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Amino Acid Positions (amino + acid_position)
Selected AbstractsProteolytic processing of the receptor-type protein tyrosine phosphatase PTPBR7FEBS JOURNAL, Issue 1 2007Gönül Dilaver The single-copy mouse gene Ptprr gives rise to different protein tyrosine phosphatase (PTP) isoforms in neuronal cells through the use of distinct promoters, alternative splicing, and multiple translation initiation sites. Here, we examined the array of post-translational modifications imposed on the PTPRR protein isoforms PTPBR7, PTP-SL, PTPPBS,42 and PTPPBS,37, which have distinct N-terminal segments and localize to different parts of the cell. All isoforms were found to be short-lived, constitutively phosphorylated proteins. In addition, the transmembrane isoform, PTPBR7, was subject to N-terminal proteolytic processing, in between amino acid position 136 and 137, resulting in an additional, 65-kDa transmembrane PTPRR isoform. Unlike for some other receptor-type PTPs, the proteolytically produced N-terminal ectodomain does not remain associated with this PTPRR-65. Shedding of PTPBR7-derived polypeptides at the cell surface further adds to the molecular complexity of PTPRR biology. [source] Cloning and Expression of Low Molecular Weight Glutenin Genes from the Chinese Elite Wheat Cultivar "Xiaoyan 54"JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 2 2006Xin-Yu Wang Abstract The low molecular weight (LMW) glutenin subunits account for 40% of wheat gluten protein content by mass and these proteins are considered to significantly affect dough quality characteristics. Five new full-length LMW glutenin genes (designated LMW-5, LMW-7, LMW-42, LMW-58, and LMW-34) were isolated from the Chinese elite wheat cultivar "Xiaoyan 54" by PCR amplification of genomic DNA using a pair of degenerate primers designed from the conserved sequences of the N- and C-terminal regions of published LMW glutenin genes. Deduced amino acid sequence analysis showed that LMW-5 belongs to the LMW-i type genes and that the other four belong to LMW-m type genes. Sequence comparisons revealed that point mutations occasionally occurred in signal peptide and N-terminus domains and often existed in domain III and domain V. Small insertions and deletions are represented in the repetitive domain. There is a stop codon after amino acid position 110 in the repetitive domain of LMW-34, indicating that it is a pseudogene. The other four genes have complete open reading frames and the putative mature regions of these genes were subcloned into pET-30a expression vector and successfully expressed in Escherichia coli. Protein sodium dodecyl sulfate-polyacrylamide gel electro-phoresis analysis showed that all proteins expressed in E. coli by the four genes could be related to B-group LMW glutenin subunits of wheat. (Managing editor: Li-Hui Zhao) [source] Cerebrotendinous xanthomatosis: molecular characterization of two Scandinavian sistersJOURNAL OF INTERNAL MEDICINE, Issue 3 2002E. Rystedt Abstract.,Rystedt E, Olin M, Seyama Y, Buchmann M, Berstad A, Eggertsen G, Björkhem I (Karolinska Institutet, Stockholm, Sweden; OchanomizuUniversity, Tokyo, Japan; Medisinsk avdeling, Haukeland sykehus, Bergen). Cerebrotendinous xanthomatosis: molecular characterization of two Scandinavian sisters (Case report). Journal of Internal Medicine 2002; 252: 259,264. Cerebrotendinous xanthomatosis (CTX) is a hereditary disorder, which is inherited as an autosomally recessive disease, causing production of cholesterol and cholestanol xanthomas and mental retardation. The disease is caused by mutations in the gene for sterol 27-hydroxylase (CYP27A1). The only CTX patients diagnosed in Scandinavia are two Norwegian sisters from a consanguineous marriage. Here we have characterized the mutation and its functional consequences for the enzyme. Analysis of genomic DNA from cultured fibroblasts identified a base exchange C > T in position 1441, causing arginine at amino acid position 441 to be replaced by tryptophan. The same mutation was introduced by mutagenesis in the complimentary DNA (cDNA) for CYP27, ligated into the expression vector pcDNA4/HisMax and transfected into HEK293 cells. The mutated enzyme had less than 5% of the enzyme activity compared with the native enzyme. No abnormal catalytic products could be identified in the cell culture medium. Probably the mutation affects the haem binding within the holoenzyme. The mutation has also previously been reported in a Japanese family. This is the second example of a CTX-causing mutation that has been recognized in more than one population. [source] Antibiotic activity of pentadecapeptides modelled from amino acid descriptorsJOURNAL OF PEPTIDE SCIENCE, Issue 2 2001Tore Lejon Abstract Pentadecapeptides based on modified murine lactoferricin (LFM) sequences show varying degrees of antibacterial activity against Escherichia coli and Staphylococcus aureus. By means of projections to latent structures (PLS), a good correlation is obtained if the biological activity is modelled as a function of variables describing peptide properties, e.g. ,-helicity, hydrophobicity/hydrophilicity and charge. Using variables derived from a principal component analysis (PCA) of all naturally occurring amino acids, it is possible to describe the amino acid content of the peptides using three variables per amino acid position. The resulting descriptor matrix is then used to develop quantitative structure,activity relationships (QSAR). It is shown that the theoretically derived descriptors model the activity of the peptides better than the earlier model, and that properties of the peptides other than antibacterial activity can be predicted. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] A Polymorphism in the ,4 Nicotinic Receptor Gene (Chrna4) Modulates Enhancement of Nicotinic Receptor Function by EthanolALCOHOLISM, Issue 5 2003Christopher M. Butt Background: Several studies indicate that ethanol enhances the activity of ,4,2 nicotinic acetylcholine receptors (nAChR). Our laboratory has identified a polymorphism in the ,4 gene that results in the substitution of an alanine (A) for threonine (T) at amino acid position 529 in the second intracellular loop of the ,4 protein. Mouse strains expressing the A variant have, in general, greater nAChR-mediated 86Rb+ efflux in response to nicotine than strains with the T variant. However, the possibility of the polymorphism modulating the effects of ethanol on the 86Rb+ efflux response has not been investigated. Methods: We have used the 86Rb+ efflux method to study the acute effects of ethanol on the function of the ,4,2 nAChR in the thalamus in six different mouse strains. Experiments were also performed on tissue samples taken from F2 intercross animals. The F2 animals were derived from A/J mice crossed with a substrain of C57BL/6J mice that carried a null mutation for the gene encoding the ,2 nAChR subunit. Results: In strains carrying the A polymorphism (A/J, AKR/J, C3H/Ibg), coapplication of ethanol (10,100 mM) with nicotine (0.03,300 ,M) increased maximal ion flux when compared with nicotine alone with no effect on agonist potency. In contrast, ethanol had little effect on the nicotine concentration-response curve in tissue prepared from strains carrying the T polymorphism (Balb/Ibg, C57BL/6J, C58/J). Experiments with the F2 hybrids demonstrated that one copy of the A polymorphism was sufficient to produce a significant enhancement of nAChR function by ethanol (50 mM) in animals that were also ,2 +/+. Ethanol had no effect on nicotine concentration-response curves in T/T ,2 +/+ animals. Conclusions: The results suggest that the A/T polymorphism influences the initial sensitivity of the ,4,2 nAChR to ethanol. [source] Expression studies on a novel type 2B variant of the von Willebrand factor gene (R1308L) characterized by defective collagen bindingJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 12 2005L. BARONCIANI Summary., A novel mutation, R1308L (3923G > T) was present in the heterozygous state in five members of a family with type 2B von Willebrand disease (VWD) characterized by a full set of von Willebrand factor (VWF) multimers in plasma and by the absence of thrombocytopenia before and after desmopressin (DDAVP). The defect (R1308L) was located at the same amino acid position of one of the most common mutations associated with type 2B VWD (R1308C), which is characterized by the loss of high molecular weight VWF multimers (HMWM) in plasma and the occurrence of thrombocytopenia. To understand the mechanisms of this defect, the novel (R1308L) and ,common' (R1308C) mutations were expressed in COS-7 cells, either alone or, to mimic the patients' heterozygous state, together with wild-type VWF. R1308L recombinant VWF (rVWF) had a higher affinity for the platelet glycoprotein Ib, (GPIb,) receptor than wild-type rVWF, R1308C rVWF showing an even higher affinity. A novel finding was that both mutant rVWFs showed a similarly reduced binding to collagen type I and type III in comparison with wild-type rVWF. The latter finding suggests a more important role than recognized so far for the VWF A1 domain in VWF binding to collagen, which may contribute to the in vivo hemostatic defect associated with type 2B VWD. [source] Interferon and ribavirin therapy does not select for resistance mutations in hepatitis C virus polymeraseJOURNAL OF VIRAL HEPATITIS, Issue 8 2008C. L. Ward Summary., Ribavirin has a minor and transient effect on hepatitis C virus (HCV) replication and has been suggested to select a novel mutation, F415Y, in the RNA-dependent RNA polymerase of subtype 1a viruses. Twenty-nine patients with chronic hepatitis C (subtyped by INNO LiPA as 1a, 17; 1b, 11; 1a/1b, 1) who were nonresponders to interferon-based therapies were identified retrospectively and screened at Baseline, week 24 of treatment, and 24 weeks post-treatment. Selection of resistance mutations, including at amino acid position 415 of the polymerase, was investigated. Using clonal sequencing and pyrosequencing of the NS5B gene, we screened for the F415Y resistance mutation among patients who received combination therapy with ribavirin and interferon ,. Of the 15 subtype 1a patients treated with interferon plus ribavirin, only one had the F415Y change at week 24, and an F/Y mixture was still present 24 weeks after therapy. Four additional patients in this group had the F415Y change 24 weeks post-therapy. The NS5B genes were sequenced in order to identify amino acid changes associated with ribavirin therapy, but no evidence was found that ribavirin selects for particular amino acids in the RNA-dependent RNA polymerase. Ribavirin, a weak inhibitor of HCV replication, does not select for resistance mutations in the sequence of the HCV RNA polymerase. [source] Characterisation of QoI-resistant field isolates of Botrytis cinerea from citrus and strawberryPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2009Hideo Ishii Abstract BACKGROUND: In 2004, field