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  • cysteine
  • This protein contains four cysteine residues, but in this state only two of them are expected to oxidize to form a single disulfide bond. (fold.it)
  • Similar studies involving chimeras between PF4 and NAP-2 localized a major antigenic site to the region between the third and fourth cysteine residues for more than half of the sera tested. (bloodjournal.org)
  • This site appears to involve a series of amino acids immediately after the third cysteine residue beginning with P37. (bloodjournal.org)
  • Rather, we propose that maintaining a region near the third cysteine residue of PF4, distal from the proposed heparin-binding domain, is required to form the epitope recognized by many HIT antibodies. (bloodjournal.org)
  • PF4 is a 70-amino acid (AA) platelet-specific protein that belongs to the CXC (or beta) chemokine subfamily, in which the first two of the four conserved cysteine residues are separated by one AA residue. (bloodjournal.org)
  • We identified multiple receptor-like protein kinases changing in abundance, including cysteine (Cys)-rich receptor-like kinases (CRKs) that are up-regulated upon the perception of flagellin. (plantphysiol.org)
  • alanine
  • We've adjusted the scoring function here so that alanine residues are more tolerable in loops (they are still restricted in helices and sheets! (fold.it)
  • Alanine substitutions at three of the four lysine residues implicated in heparin binding, K62, K65, and K66, had little effect on recognition by HIT antibodies (OD 405 = 2.2, 2.8, and 2.0, respectively), whereas an alanine substitution at position K61 led to reduced, but still significant binding (OD 405 = 1.0). (bloodjournal.org)
  • Today, key residues are typically identified by means of alanine substitution assays, which determine ΔΔ G bind , the change in the Gibbs free energy of binding caused by the substitution. (frontiersin.org)
  • Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. (mdpi.com)
  • sites for signalin
  • In the second phase, tyrosine residues that serve as docking sites for signaling proteins are phosphorylated including tyrosines in the kinase insert region (Y583, Y585), the juxtamembrane region (Y463), and in the C-terminal tail (Y766) of FGFR1. (pnas.org)
  • ligand-bindi
  • The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function. (pnas.org)
  • Similarly, they can take into account the associated conservation at the molecular signatures level (SDPs) in fundamental regions corresponding to ligand-binding sites and protein interaction sites. (pnas.org)
  • The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. (biomedcentral.com)
  • predictors
  • According to our own evaluations performed at a resolution of +/− two residues, the predictors we trained with the random forest algorithm were our top performing methods with average top 10 prediction accuracy scores of 85.13% (short range), 74.49% (medium range), and 54.49% (long range). (springer.com)
  • Our ensemble models (stacked denoising autoencoders combined with support vector machines) were our best performing deep network predictors and achieved top 10 prediction accuracy scores of 75.51% (short range), 60.26% (medium range), and 43.85% (long range) using the same evaluation. (springer.com)
  • and the results suggested that our models achieved comparable performance to contact predictors developed by groups that participated in CASP11. (springer.com)
  • accuracy
  • The evaluation was performed using standard assessment techniques such as those used by the official CASP assessors as well as two novel evaluation metrics (i.e., cluster accuracy and cluster count). (biomedcentral.com)
  • Our residue-residue contact predictor, DNcon, performed particularly well achieving an accuracy of 66% for the top L/10 long range contacts when evaluated in a neighbourhood of size 2. (biomedcentral.com)
  • We obtain 0.70 three-state accuracy for solvent accessibility, 0.33 15-state accuracy and 0.74 Pearson Correlation Coefficient (PCC) for the contact number on the 5729 monomeric soluble globular protein dataset. (biomedcentral.com)
  • We also evaluate the performance on the CASP11 benchmark dataset, DeepSacon achieves 0.68 three-state accuracy and 0.69 PCC for solvent accessibility and contact number, respectively. (biomedcentral.com)
  • If the top L /5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. (biomedcentral.com)
  • To achieve higher accuracy, SCWRL4 is somewhat slower than SCWRL3 when run in the default flexible rotamer model (FRM) by a factor of 3-6, depending on the protein. (fccc.edu)
  • The table below gives the accuracy in χ 1 and χ 1+2 dihedral angles for a test set of 379 proteins. (fccc.edu)
  • Residue types are sorted by their SCWRL4.0 χ 1 accuracy. (fccc.edu)
  • Validation results and specific examples within illustrate that SMID-BLAST has a high degree of accuracy in terms of predicting both the small molecule ligand and binding site residue positions for a query protein. (biomedcentral.com)
  • small-molecule
  • The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. (biomedcentral.com)
  • When annotation does exist, it may come from one of three places: directly from experiment, through mapping to a protein family known to bind certain molecules, or through homology to a crystal structure demonstrating small molecule binding. (biomedcentral.com)
  • Experimentally, small molecule ligands for proteins are often identified using high-throughput screening methods with chemical libraries. (biomedcentral.com)
  • subunit
  • Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. (elifesciences.org)
