The Experts below are selected from a list of 397299 Experts worldwide ranked by ideXlab platform
Jacquelyn S. Fetrow - One of the best experts on this subject based on the ideXlab platform.
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Current Protocols in Bioinformatics - Active Site profiling to identify protein functional Sites in sequences and structures using the Deacon Active Site Profiler (DASP).
Current Protocols in Bioinformatics, 2006Co-Authors: Jacquelyn S. FetrowAbstract:Methods for the annotation and analysis of functional Sites in proteins are an area of Active research, and those methods that allow detailed characterization of functional Site features are much needed. A Web Site application, DASP, which implements a previously described method (Cammer, et al., 2003) to allow users to create an Active Site profile for any protein family, is described. Two protocols for functional Site analysis of protein families using DASP are presented: 1) creation of functional Site signatures and a profile from proteins of known structure and 2) utilization of the Active Site profile to search sequences that contain fragments similar to those found in the functional Site signatures. The Active Site profile produced by Basic Protocol 1 allows the user to analyze the features of the functional Site, i.e., those characteristics that are common across the family and those that are unique to one or several members of the family. The characteristics that are unique to a subfamily might be described as specificity determinants i.e., features that impart specificity to a particular function. Basic Protocol 2 provides instructions for searching for sequences that might contain a similar functional Site. Keywords: Active Site profiling; fuzzy functional form; protein function prediction; Active Site; functional Site; functional specificity determinants
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Active Site profiling to identify protein functional Sites in sequences and structures using the Deacon Active Site Profiler (DASP).
Current protocols in bioinformatics, 2006Co-Authors: Jacquelyn S. FetrowAbstract:Methods for the annotation and analysis of functional Sites in proteins are an area of Active research, and those methods that allow detailed characterization of functional Site features are much needed. A Web Site application, DASP, which implements a previously described method (Cammer, et al., 2003) to allow users to create an Active Site profile for any protein family, is described. Two protocols for functional Site analysis of protein families using DASP are presented: 1) creation of functional Site signatures and a profile from proteins of known structure and 2) utilization of the Active Site profile to search sequences that contain fragments similar to those found in the functional Site signatures. The Active Site profile produced by Basic Protocol 1 allows the user to analyze the features of the functional Site, i.e., those characteristics that are common across the family and those that are unique to one or several members of the family. The characteristics that are unique to a subfamily might be described as specificity determinants i.e., features that impart specificity to a particular function. Basic Protocol 2 provides instructions for searching for sequences that might contain a similar functional Site.
Jack E. Dixon - One of the best experts on this subject based on the ideXlab platform.
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Active Site labeling of a receptor like protein tyrosine phosphatase
Journal of Biological Chemistry, 1992Co-Authors: Jack E. DixonAbstract:Abstract The inactivation of the cytoplasmic domain of rat LAR, a receptor-like protein tyrosine phosphatase (PTPase), by iodoacetate and not by iodoacetamide suggested that iodoacetate interacts in a highly selective manner with the enzyme. The data indicate that iodoacetate binds at the Active Site of the enzyme with a stoichiometry of 0.8 mol of iodoacetate bound per mol of rat LAR. A single [14C]iodoacetate-labeled peptide was isolated following endoproteinase Lys-C digestion of the radiolabeled PTPase. Sequence analysis of the Active Site labeled peptide demonstrates that Cys-1522 contains the radiolabel. This residue has been shown by Site-directed mutagenesis to be essential for rat LAR activity (Pot, D. A., Woodford, T. A., Remboutsika, E., Haun, R. S., and Dixon, J. E. (1991) J. Biol. Chem. 266, 19688-19696). Iodoacetate reacts only with the first domain of this double domain PTPase. These results, for the first time, directly identify the highly reActive cysteine residue at the Active Site of a PTPase and highlight the ability of this residue to participate as a nucleophile in the hydrolysis of phosphate from tyrosine.
Paul F. Fitzpatrick - One of the best experts on this subject based on the ideXlab platform.
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Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site
Biochemistry, 2014Co-Authors: Kenneth M. Roberts, Crystal A. Khan, Cynthia S. Hinck, Paul F. FitzpatrickAbstract:Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the Active Site. The location of the Site at which phenylalanine binds to activate the enzyme is unknown, and both the Active Site in the catalytic domain and a separate Site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the Active-Site iron was used to probe the accessibility of the Active Site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the Active Site is effectively abolished by mutating the Active-Site residue Arg270 to lysine. The kcat/Kphe value is down 104 for the mutant enzyme, and the Km v...
Nancy Maizels - One of the best experts on this subject based on the ideXlab platform.
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the cca adding enzyme has a single Active Site
Journal of Biological Chemistry, 1998Co-Authors: Alan M Weiner, Nancy MaizelsAbstract:Abstract The CCA-adding enzyme (tRNA nucleotidyltransferase) synthesizes and repairs the 3′-terminal CCA sequence of tRNA. The eubacterial, eukaryotic, and archaeal CCA-adding enzymes all share a single Active-Site signature motif, which identifies these enzymes as belonging to the nucleotidyltransferase superfamily. Here we show that mutations at Asp-53 or Asp-55 of theSulfolobus shibatae signature sequence abolish addition of both C and A, demonstrating that a single Active Site is responsible for addition of both nucleotides. Mutations at Asp-106 (and to a lesser extent, at Glu-173 and Asp-215) selectively impaired addition of A, but not C. We have previously demonstrated that the tRNA acceptor stem remains fixed on the surface of the CCA-adding enzyme during C and A addition (Shi, P.-Y., Maizels, N., and Weiner, A. M. (1998)EMBO J. 17, 3197–3206). Taken together with this new evidence that there is a single Active Site for catalysis, our data suggest that specificity of nucleotide addition is determined by a process of collaborative templating: as the single Active Site catalyzes addition of each nucleotide, the growing 3′-end of the tRNA would progressively refold to create a binding pocket for addition of the next nucleotide.
Yoshimura F - One of the best experts on this subject based on the ideXlab platform.
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Active Site structure of a hemagglutinating protease from Porphyromonas gingivalis: similarity to clostripain.
Iubmb Life, 1995Co-Authors: Nishikata M, Yoshimura FAbstract:The Active Site of a 44-kDa hemagglutinating arginine-specific protease from the putative periodontopathogen Porphyromonas gingivalis was specifically labeled with N alpha-[3H]acetyllysine chloromethyl ketone. After enzymatic digestion of the labeled enzyme, a labeled Active Site peptide was isolated by HPLC. The sequence of the Active Site peptide was determined, after its treatment with NaBH4 to reduce the ketone group of the reagent moiety, to be Asp-Val-Ala-Cys-Val-Asn-Gly. The cysteine residue was found to be the Site for labeling. The sequence resembled the Active Site structure of the arginine-specific cysteine protease clostripain from Clostridium histolyticum.
