322 and D321, followed by the smaller frequent mutation cluster regions at E81, R135, R148, and S246 Tiaprofenic acid of the MAPK1 (ERK2) protein (Fig. (biotech2012.org)
  • Mutations at some of these residues seem to distinguish between structurally distinct ligands and raise the possibility that GluN2B-selective ligands can be divided into multiple classes. (cshl.edu)
  • Using biolayer interferometry we showed that indeed, the E9-D4 interaction is weak and transient although very important as it has not been possible to obtain viable viruses carrying mutations of key residues in the E9-D4 interface. (biorxiv.org)
  • This 8-residue consensus allows us to rationalize all known Tankyrase substrates and explains the basis for cherubism-causing mutations in the Tankyrase substrate 3BP2. (rcsb.org)
  • Abstract: Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. (usherbrooke.ca)
  • By making deletions in the β loop we defined a 20 amino-acid sequence that is sufficient for clustering. (jneurosci.org)
  • The sequence contains a conserved tyrosine (Y390) whose phosphorylation is induced by agrin and whose mutation abolished clustering of β loop chimeras and their ability to inhibit agrin-induced clustering of the endogenous AChR. (jneurosci.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)
  • Using pattern searches and position-dependent matrices, we have extracted the AT-hook motifs present in a non-redundant protein sequence database. (embl.de)
  • We have classified these motifs into three types according to their sequence similarity and have found that they are prevalent in many eukaryotic nuclear proteins in single or multiple copies. (embl.de)
  • The HMG family of proteins comprises members with multiple HMG domains that bind DNA with low sequence specificity, and members with single HMG domains that recognize specific nucleotide sequences. (embl.de)
  • For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)
  • The most identifiable category of SNP is the small proportion (less than 1%) that change protein sequence, the most common of which is the non-synonymous SNP. (biomedcentral.com)
  • This sequence is raft associated and sufficient to target PC1 (its native molecule) or a reporter protein to the regulated secretory pathways. (nih.gov)
  • e The same X-ray crystallography structure of MAPK1 protein showing the peptide sequence of the ATP-binding domain name highlighted in yellow, and the ATP molecule shown in gray color. (biotech2012.org)
  • The year 2022 was marked by the mpox outbreak caused by human monkeypox virus (MPXV), which is about 98 % identical to vaccinia virus (VACV) at the sequence level regarding the proteins involved in DNA replication. (biorxiv.org)
  • LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. (baderlab.org)
  • LOLA allows you to generate custom sequence logos by setting parameters such as logo height, trim percentage, and residue colour scheme. (baderlab.org)
  • The chromo and SET domains are conserved sequence motifs present in chromosomal proteins that function in epigenetic control of gene expression, presumably by modulating higher order chromatin. (embl-heidelberg.de)
  • Folding a protein sequence into its minimum-energy structure represents such a problem. (lu.se)
  • Protein folding, going from sequence to structure by mini- a quadratic Hamiltonian requires additional spin variables and mizing an energy function, represents a difficult optimization implementing interactions such as self-avoidance becomes problem. (lu.se)
  • A protein complex assembly can result in the formation of homo-oligomeric or hetero-oligomeric complexes. (wikipedia.org)
  • In addition to the conventional complexes, as enzyme-inhibitor and antibody-antigen, interactions can also be established between domain-domain and domain-peptide. (wikipedia.org)
  • Homo-oligomers are macromolecular complexes constituted by only one type of protein subunit. (wikipedia.org)
  • The modeling of macromolecular complexes is an exciting and rapidly advancing niche for the protein software industry. (dnastar.com)
  • BoNTs are secreted as progenitor complexes (PTC) with a non-toxic-non-hemagglutinin protein (NTNH) and a few neurotoxin associated proteins (NAPs) with or without hemagglutinin activity (HA). (nature.com)
  • Depending on the number of proteins forming the complex, three kinds of complexes, viz . (nature.com)
  • We started hypothesizing that the most obvious interpretation of interference was from subunit poisoning by wild type proteins with mutant proteins into complexes, where maximum signal output would require both the proteins to be in the active state persistently, and that having a wild type protein would be like a sort of flat tire and would be a much less efficient complex than a sort of double barreled mutant RAS. (cancer.gov)
  • Results: It was shown that about 30% of all contacts between amino acids and nucleotides in protein-DNA complexes are not random. (isa.ru)
  • Rafts may serve to cluster protein complexes, such as those involved in signal transduction, thereby facilitating signaling. (nih.gov)