isolates of Botrytis cinerea Pers. ex Fr., resistant to strobilurin fungicides (QoIs), were first found in commercial citrus orchards in Wakayama Prefecture, Japan. Subsequently, QoI-resistant isolates of this fungus were also detected in plastic strawberry greenhouses in Saga, Ibaraki and Chiba prefectures, Japan. Biological and molecular characterisation of resistant isolates was conducted in this study. RESULTS: QoI-resistant isolates of B. cinerea grew well on PDA plates containing kresoxim-methyl or azoxystrobin at 1 mg L,1, supplemented with 1 mM of n -propyl gallate, an inhibitor of alternative oxidase, whereas the growth of sensitive isolates was strongly suppressed. Results from this in vitro test were in good agreement with those of fungus inoculation tests in vivo. In resistant isolates, the mutation at amino acid position 143 of the cytochrome b gene, known to be the cause of high QoI resistance in various fungal pathogens, was found, but only occasionally. The heteroplasmy of cytochrome b gene was confirmed, and the wild-type sequence often present in the majority of resistant isolates, indicating that the proportion of mutated cytochrome b gene was very low. CONCLUSION: The conventional RFLP and sequence analyses of PCR-amplified cytochrome b gene are insufficient for molecular identification of QoI resistance in B. cinerea. Copyright © 2009 Society of Chemical Industry [source] Validation of a real-time PCR for the quantitative estimation of a G143A mutation in the cytochrome bc1 gene of Pyrenophora teresPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 3 2007Arash Kianianmomeni Abstract A single nucleotide polymorphism (SNP) in the cytochrome b gene confers resistance to strobilurin fungicides for several fungal pathogens. Therefore, on the basis of a change at amino acid position 143 from glycine to alanine, a real-time PCR assay was established for the quantitative detection of the analogous SNP in the cytochrome b sequence of Pyrenophora teres Drechsler, which causes barley net blotch. Allelic discrimination was achieved by using allele specific primers with artificially mismatched nucleic acid bases and minor groove binding probes. Validation parameters for the lower limits of the working range, namely limits of detection (LOD) and limits of quantification (LOQ), were statistically determined by the variance of calibration data, as well as by the variance of the 100% non-strobilurin-resistant allele DNA sample (blank values). It was found that the detection was limited by the variance of blank values (five in 801 458 copies; 0.0006%), whereas the quantification was limited by the variance of calibration data (37 in 801 458 copies; 0.0046%). The real-time PCR assay was finally used to monitor strobilurin-resistant cytochrome b alleles in barley net blotch field samples, which were already classified in in vivo biotests to be fully sensitive to strobilurins. All signals for strobilurin-resistant cytochrome b alleles were below the LOD, and therefore the results are in total agreement with the phenotypes revealed by biotests. Copyright © 2006 Society of Chemical Industry [source] Opsin gene polymorphism predicts trichromacy in a cathemeral lemurAMERICAN JOURNAL OF PRIMATOLOGY, Issue 1 2009Carrie C. Veilleux Abstract Recent research has identified polymorphic trichromacy in three diurnal strepsirrhines: Coquerel's sifaka (Propithecus coquereli), black and white ruffed lemurs (Varecia variegata), and red ruffed lemurs (V. rubra). Current hypotheses suggest that the transitions to diurnality experienced by Propithecus and Varecia were necessary precursors to their independent acquisitions of trichromacy. Accordingly, cathemeral lemurs are thought to lack the M/L opsin gene polymorphism necessary for trichromacy. In this study, the M/L opsin gene was sequenced in ten cathemeral blue-eyed black lemurs (Eulemur macaco flavifrons). This analysis identified a polymorphism identical to that of other trichromatic strepsirrhines at the critical amino acid position 285 in exon 5 of the M/L opsin gene. Thus, polymorphic trichromacy is likely present in at least one cathemeral Eulemur species, suggesting that strict diurnality is not necessary for trichromacy. The presence of trichromacy in E. m. flavifrons suggests that a re-evaluation of current hypotheses regarding the evolution of strepsirrhine trichromacy may be necessary. Although the M/L opsin polymorphism may have been independently acquired three times in the lemurid,indriid clade, the distribution of opsin alleles in lemurids and indriids may also be consistent with a common origin of trichromacy in the last common ancestor of either the lemurids or the lemurid,indriid clade. Am. J. Primatol. 