• ###### tryptophan residues in proteins
• 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)
• ###### Mutation
• Mutation of Asn-43, Leu-47, and Tyr-50 residues severely affects the stable maintenance of IpaD at the Shigella surface and thus compromises the invasive phenotype of S. flexneri. (ku.edu)
• Mutation of a leucine residue in the third coiled-coil heptad impaired CWMV CRP activity for suppression of local silencing, but not for the promotion of cell-to-cell movement of Potato virus X (PVX). (biomedsearch.com)
• ###### cysteine residues
• NSs contains five highly conserved cysteine residues at positions 39, 40, 149, 178 and 194, which are thought to stabilize the tertiary and quaternary structure of the protein. (up.ac.za)
• Here, we present evidence that the conserved cysteine residues and Cys-Gly-X-X-His motif in the CRP of Chinese wheat mosaic virus (CWMV) are critical for protein stability and silencing suppression activity. (biomedsearch.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)
• We evaluated several sequence based residue-residue contact predictors that participated in the tenth Critical Assessment of protein Structure Prediction (CASP) experiment. (biomedcentral.com)
• ###### conformation
• When operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. (biomedcentral.com)
• Lateral pressure profile, spontaneous curvature frustration, and the incorporation and conformation of proteins in membranes. (semanticscholar.org)
• ###### highly conserved
• It is a highly conserved protein in eukaryotes, with a fundamental role in selective protein degradation by the ubiquitin-proteasome system (UPS). (biologists.org)
• ###### 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)
• ###### monomeric
• It is based on the nonredundant data set of 218 monomeric proteins. (hindawi.com)
• Monomeric and trimeric models of VEEV-E1 were constructed with our MPACK program, using the crystal structure of the E1 protein of Semliki forest virus as a template. (springer.com)
• A protein or a polypeptide is composed of amino acids linked together by peptide bonds, with amino acids as the monomeric units of the polypeptide. (chemistryexplained.com)
• ###### hydrophobic
• Using Data Mining Techniques to Probe the Role of Hydrophobic Residues in Protein Folding and Unfolding Simulations. (igi-global.com)
• In general, hydrophobic residues such as Val, Leu, Ile, Phe, and Met tend to be buried in the interior and polar side chains exposed to solvent. (hindawi.com)
• Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from different sizes, charges and hydrophobic characters of their side chains. (biomedcentral.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)
• The likelihood of mutations being fixed in the genome depends on various factors, such as the fitness of the phenotype or the position of the residues in the three-dimensional structure. (biochemj.org)
• ###### 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)
• 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)
• Earlier analysis [ 15 ] of the location of RNA targets within transcripts did not detect any rules to explain why particular residues within a protein sequence were affected by codon changes while other residues were not altered. (biomedcentral.com)
• ###### biological
• Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. (peerj.com)
• Determining these protein-RNA binding residues can help to elucidate the underlying mechanisms, to control biological processes, or to design RNA-based drug. (biomedcentral.com)
• Thus tryptophan residues are likely to be favourable targets for the reaction in biological systems, and the oxidation products formed may be useful biomarkers of HOSCN-mediated protein oxidation. (biochemj.org)
• ###### neural
• From the selected features, neural networks were trained to identify catalytic residues. (biomedcentral.com)
• ###### specific proteins
• One focus of the Dutch lab is to study the specific proteins in these viruses that promote fusion between the viral membranes and the host cell membranes. (murraystate.edu)
• promotes the degradation of specific proteins such as Protein Kinase R (PKR) and also induces a general transcription shut-off in infected cells. (up.ac.za)
• ###### aromatic
• Aromatic amino acids occur more often in [Formula: see text]-crystallins from vertebrates than on the average in proteins among 17 animal proteomes. (nih.gov)
• ###### globular
• Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. (biomedcentral.com)
• ###### Predicting
• Predicting the three-dimensional structure of a protein from its amino acid sequence is currently one of the most challenging problems in bioinformatics. (biomedcentral.com)
• The main reasons that predicting protein structure from sequence alone is so difficult, is that the possible ways the amino acids can twist and turn with respect to each other are enormous. (biomedcentral.com)
• Bellucci M, Agostini F, Masin M, Tartaglia GG (2011) Predicting protein associations with long noncoding RNAs. (springer.com)
• Now, Ovchinnikov, Kamisetty, and Baker have developed a method for predicting which parts of the proteins make contact with each other in a two-protein complex. (elifesciences.org)
• This article describes DP-Bind, a web server for predicting DNA-binding sites in a DNA-binding protein from its amino acid sequence. (ovid.com)
• ###### proteinaceous
• Poor cleaning can lead to proteinaceous residues. (sychem.co.uk)
• Ubiquitin A-52 residue ribosomal protein fusion product 1 ( Uba52 ), a ubiquitin-ribosomal fusion gene, is a major source of ubiquitin protein for covalent modification of proteinaceous substrates recycled by ubiquitin-proteasome system (UPS). (biologists.org)
• ###### important
• The residual protein is important because of the continuing risks of transmission of prions therefore, it is necessary to use protein detection methods to check for the efficient removal of protein from surgical instruments after processing. (sychem.co.uk)
• RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. (biomedcentral.com)
• In addition to its role in protein degradation, the non-proteolytic consequences of protein ubiquitination also play an important role in cellular functions such as signaling, cell cycle control, transcriptional regulation and apoptosis ( Komander and Rape, 2012 ). (biologists.org)
• This study reveals the residues in the conserved fingerprints to be very important for both DD-carboxypeptidase activity and penicillin-binding, and confirms them to play crucial roles in catalysis. (biochemj.org)
• Identification of the amino acid residues and domains in the cysteine-rich protein of Chinese wheat mosaic virus that are important for RNA silencing suppression and subcellular localization. (biomedsearch.com)
• ###### Nucleotide
• The much longer splice variant, caused by a deletion of exons 9 and 10, does not have the proteins coating the nucleotide binding pocket aswell as the next Ca2+ binding site. (biomasswars.com)
• ###### ribosomal
• Ubiquitin A 52 Residue Ribosomal Protein Fusion Product 1 Elisa Kit is the most suitable ELISA kit for your research - it is manufactured with the best quality antibodies and plates to provide you with high reproducible results in your lab work. (antibody-antibodies.com)
• ###### predictions
• 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)
• ###### mutant
• The V247N mutant also constitutively activated the $$G\alpha_i$$ protein. (harvard.edu)
• The mutant proteins were assayed for their penicillin-binding capacity and DD-carboxypeptidase activity. (biochemj.org)
• As a result, the mutant INNO-406 does not have GTPase activity and isn't controlled by guanine nucleotides, however it retains 25% transglutaminase activity weighed against the full-length proteins. (biomasswars.com)
• In planta and in vitro analysis of wild-type and mutant proteins indicated that the ability of the CRP to self-interact was correlated with its suppression activity. (biomedsearch.com)
• ###### methods
• The coverage of residue-residue contact areas was also greater with DNcon when compared to other methods. (biomedcentral.com)
• On the other hand, the Pfam database of protein families [ 2 ] represents about 12,000 families, and about 20% of these are domains of unknown function (DUFs), revealing that state-of-the-art sequence similarity-based and even profile-based annotation methods have had limited success in assigning functions to novel proteins. (biomedcentral.com)
• Improved methods for building protein models in electron density maps and the location of errors in these models. (psu.edu)
• ###### pairs
• As such, when pairs of interacting proteins from different species are compared, there will be many positions in the two proteins that vary. (elifesciences.org)