  • These proteins inhibit the C3 and C5 convertases (multi-subunit proteases), by promoting dissociation of the multisubunit complexes and/or by inactivating the complexes through proteolysis (catalyzed by factor I). Several pharmacological agents that regulate or modulate complement activity have been identified by in vitro assay, but most have been shown in vivo to be of low activity or toxic. (justia.com)
  • In one study of a large set of protein-ligand complexes, we tried to improve the free energies of binding by using MD simulations with QM-derived charges, which sometimes led to improved results, but not always. (lu.se)
  • Many molecular processes within a cell are carried out by molecular machines that are built from numerous protein components organized by their PPIs. (wikipedia.org)
  • All this information enables the creation of large protein interaction networks - similar to metabolic or genetic/epigenetic networks - that empower the current knowledge on biochemical cascades and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. (wikipedia.org)
  • In the cellular environment, molecular recognition occurs when one protein binds with another in a specific fashion based on traits such as steric complementarity ("shape recognition"), charge complementarity, and other nonbonded forces (e.g., van der Waals forces, hydrogen binding, electrostatic, solvation contributions). (dnastar.com)
  • A docking algorithm must consider the structure of each individual protein molecule and use this information to predict the structure of the bound complex, while also considering protein flexibility, multiple point interactions between the ligand and receptor, molecular energy and biophysical interactions. (dnastar.com)
  • The 90 KDa heat shock protein (Hsp90) is a highly conserved molecular chaperone crucially involved in maintaining cellular homoeostasis in organisms from most kingdoms of life with the exception of archea 1 . (nature.com)
  • The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. (nature.com)
  • We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. (springer.com)
  • Here, we sought to uncover the structural details of this interaction through molecular dynamics (MD) simulations of a dimeric model system, coarse grained using the AWSEM force field. (mathtube.org)
  • These results provide the first detailed analysis of the interaction determinants of MipZ and deepen our knowledge of the molecular mechanism underlying the function of this intriguing cell division regulator. (mpg.de)
  • Molecular modeling of these enzymes has revealed an amphipathic alpha helix within the C-terminal domains of these proteins. (nih.gov)
  • IntAct provides a database system and analysis tools for molecular interaction data. (biokeanos.com)
  • A cluster of residues distant to the binding site also control ligand potency, the degree of inhibition, and show ligand-induced increases in motion during molecular dynamics simulations. (cshl.edu)
  • However, each substance possesses the disadvantage of being large molecular weight proteins (240 kDa and 26,000 kDa, respectively) that are difficult to manufacture and must be administered by infusion. (justia.com)
  • The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe. (cornell.edu)
  • Here, we provide molecular and functional studies revealing the basis of this Ibp/immunoglobulin (Ig) interaction. (cornell.edu)
  • To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore interactions and movements that define the conformational landscape of the AT[subscript 1] receptor. (usherbrooke.ca)
  • However, in the mid 1990s, other proteins were also found to accumulate in the abnormal muscle fibers, and molecular genetic studies revealed several chromosomal loci. (medscape.com)
  • 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)
  • 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)
  • Our study maps the important ISD11 amino acid residues critical for in vivo Fe-S cluster biogenesis. (iisc.ac.in)
  • In vivo, regulation of complement at the C3 and C5 activation steps is provided by both plasma and membrane proteins. (justia.com)
  • We used targeted mutagenesis of contact residues and affinity measurements and performed studies of the Fab-IbpA complex to determine the stoichiometry between Ibp and VH domains, suggesting Ibp may serve to cluster full-length IgA antibodies in vivo. (cornell.edu)
  • Assembly of the binuclear iron center in the oxygenase component of phenol hydroxylase was examined in the presence and absence of DmpK, a protein required for in vivo synthesis of active oxygenase. (concordia.ca)
  • In many metabolic reactions, a protein that acts as an electron carrier binds to an enzyme that acts as its reductase. (wikipedia.org)
  • 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)
  • Viral DNA synthesis involves a DNA repair enzyme, the uracil-DNA glycosylase D4 linked to the structural protein A20 forming the processivity factor, which in turn binds to E9 forming the complex required for processive DNA synthesis. (biorxiv.org)
  • describes the use of a phage-displayed combinatorial random peptide library to identify a 27-residue peptide that binds to C3 and inhibits complement activation. (justia.com)