71:86,90, 2009. © 2008 Wiley-Liss, Inc. [source] Characterization and genetic analysis of bovine ,s1 -casein I variantANIMAL GENETICS, Issue 4 2009G. Lühken Summary The aim of this study was to identify the molecular genetic origin underlying the I variant of ,s1 -casein and to develop a DNA-based test for this polymorphism as a tool for genetic analyses independent of milk sample testing. All coding exons and flanking regions of the ,s1 -casein gene were sequenced in DNA samples from cattle of known ,s1 -casein genotypes (BI, CI, II, CC), determined by isoelectric focusing of milk samples. A nucleotide substitution (A>T) in exon 11 (g.19836A>T) leads to the exchange of Glu with Asp at amino acid position 84 of the mature protein (p.Glu84Asp) and perfectly co-segregated with the presence of the ,s1 -casein I variant in the milk of the analysed animals. Genotyping of a total of 680 DNA samples from 31 Bos taurus and Bos indicus cattle breeds and from Bos grunniens, Bison bison and Bison bonasus by restriction fragment length polymorphism analysis revealed the occurrence of Asp at position 84 at low frequencies in Bos taurus and Bos indicus breeds and established its origin from the ,s1 -casein C variant (p.Glu192Gly). Ten different intragenic haplotypes in the gene region from intron 8 to intron 12 were observed by sequencing, of which two occurred in Bison bison and one in Bison bonasus only. Using available casein gene complex information, an association of Asp at position 84 to ,-casein A2 and ,-casein B was shown in the Bos indicus breed Banyo Gudali. Taken together, we can postulate that the ,s1 -casein variant I is caused by a non-synonymous nucleotide substitution in exon 11 of the gene and that it originated within Bos indicus and spread to Bos taurus subsequently. [source] R58fs Mutation in the HGD Gene in a Family with Alkaptonuria in the UAEANNALS OF HUMAN GENETICS, Issue 1 2009Yousef M Abdulrazzaq Summary This study was conducted to determine the prevalence of alkaptonuria in the UAE population and to identify the genotype of affected individuals. In a 3 stage sampling technique 2981 pupils from Government schools in Al Ain and private schools in Dubai were selected to take part in the study, of whom 2857 provided urine samples. Urine collected was analysed for homogentisic acid by gas chromatography-mass spectrometry. Genomic DNA was isolated from the white blood cells of all family members of the affected case following standard established protocols. Specific PRC primers were designed to amplify all 14 exons of the HGD gene with the flanking intronic sequences including the splice site sequences. 2857 children returned a viable urine sample, of which one was highly positive for homogentisic acid. All 12 members of this girl's family were studied and one, a 22 year old brother, was found to excrete HGA. Another, a sister who had not provided a urine sample, was discovered by genetic testing. There were no complaints of joint pain or other symptoms in any member of this family. Parents were first cousins. We found a single nucleotide deletion c.342delA, located in exon 3, which resulted in a frameshift at amino acid position 58 (p.Arg58fs or p.R58fs). Alkaptonuria may be more common than it is thought to be with an allele prevalence estimated at 0.0107 (95% CI 0.000392 , 0.03473). The R58fs mutation is old, perhaps having occurred several thousand years ago, and has spread over a large geographical area. [source] A nonsense mutation in exon 8 of the APC gene (Arg283Ter) causes clinically variable FAP in a Malaysian Chinese familyCANCER SCIENCE, Issue 8 2003Zulqarnain Mohamed The present study was carried out to characterize the causative genetic mutation in a medium-sized Malaysian Chinese pedigree of three generations affected with familial adenomatous polyposis (FAP). Clinical data and genetic studies revealed considerable phenotypic variability in affected individuals in this family. Blood was obtained from members of the FAP-01 family and genomic DNA was extracted. Mutation screening of the adenomatous polyposis coli (APC) gene was carried out using the single strand conformation polymorphism (SSCP) technique. The possibility of exon skipping was predicted by splicing motif recognition software (ESEfinder release2.0). SSCP results showed mobility shifts in exon 8 of the APC gene which segregated with affected members of the family. Sequence analysis revealed that the affected individuals are heterozygous for a C847T transition, whilst all the unaffected family members and control individuals are homozygous C at the same position. This nucleotide substitution generates a stop codon at amino acid position 283, in place of the usual arginine (Arg283Ter). We conclude that an Arg283Ter mutation in the APC gene is causative of the FAP phenotype in this family, although there is considerable variation in the presentation of this disease among affected individuals. Computational analysis predicts that this mutation occurs within sequences that may function as splicing signals, so that the sequence change may affect normal splicing. [source] Lep d 2 polymorphisms in wild and cultured Lepidoglyphus destructor mitesFEBS JOURNAL, Issue 4 2003Liselotte Kaiser We have previously cloned, expressed and characterized two variants of the major allergen Lep d 2 from cultured Lepidoglyphus destructor mites. These variants, Lep d 2.0101 and Lep d 2.0201, differ at 13 amino acid positions. In this study we investigated Lep d 2 sequence diversity between wild and cultured mites. PCR, Southern blot and DNA sequence analysis revealed the presence of two different Lep d 2 genes, one with and one without an intron. In addition, two new variants of Lep d 2, Lep d 2.0102 and Lep d 2.0202, were found at different frequencies in wild and cultured mites. When we expressed the Lep d 2 variants and compared their IgE binding properties by ELISA inhibition, we found that Lep d 2.0102 was a more potent inhibitor than Lep d 2.0101, and to a lesser extent Lep d 2.0202 was more potent than Lep d 2.0201. Long-term cultures of peripheral blood mononuclear cells were used to assess the ability of the expressed Lep d 2 variants to induce cytokine release. Although cells from different individuals released different amounts of interferon-, and