  • protein's
  • However, mutations that are neutral with respect to a protein's capacity to perform its biological function often affect protein thermodynamics. (genetics.org)
  • and their effects on stability (measured as ΔΔ G , the Δ G f of the mutant protein minus the Δ G f of the wild-type protein) are frequently of the same magnitude as a protein's net stability. (genetics.org)
  • The impact of a mutation on a protein's function can therefore depend on the protein's stability: a moderately destabilizing mutation that is easily tolerated by a stable parent protein may completely disrupt the folding of a less stable parent. (genetics.org)
  • The fact that mutations that are neutral with respect to direct selection for protein function can affect a protein's tolerance to subsequent mutations is not consistent with the simplest formulation of the neutral theory of evolution, which tends to assume that the fraction of mutations that is neutral remains constant in time. (genetics.org)
  • characteristic
  • In analogous with solvent accessibility, the contact number is another important structural characteristic. (biomedcentral.com)
  • The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. (pnas.org)
  • correctly
  • For a testing set of 379 proteins, 86% of chi1 angles and 75% of chi1+2 are predicted correctly within 40 degrees of the X-ray positions. (fccc.edu)
  • membrane-bound
  • Cellulose microfibrils are synthesized by a large membrane-bound protein complex. (plantphysiol.org)
  • Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. (peerj.com)
  • The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. (peerj.com)
  • encodes
  • Here, we report the identification of a Drosophila Pax gene that encodes a protein with only a RED domain and no PAI domain. (pnas.org)
  • Recombinant
  • To address this issue, we studied the binding of HIT antibodies to a series of recombinant proteins containing either point mutations in PF4 or chimeras containing various domains of PF4 and the related protein, neutrophil activating peptide-2 (NAP-2). (bloodjournal.org)
  • structurally
  • Note that Spo0B along with SK proteins are structurally distinct from Hpt-type phosphotransferases, commonly utilized as intermediary proteins in phosphorelays. (pnas.org)
  • In the Tat system, which is structurally and mechanistically unrelated to the Sec translocase, proteins are translocated in a fully folded form ( 2 , 3 ). (pnas.org)
  • experimental
  • Furthermore, as more and more genomes are sequenced, only a fraction of proteins will have additional data to complement any experimental HTP study. (biomedcentral.com)
  • Although contact maps based on the static structure of the complex give an initial approximation to the physical communication network, the inclusion of dynamical correlations provides a more accurate picture of the network topology and approximates the strength of the allosteric signal that can be related to experimental observations. (pnas.org)
  • Experimental methods such as directed evolution have shown success in protein design. (jove.com)
  • distance restraints
  • One of the major advantages of these two programs over the others is that both depend on contacts and distance restraints, extracted from multiple templates, to refine the template-based models. (biomedcentral.com)
  • rigid
  • It means that a probe sphere of 1.4A radius (representing a water molecule) can not pass in or out of the cavity (considering protein as completely rigid of course). (molsoft.com)
  • stability
  • We present a mathematical theory that predicts the number of accumulated mutations, the index of dispersion, and the distribution of stabilities in an evolving protein population from knowledge of the stability effects (ΔΔ G values) for single mutations. (genetics.org)
  • Our theory quantitatively describes how neutral evolution leads to marginally stable proteins and provides formulas for calculating how fluctuations in stability can overdisperse the molecular clock. (genetics.org)
  • This indicates that the recurrent structural motifs, as we define them, describe recurrent structural patterns that are important for protein stability. (mdpi.com)
  • monomeric
  • The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. (plantphysiol.org)
  • important
  • The yeast splicing factor Cwc2 contacts several catalytically important RNA elements in the active spliceosome, suggesting that Cwc2 is involved in determining their spatial arrangement at the spliceosome's catalytic centre. (embopress.org)
  • The most obvious example is the study of fully conserved positions that pinpoint important residues for the structure and function of the family members ( 5 ). (pnas.org)
  • Residues and nucleotides in the majority of pathways for intercommunity signal transmission are evolutionarily conserved and are predicted to be important for allosteric signaling. (pnas.org)
  • Conserved residues that greatly affect the CPL upon removal have been hypothesized to be important for allosteric signal transmission ( 10 ). (pnas.org)
  • The Tat pathway is required for important cellular processes, including energy metabolism (Tat can export cofactor-containing proteins), cell division, cell motility, quorum sensing, heavy metal resistance, iron acquisition, and biofilm formation ( 3 ). (pnas.org)
  • largely
  • The absolute number of CESA proteins present in a CSC remains a subject of much speculation, largely because the stoichiometry of the cellulose microfibril remains unresolved ( Cosgrove, 2014 ). (plantphysiol.org)
  • PROTEINS evolve largely through the slow accumulation of amino acid substitutions. (genetics.org)