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  • highly conserved
  • Sequence conservation and motif prediction studies show that even though most of the highly conserved residues have been characterized biochemically in previous studies, a significant number of novel putative sites and motifs are discovered that vary in a clade specific manner. (biomedcentral.com)
  • Furthermore, at least one portion of the protein has been extremely highly conserved - e.g ., only two of the 60 positions in the homeodomain differ between Nematostella (a sea anemone) and Branchiostoma (a chordate), two taxa that diverged over 600 million years ago. (biomedcentral.com)
  • mutations
  • Disease‐associated mutations often affect protein-protein binding affinities that can be measured with high accuracy in vitro using purified proteins by a variety of biophysical techniques. (els.net)
  • We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. (springer.com)
  • Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. (springer.com)
  • To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. (biomedcentral.com)
  • ligands
  • Such residues turn out to be often directly involved in binding ligands or interfacing with other proteins. (biomedcentral.com)
  • Protein Explorer has convenience buttons to toggle continuous slow spinning**, visibility of water or ligands, slab and stereo, as well as buttons to zoom up or down, change between white and black background, center any atom, or reset the initial view. (umass.edu)
  • selective
  • The structure of protein families is shaped by the sequence divergence accumulated as a consequence of speciation, gene duplication, and deletion events, as well as by the evolutionary selective pressure exerted on each protein in accordance with the corresponding 3D structure and the specific function performed ( 1 , 2 ). (pnas.org)
  • Bjerrum PJ, Wieth JO, Minakami S (1983) Selective phenyllyoxalation of functionally essential arginyl residues in the erythrocyte anion transport protein. (springer.com)
  • molecule
  • Protein Explorer's first image of any molecule is maximally informative . (umass.edu)
  • Protein Explorer has a molecule information window accessible at all times, with direct links to the PDB file header and RCSB Structure Explorer for the PDB ID code currently loaded, as well as links to external resources for viewing specific oligomers, fewer or single chains, evolutionary rate (ConSurf), and information about crystal contacts and model quality. (umass.edu)
  • The conserved arginine residue is positioned at the side of the narrow cleft on the concave site of the V-shaped molecule. (ebi.ac.uk)
  • metazoan
  • We also found transcripts encoding a nearly complete integrin adhesome from Pygsuia , indicating that this protein complex involved in metazoan multicellularity may have evolved earlier in eukaryote evolution than previously thought. (royalsocietypublishing.org)
  • pathways
  • Xenopus egg extract has been used to study protein turnover in many cellular contexts, including the cell cycle and signal transduction pathways 1-3 . (jove.com)
  • experiments
  • Protein binding experiments validate this assertion by demonstrating pseudo-phosphorylated Ser-150 decreases the affinity of isolated TnI for actin, whereas Ser-23/24 pseudo-phosphorylation is not different from unphosphorylated. (frontiersin.org)
  • We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. (angiogenesis-blog.com)
  • constitute
  • A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. (jove.com)
  • results
  • A plot of runtimes for the most time-intensive (non-parallelizable) part of the algorithm indicates a nearly linear time complexity so that, even for the extremely large Rossmann fold protein class, results were obtained in about a day. (biomedcentral.com)
  • This distinction must be kept in mind when analysing results from protein-protein interaction databases. (els.net)
  • 2002
  • Version 2.0 of Protein Explorer, released in increments in 2000-2002, is much easier to use, and much more powerful than RasMol. (umass.edu)
  • describe
  • In Auditory and Vestibular Research: Methods and Protocols , specialists in the field describe current RNA, protein, and imaging protocols that have provided insights into genetic regulation as well as a greater understanding of the genes and pathogens involved in diseases of the ear. (springer.com)
  • We describe the isolation of a novel murine CC chemokine that, based on its biological and structural features, we have named monocyte chemoattractant protein (MCP)-5. (rupress.org)
  • known
  • The dimerization domain adopts a conformation that bears no resemblance to any other known protein structure. (sciencemag.org)
  • The TBC/rab GAP domain has also been named PTM after three proteins known to contain it: the Drosophila pollux, the human oncoprotein TRE17 (oncoTRE17), and a myeloid cell line-expressed protein [ PMID: 8654926 ]. (ebi.ac.uk)
  • motif
  • A conserved arginine residue in the sequence motif B has been shown to be critical for the full GAP activity [ PMID: 10508155 ]. (ebi.ac.uk)
  • specific
  • We propose that delineating the residues responsible for the functional diversity associated with these proteins could help in design of species/clade specific inhibitors. (biomedcentral.com)
  • Bolton AE, Hunter WM (1973) The labelling of proteins to high specific radioactivities by conjugation to a 125I-containing acylating agent. (springer.com)
  • A shared domain between a spindle assembly checkpoint protein and Ypt/Rab-specific GTPase-activators. (ebi.ac.uk)
  • family
  • A commonly accepted working hypothesis is that whereas fully conserved positions are related to functional features common to all the members of the family, these other residues are related to functional specificity (e.g., binding of different cofactors). (pnas.org)
  • Members of the GGT protein family share a conserved "sandwich like" 3D structural domain which is made up of four layered αββα fold, except in case of CapD protein from B. anthracis, which has been reported to have six layered ααββαα like fold. (biomedcentral.com)
  • The other members of the family are the bifunctional enzyme peptidylglycine α-hydroxylating (and α-amidating) monooxygenase (PHM) ( 10 , 11 ), monooxygenase X (DBH-like monooxygenase protein 1, MOXD1) ( 12 ), and tyramine β-monooxygease (TBH) ( 13 ), which is the insect homolog of DBH. (sciencemag.org)