interleukin-5, no consistent cytokine release pattern could be linked to any specific Lep d 2 variant. In conclusion, we show that both cultured and wild Lepidoglyphus destructor mites contain the same pattern of polymorphism. Furthermore, this Lep d 2 sequence diversity seems not to have any significant impact on the allergens IgE binding or its ability to induce T cell cytokine release. [source] Recognition of HLA-A*0248 in a Chinese donorINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 3 2003K. L. Yang Summary HLA-A*0248, a rare allele originally found in an individual of Filipino background, was detected in a Chinese donor. We confirmed the novel sequence and analysed its serological reaction pattern. The exon 2 sequence of A*0248 was apparently generated in a gene conversion event with an A2 gene, receiving a sequence segment comprising codons 56 to 74 from an A*24 donor gene. Serological typing showed a clear-cut A2 reaction pattern, indicating that the three amino acid positions 62, 65 and 74, are probably not a critical part of the A2 epitope. Our typing experience also demonstrated that different typing technologies often complement each other in fine HLA typing. [source] Molecular epidemiology of hepatitis A virus in Korea,JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 5 2001Kwan Soo Byun Abstract Background: The prevalence of antibodies for hepatitis A virus (anti-HAV) in adolescents and young adults has decreased remarkably following the economic growth in Korea. As a result, this age group has a high risk for HAV infection paradoxically, and over 1500 cases of clinically overt hepatitis A occurred in 1998. Human isolates of hepatitis A virus (HAV) are categorized within four genotypes (I, II, III, and VII). In some geographic regions, closely related isolates cluster, suggesting endemic spread of the virus, while in other regions multiple genotypes circulate. Virtually no data are available with regard to the genetic relatedness of Korean strains of HAV. Methods and Results: A 168 base pair segment encompassing the putative VP1/2A junction of the HAV genome was amplified by RT-PCR and sequenced in sera of 18 Korean patients with a sporadic form of acute hepatitis A. Pairwise comparisons of the nucleic acid and amino acid sequences of 18 Korean isolates with one another revealed that the Korean isolates showed > 94.6% and > 96.4% identity, respectively. All of the 18 Korean isolates clustered within genotype IA, irrespective of the geographic locations and the time that hepatitis occurred. Unique amino acid sequence changes that had never been reported in genotype IA were found in nine of the 18 isolates. These changes were Gln,Ser and Lys,Arg in 2A-19 and 2A-10 amino acid positions. Conclusion: The presence of single genotype and unique mutations may be related with the circulation of endemic HAV over a long period of time in Korea. [source] Changes in the Vif protein of HIV-1 associated with the development of resistance to inhibitors of viral proteaseJOURNAL OF MEDICAL VIROLOGY, Issue 2 2005Melanie A. Adekale Abstract The protease (PR) and virus infectivity factor (vif) gene sequences of a cohort of HIV-1 infected patients showing evidence of developing protease inhibitor (PI) resistance whilst undergoing highly active antiretroviral therapy (HAART) have been determined. The PR sequences showed the presence of the classical mutations associated with resistance to PIs. The sequence of the Vif protein showed less variation in samples from PI treated patients than in specimens prepared from treatment-naïve patients. In addition a number of amino acid positions within Vif showed highly significant preferences for a particular amino acid in the PI-treated cohort compared to the untreated control cohort. J. Med. Virol. 75:195,201, 2005. © 2004 Wiley-Liss, Inc. [source] An in silico method using an epitope motif database for predicting the location of antigenic determinants on proteins in a structural contextJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2006Vincent Batori Abstract Presently X-ray crystallography of protein,antibody complexes is still the most direct way of identifying B-cell epitopes. The objective of this study was to assess the potential of a computer-based epitope mapping tool (EMT) using antigenic amino acid motifs as a fast alternative in a number of applications not requiring detailed information, e.g. development of pharmaceutical proteins, vaccines and industrial enzymes. Using Gal d 4 as a model protein, the EMT was capable of identifying, in the context of the folded protein, amino acid positions known to be involved in antibody binding. The high sensitivity and positive predictive value of the EMT as well as the relevance of the structural associations suggested by the EMT indicated the existence of amino acid motifs that are likely to be involved in antigenic determinants. In addition, differential mapping revealed that sensitivity and positive predictive value were dependent on the minimum relative surface accessibility (RSA) of the amino acids included in the mapping, demonstrating that the EMTs accommodated for the fact that epitopes are three-dimensional entities with various degrees of accessibility. The comparison with existing prediction scales demonstrated the superiority of the EMT with respect to physico-chemical scales. The mapping tool also performed better than the available structural scales, but the significance of the differences remains to be established. Thus, the