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Residue Positions (residue + position)
Selected AbstractsCattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb regionINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 3 2001A. Gelhaus Summary In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and - DOB genes enable these loci to be used as markers in genetic trait analyses. [source] Detection of quinolone-resistance genes in Photobacterium damselae subsp. piscicida strains by targeting-induced local lesions in genomesJOURNAL OF FISH DISEASES, Issue 8 2005M-J Kim Abstract Quinolone-resistant strains of the fish-pathogenic bacterium, Photobacterium damselae subsp. piscicida are distributed widely in cultured yellowtail, Seriola quinqueradiata (Temminck & Schlegel), in Japan. The quinolone resistance-determining region (QRDR) was amplified with degenerate primers, followed by cassette ligation-mediated PCR. Open reading frames encoding proteins of 875 and 755 amino acid residues were detected in the gyrA and parC genes, respectively. Resistant strains of P. damselae subsp. piscicida carried a point mutation only in the gyrA QRDR leading to a Ser-to-Ile substitution at residue position 83. No amino acid alterations were discovered in the ParC sequence. A mutation in the gyrA gene was also detected in nalidixic acid-resistant mutants of strain SP96002 obtained from agar medium containing increased levels of quinolone. These results suggest that GyrA, as in other Gram-negative bacteria, is a target of quinolone in P. damselae subsp. piscicida. Furthermore, we attempted to detect a point mutation using targeting-induced local lesions in genomes (TILLING), which is a general strategy used for the detection of a variety of induced point mutations and naturally occurring polymorphisms. We developed a new detection method for the rapid and large-scale identification of quinolone-resistant strains of P. damselae subsp. piscicida using TILLING. [source] Structural interpretation of mutations and SNPs using STRAP-NTPROTEIN SCIENCE, Issue 1 2006Christoph Gille Abstract Visualization of residue positions in protein alignments and mapping onto suitable structural models is an important first step in the interpretation of mutations or polymorphisms in terms of protein function, interaction, and thermodynamic stability. Selecting and highlighting large numbers of residue positions in a protein structure can be time-consuming and tedious with currently available software. Previously, a series of tasks and analyses had to be performed one-by-one to map mutations onto 3D protein structures; STRAP-NT is an extension of STRAP that automates these tasks so that users can quickly and conveniently map mutations onto 3D protein structures. When the structure of the protein of interest is not yet available, a related protein can frequently be found in the structure databases. In this case the alignment of both proteins becomes the crucial part of the analysis. Therefore we embedded these program modules into the Java-based multiple sequence alignment program STRAP-NT. STRAP-NT can simultaneously map an arbitrary number of mutations denoted using either the nucleotide or amino acid sequence. When the designations of the mutations refer to genomic sites, STRAP-NT translates them into the corresponding amino acid positions, taking intron,exon boundaries into account. STRAP-NT tightly integrates a number of current protein structure viewers (currently PYMOL, RASMOL, JMOL, and VMD) with which mutations and polymorphisms can be directly displayed on the 3D protein structure model. STRAP-NT is available at the PDB site and at http://www.charite.de/bioinf/strap/ or http://strapjava.de. [source] Alternative type I and I, turn conformations in the ,8/,9 ,-hairpin of human acidic fibroblast growth factorPROTEIN SCIENCE, Issue 3 2002Jaewon Kim Abstract Human acidic fibroblast growth factor (FGF-1) has a ,-trefoil structure, one of the fundamental protein superfolds. The X-ray crystal structures of wild-type and various mutant forms of FGF-1 have been solved in five different space groups: C2, C2221, P21 (four molecules/asu), P21 (three molecules/asu), and P212121. These structures reveal two characteristically different conformations for the ,8/,9 ,-hairpin comprising residue positions 90,94. This region in the wild-type FGF-1 structure (P21, four molecules/asu), a his-tagged His93,Gly mutant (P21, three molecules/asu) and a his-tagged Asn106,Gly mutant (P212121) adopts a 3:5 ,-hairpin known as a type I (1,4) G1 ,-bulge (containing a type I turn). However, a his-tagged form of wild-type FGF-1 (C2221) and a his-tagged Leu44,Phe mutant (C2) adopt a 3:3 ,-hairpin (containing a type I, turn) for this same region. A feature that distinguishes these two types of ,-hairpin structures is the number and location of side chain positions with eclipsed C, and main-chain carbonyl oxygen groups (, , +60°). The effects of glycine mutations upon stability, at positions within the hairpin, have been used to identify the most likely structure in solution. Type I, turns in the structural data bank are quite rare, and a survey of these turns reveals that a large percentage exhibit crystal contacts within 3.0 Å. This suggests that many of the type I, turns in X-ray structures may be adopted due to crystal packing effects. [source] Single nucleotide polymorphisms in the corticotrophin - releasing hormone and pro - opiomelancortin genes are associated with growth and carcass yield in beef cattleANIMAL GENETICS, Issue 2 2005F. C. Buchanan Summary A single nucleotide polymorphism (SNP) in the corticotrophin - releasing hormone gene (CRH C22G) alters the fourth amino acid in the signal sequence from proline to arginine. Two other SNPs (CRH A145G and C240G) occur in the propeptide region at residue positions 45 and 77, respectively, that result in serine/asparagine and histidine/aspartic acid substitutions respectively. These SNPs, as well as SNPs in pro - opiomelancortin (POMC), leptin (LEP) and melanocortin - 4 receptor (MC4R), were evaluated for associations with average daily gain, end-of-test rib-eye area, shipping weight and hot carcass weight in a group of 256 steers using a general linear model. The CRH C22G SNP was associated with end-of-test rib-eye area (P < 0.034) and hot carcass weight (P < 0.0015). The SNP in POMC was associated with shipping weight (P < 0.0078) and hot carcass weight (P = 0.006) while it approached significance for average daily gain (P < 0.07). The SNP in MC4R approached significance for hot carcass weight (P < 0.085) while no significance was observed between the leptin SNP and the above listed traits. Because both CRH and POMC regulate appetite, potential interaction effects between these two genes were assessed. The absence of an interaction effect between CRH and POMC with hot carcass weight suggests that these genes act independently to increase carcass yield. These gene effects used singularly or together could result in an economic benefit to the beef industry. [source] Translational Mini-Review Series on Complement Factor H: Structural and functional correlations for factor HCLINICAL & EXPERIMENTAL IMMUNOLOGY, Issue 1 2008C. Q. Schmidt Summary The 155-kDa glycoprotein, complement factor H (CFH), is a regulator of complement activation that is abundant in human plasma. Three-dimensional structures of over half the 20 complement control protein (CCP) modules in CFH have been solved in the context of single-, double- and triple-module segments. Proven binding sites for C3b occupy the N and C termini of this elongated molecule and may be brought together by a bend in CFH mediated by its central CCP modules. The C-terminal CCP 20 is key to the ability of the molecule to adhere to polyanionic markers on self-surfaces where CFH acts to regulate amplification of the alternative pathway of complement. The surface patch on CCP 20 that binds to model glycosaminoglycans has been mapped using nuclear magnetic resonance (NMR), as has a second glycosaminoglycan-binding patch on CCP 7. These patches include many of the residue positions at which sequence variations have been linked to three complement-mediated disorders: dense deposit disease, age-related macular degeneration and atypical haemolytic uraemic syndrome. In one plausible model, CCP 20 anchors CFH to self-surfaces via a C3b/polyanion composite binding site, CCP 7 acts as a ,proof-reader' to help discriminate self- from non-self patterns of sulphation, and CCPs 1,4 disrupt C3/C5 convertase formation and stability. [source] | ||||||||||