  • We systematically exchanged surface-exposed residues using alanine-scanning mutagenesis. (mpg.de)
  • Site-directed and random mutagenesis were performed on DmpM to identify residues involved in its interaction with the oxygenase. (concordia.ca)
  • Although mutation of six conserved residues activated phenol hydroxylase in steady-state assays, the double mutant M37T/V77A, resulting from random mutagenesis, did not activate phenol hydroxylase. (concordia.ca)
  • Immunodetection of endogenous Suv39h1/SUV39H1 proteins in a variety of mammalian cell lines reveals enriched distribution at heterochromatic foci during interphase and centromere-specific localization during metaphase. (embl-heidelberg.de)
  • The angiotensin-II type 1 (AT[subscript 1]) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the G[subscript q/11] protein and β-arrestins. (usherbrooke.ca)
  • Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
  • Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. (upf.edu)
  • The results of this research provide insight into recent work regarding the physical chemistry of amino acids and their role in the structure, function and evolution of proteins. (purdue.edu)
  • The paper deals with the amino acid residues classification on the basis of the amino acids proteins - DNA nucleotides contacts parameters. (isa.ru)
  • Crisp classification methods showed the existence of clustering invariants of amino acids at the lowest level of association. (isa.ru)
  • Conclusions: Fuzzy classification of amino acids data can be used to construct the substitution matrix for DNA-binding protein sequences and protein-DNA binding analysis. (isa.ru)
  • The plasma protein inhibitors are factor H and C4-binding protein, and the regulatory membrane proteins located on cell surfaces are complement receptors 1 (CR1), decay-accelerating factor (DAF), and membrane cofactor protein (MCP). (justia.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)
  • Two highly conserved phenylalanine residues are found in the middle of the first and third helices, and help form the hydrophobic core of the protein. (mshri.on.ca)
  • 1. Gurskii G. V., Tumanian V. G., Zasedatelev A. S., Zhuze A. L., Grokhovskii S. L., Gottikh B. P. A code governing specific binding of regulatory proteins to DNA and structure of stereospecific sites of regulatory proteins // Mol Biol (Mosk), 1975. (isa.ru)
  • The AT-hook is a small DNA-binding protein motif which was first described in the high mobility group non-histone chromosomal protein HMG-I(Y). Since its discovery, this motif has been observed in other DNA-binding proteins from a wide range of organisms. (embl.de)
  • It is most interesting that this motif seems to be quite specific to known or predicted chromosomal/DNA-binding proteins, suggesting that it may act as a versatile minor groove tether. (embl.de)
  • This alternation results in a dynamic localization cycle, in which MipZ continuously oscillates between non-specific chromosomal DNA and the polarly localized ParB protein. (mpg.de)
  • Two of them are likely responsible for contacting FtsZ and chromosomal DNA, respectively, whereas the other two appear to be involved in the interaction with ParB. (mpg.de)
  • HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. (embl.de)
  • Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). (embl.de)
  • The study also examined the genetic-epigenetic interactions with treatment response through differential methylation analysis, methylation quantitative trait loci, colocalization, and promoter-anchored chromatin interaction. (inra.fr)
  • As a main result, we found that clusters of co-evolving residues related to the catalytic site of an enzyme have distinguishable topological properties in the network. (upf.edu)
  • On the contrary, they form clusters interconnecting β-sheets of the catalytic domain. (rcsb.org)
  • The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. (rcsb.org)
  • Cas9 nuclease can be converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains 12 , 13 and then fused to transcription activation domains. (cdc.gov)
  • Using chimeric proteins in which CD4 is fused to the large intracellular loop of each of the AChR subunits we found that agrin induced clustering of only chimeras containing the β subunit loop. (jneurosci.org)
  • Phosphorylation of the AChR β subunit is correlated with increased rapsyn/AChR binding, suggesting that the effect of βY390 phosphorylation on clustering is mediated by rapsyn. (jneurosci.org)
  • Together, these findings suggest that agrin-induced phosphorylation of the β subunit motif increases the stoichiometry of rapsyn binding to the AChR, thereby helping to stably cluster the receptor and anchor it at high density in the postsynaptic membrane. (jneurosci.org)
  • Each subunit has a large intracellular loop between the third and fourth transmembrane domains that is the likely site for regulated interactions with postsynaptic scaffolding proteins. (jneurosci.org)
  • Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. (mdpi.com)
  • Following this endoproteolytic cleavage, the C-terminal basic residues are trimmed by the enzymatically active form of CPE to yield mature, bioactive peptide hormones. (nih.gov)