EMT has the potential of becoming a fast and simple alternative to X-ray crystallography for predicting structural antigenic determinants, if detailed epitope information is not required. Copyright © 2005 John Wiley & Sons, Ltd. [source] IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid propertiesJOURNAL OF MOLECULAR RECOGNITION, Issue 1 2004Christelle Pommié Abstract IMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr) is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates. IMGT comprises IMGT/LIGM-DB, the comprehensive database of IG and TR sequences from human and other vertebrates (76,846 sequences in September 2003). In order to define the IMGT criteria necessary for standardized statistical analyses, the sequences of the IG variable regions (V-REGIONs) from productively rearranged human IG heavy (IGH) and IG light kappa (IGK) and lambda (IGL) chains were extracted from IMGT/LIGM-DB. The framework amino acid positions of 2474 V-REGIONs (1360 IGHV, 585 IGKV, 529 IGLV) were numbered according to the IMGT unique numbering. Two statistical methods (correspondence analysis and hierarchic classification) were used to analyze the 237 framework positions (80 for IGHV, 79 for IGKV, 78 for IGLV), for three properties (hydropathy, volume and chemical characteristics) of the 20 common amino acids. Results of the analyses are shown as standardized two-dimensional representations, designated as IMGT Colliers de Perles statistical profiles. They provide a characterization of the amino acid properties at each framework position of the expressed IG V-REGIONs, and a visualization of the resemblances and differences between heavy and light, and between kappa and lambda sequences. The standardized criteria defined in this paper, amino acid positions and property classes, will be useful to study the mutations and allele polymorphisms, to establish correlations between amino acids in the IG and TR protein three-dimensional structures and to extract new knowledge from V-like domains of chains, other than IG and TR, belonging to the immunoglobulin superfamily. Copyright © 2004 John Wiley & Sons, Ltd. [source] Topological analysis of the complex formed between neurokinin A and the NK2 tachykinin receptorJOURNAL OF NEUROCHEMISTRY, Issue 2 2007Sannah Zoffmann Abstract Neurokinin A stimulates physiological responses in the peripheral and central nervous systems upon interacting primarily with the tachykinin NK2 receptor (NK2R). In this study, the structure of NKA bound to the NK2R is characterised by use of fluorescence resonance energy transfer. Four fluorescent NKA analogues with Texas red introduced at amino acid positions 1, 4, 7 and 10 were prepared. When bound to a NK2R carrying enhanced green fluorescent protein at the N-terminus, all peptides reduce green fluorescent protein fluorescence from 10% to 50% due to energy transfer. The derived donor-acceptor distances are 46, 55, 59 and 69 Å for the fluorophore linked to positions 1,10, respectively. The monotonic increase in distance clearly indicates that the peptide adopts an extended structure when bound to its receptor. The present data are used, in combination with rhodopsin structure, fluorescence studies, photoaffinity labelling and site-directed mutagenesis data to design a computer model of the NKA-NK2R complex. We propose that the N-terminus of NKA is exposed and accessible to the extracellular medium. Subsequent amino acids of the NKA peptide become progressively more buried residues up to approximately one-third of the transmembrane-spanning domain. [source] Site-specific mutation of the interferon sensitivity-determining region (ISDR) modulates hepatitis C virus replicationJOURNAL OF VIRAL HEPATITIS, Issue 9 2006T. Kohashi Summary., The number of amino acid substitutions in the interferon sensitivity-determining region (ISDR) in the nonstructural 5A (NS5A) gene of hepatitis C virus (HCV) is closely associated with the interferon (IFN) response and viral load. Several HCV replicon-based studies have reported that ISDR sequences had an influence on viral replication in vitro. However, it is unclear as to how different ISDR sequences affect HCV replication. Various clinically observed ISDR sequences were introduced into HCV replicons and their contribution to viral replication was investigated using a colony formation assay and/or a transient replication assay. A mapping study of the ISDR was performed to identify the amino acid positions that critically affect replication. While no colonies were formed in the colony formation assay using HCV replicons with few mutations (0, 1 and 3) in the ISDR, numerous colonies (>200) appeared when using constructs with six mutations. Introduction of various distinct ISDR sequences with multiple mutations resulted in replication enhancement in transient assays. A mapping study identified several specific sites in the ISDR that critically affected replication, including codon 2209 which, in patients, was closely associated with a strong response to IFN. ISDR sequences associated with a clinical IFN response and viral load modulated the replication of HCV replicons, suggesting the importance of the ISDR sequence in HCV infection. [source] The active site of HIV-1 proteaseMEDICINAL RESEARCH REVIEWS, Issue 4 2001Peter P. Mager Abstract The active site of the homodimeric HIV-1 protease includes six amino acids (triads AspThrGly found in each monomer) in amino acid positions 25 to 27 and 25, to 27,. Up to now, the role of Thr26 and Thr26,, and Gly27 and Gly27,, is unknown. It is hypothesized that strong hydrogen-bonding forces between the Thr26 and Thr26, residues stabilize the conformational state of the active site, and that the function of Gly27 and Gly27, is to accommodate and bind a substrate in a position in which the catalytic Asp25 and Asp25, carboxylate groups can attack the amide moiety of a substrate. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 4, 348,353, 2001 [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] SHORT COMMUNICATION: Recurrent Pregnancy Loss and Apolipoprotein E Gene Polymorphisms: A Case,Control Study from North IndiaAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 3 2010Meenal Agarwal Citation Agarwal M, Parveen F, Faridi RM, Phadke SR, Das V, Agrawal S. Recurrent pregnancy loss and apolipoprotein E gene polymorphisms: a case,control study from North India. Am J Reprod Immunol 2010; 64: 172,178 Problem, The role of apolipoprotein E gene polymorphisms in the etiology of recurrent pregnancy loss (RPL) is not clearly understood. We evaluated this polymorphism in unexplained pregnancy losses among North Indian women. Method of study, In a retrospective case,control study, 200 well-characterized RPL cases were examined for their APO-E genotypes based on restriction fragment length polymorphism analysis of PCR-amplified fragments including amino acid positions 112 and 158. The observed genotypes were compared with those obtained from an equal number of ethnically matched negative controls. Results, We found similar APO-E genotypes and E2, E3, and E4 allele frequency distribution among RPL patients and controls. The allele frequencies obtained in patients and controls respectively were as follows: E2 = 7.5% and 9.0% (P = 0.52; OR = 0.81; 95%CI = 0.49,1.35), E3 = 89.7% and 90% (P = 1.00; OR = 0.97; 95%CI = 0.61,1.54), and E4 = 2.8% and 1% (P = 0.12; OR = 2.79; 95%CI = 0.88,8.86). Conclusions, Our data did not support the association of APO-E gene polymorphisms with recurrent pregnancy loss as reported by some of the previous studies. We endorse adequate characterization of RPL cases, inclusion of appropriate negative controls, and adequate sample size prior to addressing such studies. [source] Polymorphisms in MHC- DRA and - DRB alleles of water buffalo (Bubalus bubalis) reveal different features from cattle DR allelesANIMAL GENETICS, Issue 1 2003L. Sena Summary Seventy-five individuals of Bubalus bubalis belonging to four different breeds, three of river buffalo and one of swamp buffalo, were studied for polymorphism in MHC DRB (Bubu-DRB) and DRA (Bubu-DRA) loci. Eight alleles of Bubu-DRB were found, and all alleles in the swamp type were shared with the three river breeds. All alleles sampled from the breed of European origin (Mediterranean) were present in breeds sampled in Brazil, thus variability of this locus may have been preserved to a great extent in the more recently founded Brazilian population. Bubu-DRB alleles contained higher proportions of synonymous vs. non-synonymous substitutions in the non-peptide-binding sites (PBS) region, in contrast to the pattern of variation found in BoLA-DRB3, the orthologous locus in cattle. This indicated that either the first domain exon (exon 2) of Bubu-DRB has not undergone as much recombination and/or gene conversion as in cattle alleles, or Bubu-DRB may be more ancient than BoLA-DRB3 alleles. Phylogenetic analysis of DRB alleles from Bubalus, Syncerus c. caffer, the Cape buffalo, and domestic cattle demonstrated transspecies polymorphism. Water buffalo contained two alleles of DRA that differed from each other in two amino acid positions, including one in the PBS (,22) that was also shared with Anoa depressicornis, the anoa. Discovery of variation in DRA was surprising as the first domain of DRA is a highly conserved polypeptide in mammals in general and especially in ruminants, where no other substitution in PBS was seen. [source] Genome Scanning Tests for Comparing Amino Acid Sequences Between GroupsBIOMETRICS, Issue 1 2008Peter B. Gilbert Summary Consider a placebo-controlled preventive HIV vaccine efficacy trial. An HIV amino acid sequence is measured from each volunteer who acquires HIV, and these sequences are aligned together with the reference HIV sequence represented in the vaccine. We develop genome scanning methods to identify positions at which the amino acids in infected vaccine recipient sequences either (A) are more divergent from the reference amino acid than the amino acids in infected placebo recipient sequences or (B) have a different frequency distribution than the placebo sequences, irrespective of a reference amino acid. We consider t -test-type statistics for problem A and Euclidean, Mahalanobis, and Kullback,Leibler-type statistics for problem B. The test statistics incorporate weights to reflect biological information contained in different amino acid positions and mismatches. Position-specific p -values are obtained by approximating the null distribution of the statistics either by a permutation procedure or by a nonparametric estimation. A permutation method is used to estimate a cut-off p -value to control the per comparison error rate at a prespecified level. The methods are examined in simulations and are applied to two HIV examples. The methods for problem B address the general problem of comparing discrete frequency distributions between groups in a high-dimensional data setting. [source] The distribution of neuroglobin in mouse eyeACTA OPHTHALMOLOGICA, Issue 