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  • detect
  • Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13 C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13 C chemical shifts from the expected (mean) experimental value of the non-modified residue. (peerj.com)
  • recently proposed a novel NMR-based methodology to detect glycosylation of residues in proteins under urea-denaturing conditions. (peerj.com)
  • The Hygiene Monitoring System Chemdye® PRO1 MICRO has been designed to detect proteins and to reduce iatrogenic agents on surgical instruments after their cleaning, in real time. (sychem.co.uk)
  • Chemdye® PRO1 MICRO has high sensitivity and can detect up to 1.0 micrograms of protein. (sychem.co.uk)
  • This Pen system is designed to detect and quantify proteins, allergens and reducing agents with high sensitivity on surfaces and difficult-to access areas after the cleaning process. (sychem.co.uk)
  • The objective of the current analysis is to detect plant and animal protein residues on the 15 stone artifacts using cross-over immunoelectrophoresis (CIEP). (tdar.org)
  • Since the number of related copies for eukaryotic proteins tends to be smaller, there are fewer proteins to compare and it is therefore harder to detect 'covariation' when it occurs. (elifesciences.org)
  • coiled-coil
  • MxiH (8.3 kDa) is a helix-turn-helix, whereas IpaD (36.6 kDa) has a dumbbell shape with two globular domains flanking a central coiled-coil that stabilizes the protein. (ku.edu)
  • functional
  • The pathogenesis of Shigella flexneri requires a functional type III secretion apparatus to serve as a conduit for injecting host-altering effector proteins into the membrane and cytoplasm of the targeted cell. (ku.edu)
  • We interpret the observed length scale of clustering as a statistical reflection of the functional locality (or modularity) of proteins: amino acids that are near each other on the protein backbone are more likely to contribute to, and collaborate toward, a common subfunction. (prolekare.cz)
  • Although two selective mutants on Leu128, Leu128Ala (L128A) and Leu128Arg (L128R), demonstrated high binding affinity to IL-8, they were not capable of coupling to G proteins and consequently lost the functional response of the receptors. (harvard.edu)
  • We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. (biomedcentral.com)
  • Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. (biomedcentral.com)
  • recombinant
  • AJOU Open Repository: Enzymatic methylation of recombinant TIS21 protein-arginine residues. (ajou.ac.kr)
  • Recombinant TIS21 protein was overexpressed in Escherichia coli harboring the expression vector plasmid pQE-30 carrying the TIS21 cDNA coding sequence containing an extra 120 nucleotides upstream. (ajou.ac.kr)
  • Molecular
  • Moreover, the identification of a series of neurodegenerative diseases as protein unfolding/misfolding disorders highlights the importance of a detailed characterisation of the molecular events driving the unfolding and misfolding processes in proteins. (igi-global.com)
  • Considering the central role of the hydrophobic effect in protein folding, we show here the application of two data mining methods - hierarchical clustering and association rules - for the analysis and comparison of the solvent accessible surface area (SASA) variation profiles of each one of the 127 amino-acid residues in the amyloidogenic protein Transthyretin, across multiple molecular dynamics protein unfolding simulations. (igi-global.com)
  • Molecular dynamics (MD) is one of the most realistic simulation techniques available to study protein folding in silico . (igi-global.com)
  • Ubiquitin (UBB/UBC/UBD) is a 76-amino acid small protein with molecular mass of 8.5 kDa. (biologists.org)
  • A residue is a single molecular unit within a polymer. (chemistryexplained.com)
  • predictions
  • Many different protein structure prediction methods exist and each uses different tools and auxiliary predictions to help determine the native structure. (biomedcentral.com)
  • A thorough study of the quality of current residue-residue contact predictions and the evaluation metrics used as well as an analysis of current methods is needed to stimulate further advancement in contact prediction and its application. (biomedcentral.com)
  • Such a study will better explain the quality and nature of residue-residue contact predictions generated by current methods and as a result lead to better use of this contact information. (biomedcentral.com)
  • An in-depth analysis revealed that while most residue-residue contact predictions generated are not accurate at the residue level, there is quite a strong contact signal present when allowing for less than residue level precision. (biomedcentral.com)
  • Our novel evaluation metrics demonstrate that current residue-residue contact predictions do contain a strong contact signal and are of better quality than standard evaluation metrics indicate. (biomedcentral.com)
  • However, recent population genetic analyses of closely related Drosophila species suggest that protein divergence between species is substantially in excess of the neutral model's predictions , . (prolekare.cz)
  • Transmembrane
  • In this study, two conserved amino acid residues of CXCR1 on the transmembrane domain (TM) 3 and TM6, \(Leu128^{3.43}\) (L128) and \(Val247^{6.40}\) (V247), respectively, were selectively substituted with other amino acids to investigate the role of these conserved residues in CXCR1 activation. (harvard.edu)
  • isoleucine
  • Gardner KH, Kay LE (1997) Production and incorporation of 15N, 13C, 2H (1H-1 methyl) isoleucine into proteins for multidimensional NMR studies. (springer.com)
  • correlation
  • Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. (springer.com)
  • No such clustering is observed for synonymous substitutions, supporting a "correlation length" associated with selection on proteins as the causative mechanism. (prolekare.cz)
  • The role of epistasis is directly supported by the tendency of nearby substitutions that arose on the same lineage to preserve the total charge of the residues within the correlation length and by the preferential cosegregation of neighboring derived alleles in our population sample. (prolekare.cz)
  • lysine
  • Moreover, as a validation test of this approach, we compare our theoretical computations of the 13 C ε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. (peerj.com)
  • recurrent
  • Secondly, the dihedral angles of residues in coil segments are very flexible and they do not show any simple recurrent pattern like those in helices and sheets. (biomedcentral.com)
  • histidine
  • We are just beginning to appreciate that such signaling mechanisms are extended and enriched by the reversible phosphorylation of histidine residues. (sciencemag.org)
  • The most exciting developments in this field to date come from studies on the β subunit of heterotrimeric guanosine triphosphate-binding proteins (G proteins), the enzyme adenosine 5′-triphosphate-citrate lyase, and now the Ca 2+ -activated K + channel KCa3.1, all of which are targeted by nucleoside diphosphate kinase (which phosphorylates histidines) and protein histidine phosphatase (which dephosphorylates phosphorylated histidines). (sciencemag.org)
  • The importance of kinases and phosphatases to signaling mechanisms is extended by their regulation of histidine residues. (sciencemag.org)
  • backbone
  • Chen K, Delaglio F, Tjandra N (2010) A practical implementation of cross-spectrum in protein backbone resonance assignment. (springer.com)
  • Mutations
  • The neutral theory posits that protein evolution is chiefly governed by the fraction of newly arising mutations that are not detrimental enough to be removed by natural selection. (prolekare.cz)
  • exposure
  • Fluorescence quenching reactions, using such quenchers as oxygen and acrylamide, have been used to obtain information about the kinetic exposure of tryptophan residues in proteins. (spie.org)
  • sequence identity
  • Previous studies argued that sequence based approaches are reliable only if at least 40-50% sequence identity exists between two proteins. (biomedcentral.com)
  • For example, in the case of enzymes, a similar (but not necessarily identical) function can be assumed between two proteins if their sequence identity is above 40%, but if the sequence identity drops in between 30-40% then only the first three Enzyme Commission (EC) numbers can be predicted reliably, and only at 90% accuracy level. (biomedcentral.com)