  • The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments). (baderlab.org)
  • BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network. (baderlab.org)
  • This peptide was truncated to a 13-residue cyclic segment that maintained complete activity, which is referred to in the art as Compstatin. (justia.com)
  • A cell-penetrant peptide blocking C9ORF72-repeat RNA nuclear export reduces the neurotoxic effects of dipeptide repeat proteins. (le.ac.uk)
  • We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. (nature.com)
  • Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. (weizmann.ac.il)
  • Targeting EPPIN's essential residues for its biomolecular interactions may improve the rational design of EPPIN ligands as spermiostatic compounds. (bvsalud.org)
  • This may function in coupling the processes of transcription and splicing, as these WW domains can interact with essential splicing proteins such as mBBP/SF1. (mshri.on.ca)
  • Frank, would you like to summarize the data from your lab, and from the RAS Initiative here at the FNL, that have influenced your thinking about how RAS proteins might interact? (cancer.gov)
  • Further, we showed in cultured cells that several mutant SOD1 proteins, but not wild type SOD1 protein, interact with TRAF6 via the MATH domain. (mathtube.org)
  • 1997) at higher how proteins interact with themselves in solution. (lu.se)
  • This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. (weizmann.ac.il)
  • Compounds comprising peptides and peptidomimetics capable of binding the C3 protein and inhibiting complement activation are disclosed. (justia.com)
  • In particular, this invention provides peptides and peptidomimetics capable of binding the C3 protein and inhibiting complement activation. (justia.com)
  • The aggregation of both amyloid beta (Abeta) peptides extracellularly and Tau proteins intracellularly plays key roles in the pathological consequences of AD, which lead to cholinergic neurodegeneration and eventually death. (inra.fr)
  • Protein subunits assembly is guided by the establishment of non-covalent interactions in the quaternary structure of the protein. (wikipedia.org)
  • Notably, the DNA-binding and FtsZ-binding interfaces of MipZ comprise residues from both monomeric subunits and are located on opposite sides of the dimer. (mpg.de)
  • A more recent NMR pulsed-gradient, spin-echo misfolded proteins (Kelly, 1998), and the nucleation, growth, (PGSE) self-diffusion study concluded that BPTI is pre- and polymorphism of protein crystals (Rosenberger et al. (lu.se)
  • Second, we have investigated how this information can be used to improve methods of prediction of functional residues by reducing the search space. (upf.edu)
  • It would be an advantage if the functional effects of an nsSNP on protein structure and function could be predicted, both for the final identification process of a causal variant in a disease-associated chromosome region, and in further functional analyses of the nsSNP and its disease-associated protein. (biomedcentral.com)
  • The interactions include direct (physical) and indirect (functional) associations. (biokeanos.com)
  • PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. (biokeanos.com)
  • The most diversity in atomic interactions between protein and ligand occur in the B ring, with functional groups that contain electron donors and acceptors providing additional atomic contacts within the pocket. (cshl.edu)
  • Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. (embl-heidelberg.de)
  • The goal of this work is two-fold: first, we have combined mutual information and structural data to describe the amino acid networks within a protein and their interactions. (upf.edu)
  • The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases. (rcsb.org)
  • The clustering study revealed spatial arrangements of residues that were grouped roughly into a number of structural motifs. (purdue.edu)
  • The A and B class Eph proteins have a common structural organization. (rndsystems.com)
  • 1991), none of the the structural details of the heterogeneous protein surface and experimental studies mentioned so far could provide un- takes into account a variety of short-range interactions, direct ambiguous information about oligomer structure. (lu.se)
  • Protein-protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. (wikipedia.org)
  • Decamer formation is opposed by electrostatic repulsion among numerous cationic residues confined within a narrow channel. (lu.se)
  • The cytoplasmic domain contains a juxtamembrane motif with two tyrosine residues, which are the major autophosphorylation sites, a kinase domain, and a conserved sterile alpha motif (SAM) (5). (rndsystems.com)
  • Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. (baderlab.org)
  • Limb-girdle muscular dystrophy (LGMD) protein defects occur in several pathways involved in the biologic function of muscle and can be divided into groups based on cellular localization. (medscape.com)