2009Y YOU Purpose To determine the distribution of neuroglobin (Ngb) in mouse eye. Ngb is predominantly expressed in the nervous system,and at particularly high levels in the retina. Ngb may serve as a reactive oxygen scavenger and may protect the tissue of eye from ischemia/hypoxia injuries. However,the distribution of Ngb in the eye is still controversial. Methods Two polyclonal antibodies against Ngb were used in this immunohistochemical study, both of which were raised in rabbits. One of these two antibodies was generated against the whole recombinant protein of mouse Ngb and the other was generated against amino acid positions 55-70 of mouse and human Ngb. The expression of Ngb was analyzed with light microscopy on tissue sections. Results These two antibodies showed comparable results. Ngb was expressed in the layers of the retina, including the ganglion cell layer, inner and outer nuclear layers, inner and outer plexiform layers, the inner segments of the photoreceptors and the retinal pigment epithelium. Ngb was also detected in other structures of the eye, including the epithelium and endothelium of cornea,the stroma of iris,the ciliary body, the lens epithelium, and the sclera. However, Ngb was not expressed in the corneal stroma, the lens capsule, the lamellar fibers of lens, the pigment epithelium of ciliary body or the pigment layer of iris. Conclusion Ngb was found widely distributed in mouse eye. This finding can be explained by the fact that most of the structures of the eye originated from neural crest/neural ectoderm. Future experiments will focus on the distribution of Ngb at the mRNA level (in situ hybridization),and the quantitative expression levels at baseline and after hypoxic/ischemic challenge. [source] Cloning, expression and immunological characterization of full-length timothy grass pollen allergen Phl p 4, a berberine bridge enzyme-like protein with homology to celery allergen Api g 5CLINICAL & EXPERIMENTAL ALLERGY, Issue 1 2006Å. Marknell DeWitt Summary Background Timothy grass pollen is a common cause of respiratory allergy in the temperate regions. The major group 4 allergen, Phl p 4, has previously been purified and studied biochemically and immunologically, but has so far not been produced and characterized as a recombinant protein. Objective To clone and characterize timothy grass pollen allergen Phl p 4. Methods Full-length Phl p 4 cDNA was cloned using a PCR-based strategy including 3,-and 5,-RACE. Recombinant Phl p 4 was expressed in Escherichia coli and purified by immobilized metal ion affinity chromatography. Its immunological activity was investigated using experimental ImmunoCAP tests, sera from Phl p 4 sensitized individuals and Phl p 4 reactive polyclonal and monoclonal animal antibodies. Results Five full-length Phl p 4 cDNA clones were analysed. Sequence deviations between the clones were present at nine amino acid positions, and the consensus sequence comprised an open reading frame of 525 amino acids, including a predicted 25-residue signal peptide. The calculated molecular weight of the deduced mature protein was 55.6 kDa and the isoelectric point 9.9, both consistent with previously observed properties of purified nPhl p 4. Close sequence similarity was found to genomic clones from several other Pooideae grass species and to Bermuda grass pollen allergen BG60. Further, similarity was found to members of the berberine bridge enzyme (BBE) family, including celery allergen Api g 5. Recombinant Phl p 4 bound specific immunoglobulin (Ig)E from 31 of 32 nPhl p 4-reactive sera, and the IgE binding to rPhl p 4 could be inhibited by nPhl p 4 in a dose-dependent manner. Conclusions Full-length Phl p 4 cDNA was cloned and showed sequence similarity to members of the BBE family. Recombinant Phl p 4 was produced and shared epitopes with natural Phl p 4. [source] Genetics of individual differences in bitter taste perception: lessons from the PTC geneCLINICAL GENETICS, Issue 4 2005UK Kim The ability or inability to taste the compound phenylthiocarbamide (PTC) is a classic inherited trait in humans and has been the subject of genetic and anthropological studies for over 70 years. This trait has also been shown to correlate with a number of dietary preferences and thus may have important implications for human health. The recent identification of the gene that underlies this phenotype has produced several surprising findings. This gene is a member of the T2R family of bitter taste receptor genes. It exists in seven different allelic forms, although only two of these, designated the major taster and major non-taster forms, exist at high frequency outside sub-Saharan Africa. The non-taster allele resides on a small chromosomal region identical by descent, indicating that non-tasters are descended from an ancient founder individual, and consistent with an origin of the non-taster allele preceding the emergence of modern humans out of Africa. The two major forms differ from each other at three amino acid positions, and both alleles have been maintained at high frequency by balancing natural selection, suggesting that the non-taster allele serves some function. We hypothesize that this function is to serve as a receptor for another, as yet unidentified toxic bitter substance. At least some of the remaining five haplotypes appear to confer intermediate sensitivity to PTC, suggesting future detailed studies of the relationships between receptor structure and taste function. [source] | ||||||||||||||||||||||||||||