  • In the case of the mitochondrial P450 systems, the specific residues involved in the binding of the electron transfer protein adrenodoxin to its reductase were identified as two basic Arg residues on the surface of the reductase and two acidic Asp residues on the adrenodoxin. (wikipedia.org)
  • Defects in Fe-S cluster biogenesis process leads to mitochondrial dysfunction and that eventually results in various human mitochondrial disorders. (iisc.ac.in)
  • One of the major mitochondrial disorders associated with Fe-S cluster biogenesis impairment is exercise intolerance disorder ISCU myopathy, which is a result of loss of function of Fe-S cluster scaffold protein ISCU. (iisc.ac.in)
  • Our biochemical results using yeast model system and HeLa cells lines suggests that ISCU Myopathy results in defective Fe-S cluster biogenesis in mitochondrial compartment. (iisc.ac.in)
  • This study shows that the expression of both myeloid zinc finger 1 (MZF-1) and Ets-like protein-1 (Elk-1) correlates with PKCα expression in TNBC. (oncotarget.com)
  • The 32-aa MYND domain (for myeloid, Nervy, and Deaf-1) contains non-DNA-binding zinc fingers that are thought to mediate protein-protein interactions (Gross, 1996). (sdbonline.org)
  • These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. (embl-heidelberg.de)
  • Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)
  • Our experimental data on photoactive yellow protein argue against a role in allosteric switching or protein stability. (aps.org)
  • Adding a carrier protein enhances protein stability, increases shelf-life, and allows the recombinant protein to be stored at a more dilute concentration. (rndsystems.com)
  • The poly(ADP-ribose)polymerases Tankyrase 1/2 (TNKS/TNKS2) catalyze the covalent linkage of ADP-ribose polymer chains onto target proteins, regulating their ubiquitylation, stability, and function. (rcsb.org)
  • Importantly, mutation of these critical ISD11 residues to alanine leads to its compromised interaction with NFS1, which results in reduced stability and enhanced aggregation of NFS1 in the mitochondria. (iisc.ac.in)
  • The 9 most strongly PAS-conserved residues are located at structurally inconspicuous positions that remain largely unstudied. (aps.org)
  • We found that interaction of the A ring within the binding pocket seems largely invariant for a variety of structurally distinct ligands. (cshl.edu)
  • In addition, a range of structurally diverse linkers between the two aryl rings can be accommodated by the binding site, providing a potential opportunity to tune interactions with the ligand binding pocket via changes in hydrogen bond donors, acceptors, as well as stereochemistry. (cshl.edu)
  • The presence of these proteins in a commensal microbe suggest that binding a broad repertoire of immunoglobulins, particularly in the gut/microbiome environment, may provide an important function in the maintenance of host/microbiome homeostasis contrasting with the pathogenic role of structurally homologous superantigens expressed by pathogens. (cornell.edu)
  • Several enzymes, carrier proteins, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers. (wikipedia.org)
  • In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)
  • and at agrin-induced clusters in cultured myotubes ( Wallace, 1989 ). (jneurosci.org)
  • We also found that the DNA-binding region mainly consists of positively charged arginine and lysine residues. (mpg.de)
  • The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. (embl-heidelberg.de)
  • Gradient formation is driven by the alternation of MipZ between a monomeric and dimeric state with distinct interaction patterns and diffusion rates. (mpg.de)
  • Hsp90's diverse array of clientele implicate the chaperone in several associated biological functions and place it at the intersection of various fundamental cellular pathways, where it acts as a central hub in maintaining numerous protein interaction networks 1 . (nature.com)
  • Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. (weizmann.ac.il)
  • In this report, an information-theoretic method is introduced for the purpose of detecting and quantifying distance-dependent through-space multibody relationships between the side chains of three residues. (purdue.edu)
  • This new technique is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen and experimentally solved protein structures. (purdue.edu)
  • MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. (biokeanos.com)
  • Using affinity chromatography coupled to multidimensional protein identification technology (MudPIT), DEAF-1 was identified as a candidate regulator. (sdbonline.org)
  • Moreover, our findings highlight that, COXPD19 associated R68L ISD11 mutant displays reduced affinity to form a stable sub-complex with NFS1, thereby fails to prevent NFS1 aggregation, resulting impairment of Fe-S cluster biogenesis. (iisc.ac.in)
  • It was shown by fuzzy classification methods that six classes are optimal for protein-DNA recog¬nition task. (isa.ru)
  • The surface of the GABP alpha OST domain contains two predominant clusters of negatively-charged residues suggestive of electrostatically driven interactions with positively-charged partner proteins. (ubc.ca)
  • It has been proposed that interactions with ligand might be mediated through a cluster of positively charged residues between helices 1 and 4. (mshri.on.ca)
  • Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. (expasy.org)
  • The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications. (biokeanos.com)
  • Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. (expasy.org)
  • Orange protein (ORP) is a small bacterial protein, of unknown function, that contains a unique molybdenum/copper heterometallic cluster, [S 2 Mo VI S 2 Cu I S 2 Mo VI S 2 ] 3- (Mo/Cu), non-covalently bound. (unl.pt)
  • Activation of kinase activity occurs after membrane-bound or clustered ligand recognition and binding. (rndsystems.com)
  • The HP model has favorable interactions between adjacent, not directly bound hydrophobic residues. (lu.se)
  • So that was the first observation that this inhibitory effect was somehow mediated by interaction of wild type with mutant KRAS. (cancer.gov)
  • A couple of papers have shown that overexpression of wild-type RAS can interfere with mutant in some ways, but it's always been very complicated to interpret because obviously the wild type protein can signal as well, so seeing interference of the mutant is difficult. (cancer.gov)
  • Analyzing the subcellular distribution of the mutant proteins as well as their ability to support division site placement, we identified four clusters of residues that are important for MipZ activity. (mpg.de)
  • There are conflicting data on whether KRAS protein molecules form dimers. (cancer.gov)
  • Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. (weizmann.ac.il)
  • These clustered hot spots form hot regions. (biokeanos.com)
  • Antibodies are heavy (~150 k Da ) proteins of about 10 nm in size, [7] arranged in three globular regions that roughly form a Y shape. (wikipedia.org)
  • These ankyrin repeats form five domains termed ankyrin repeat clusters (ARCs), each predicted to bind substrate. (rcsb.org)
  • Dissociation of the dimeric form of DmpM was shown to precede denaturation at low protein concentrations resulting in activation. (concordia.ca)
  • Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. (rcsb.org)
  • You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. (baderlab.org)
  • These interactions between proteins are dependent on highly specific binding between proteins to ensure efficient electron transfer. (wikipedia.org)
  • One of the major biosynthetic processes in human mitochondria is the biogenesis of Iron-Sulfur (Fe-S) clusters which primarily involves in electron transfer reactions during oxidative phosphorylation (OXPHOS). (iisc.ac.in)
  • 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)
  • The domains are well conserved from yeast to humans, and are also found in plant proteins. (mshri.on.ca)
  • Interestingly, all of the nuclear FF domain-containing proteins also possess WW domains towards their N-terminus. (mshri.on.ca)
  • Referenced in part on Cell Signaling Technology Website, Reference Section on Protein Domains. (mshri.on.ca)
  • The 576-aa DEAF-1 protein possesses two conserved domains, SAND and MYND. (sdbonline.org)
  • High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. (embl.de)
  • There are 46627 HMG domains in 39088 proteins in SMART's nrdb database. (embl.de)
  • Moreover, hydrophobic and hydrophilic residues in the WFDC and Kunitz domains allow plasma membrane anchoring, orienting the EPPIN binding pocket to the solvent. (bvsalud.org)
  • There are 16430 PostSET domains in 16148 proteins in SMART's nrdb database. (embl-heidelberg.de)
  • These include proteins associated with the sarcolemma (see image below), proteins associated with the contractile apparatus (see image below), and various enzymes involved in muscle function. (medscape.com)
  • More recent work on the phylogeny of the reductase has shown that these residues involved in protein-protein interactions have been conserved throughout the evolution of this enzyme. (wikipedia.org)
  • Each binding partner can consist of one or multiple protein chains. (dnastar.com)
  • The crystal structure and biochemical assays of a truncated IbpA construct in complex with mouse VH5 antigen-binding fragment (Fab) shows a binding of Ig heavy chain framework residues to the Ibp Domain D and the C-terminal heavy chain binding domain (HCBD). (cornell.edu)
  • In summary, our findings provide compelling evidence that respiration defect due to impaired biogenesis of Fe-S clusters in ISCU myopathy patients, leads to manifestation of complex clinical symptoms. (iisc.ac.in)
  • Raft association of CPE likely facilitates its interaction with its prohormone cargo. (nih.gov)
  • 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)
  • In this study, we investigated the function of MipZ by mapping its interaction interfaces with FtsZ, ParB and DNA. (mpg.de)
  • Specific protein function and abnormalities are discussed below with each LGMD. (medscape.com)
  • To date, various genome-scale loss-of-function screening methods have been developed, including approaches employing RNA interference 1 , 2 and the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) adaptive immune system 3 , 4 . (cdc.gov)