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1.
An ApaLI restriction site polymorphism is associated with the MB19 polymorphism in apolipoprotein B 总被引:6,自引:0,他引:6
An apolipoprotein (apo) B-specific monoclonal antibody, MB19, detects a commonly occurring two-allele genetic polymorphism in human apoB (Young, S. G., S. J. Bertics, L. K. Curtiss, D. C. Casal, and J. L. Witztum. 1986. Proc. Natl. Acad. Sci. USA. 83: 1101-1105). Antibody MB19 binds to two different allotypes of apoB, MB19(1) and MB19(2), with high and low affinity, respectively. The epitope for antibody MB19 is located within apoB-100 thrombolytic fragment T4 (apoB-100 amino acid residues 1-1297). In this study, we examined the relationship of the MB19 polymorphism to a C----T nucleotide substitution at apoB cDNA nucleotide 421. This nucleotide substitution results in a Thr----Ile substitution at apoB-100 amino acid 71, and it changes an ApaLI restriction endonuclease site in the apoB gene. The nucleotide substitution was easily detectable by ApaLI digestion of a 141-base pair fragment of the apoB gene obtained by enzymatic amplification of genomic DNA. In 62 subjects, the MB19 phenotype, as determined by radioimmunoassays, correlated perfectly with the ApaLI restriction site polymorphism in the amplified DNA. The apoB allotype MB19(1) is associated with an Ile at residue 71 and the absence of the ApaLI site, whereas the apoB allotype MB19(2) is associated with a Thr at residue 71 and the presence of the ApaLI site. We conclude that the amino acid substitution at residue 71 probably accounts for the MB19 polymorphism in apoB. 相似文献
2.
Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html. 相似文献
3.
G. Arlet G. Brami D. Deere A. Flippo O. Gaillot P.H. Lagrange A. Philippon 《FEMS microbiology letters》1995,134(2-3):203-208
Abstract To rapidly characterise TEM-derived extended-spectrum β-lactamases a fast and easy method using polymerase chain reaction-restriction fragment length polymorphism was developed. This method was validated with ten reference TEM-type extended-spectrum β-lactamases. The mutations involved in TEM-20 and TEM-21, which were previously reported only with biochemical analysis, were then characterised. TEM-20 differed from TEM-19 by a silent mutation at position 925 (A for G), and TEM-21 differed from TEM-3 and TEM-14 by a single mutation (G for A) in an unreported position 660, involving an amino acid substitution, arginine for histidine, at position 153. Moreover, a new extended-spectrum β-lactamase conferring low resistance to ceftazidime (TEM-29), was described. TEM-29 derived from TEM-1, with an amino acid substitution, his-164. Finally, the combination of polymerase chain reaction-restriction fragment length polymorphism and plasmid analysis allowed us to investigate nosocomial outbreaks due to clinical isolates of multi-resistant Klebsiella pneumoniae in three hospitals. 相似文献
4.
The molecular basis of an acetyl-CoA carboxylase (ACCase) target-based resistant Lolium rigidum population (WLR 96) was studied here. The carboxyl-transferase domain of the plastidic ACCase gene from resistant individuals was amplified by PCR and sequenced. The DNA sequences were aligned and compared with a susceptible population. Six amino acid substitutions were identified in the resistant population. The substitution Ile-2041-Asn, known to confer resistance to ACCase-inhibiting herbicides aryloxyphenoxypropionate (APP) in Alopecurus myosuroides, was identified in most resistant plants but it is always linked with other amino acid substitutions. This was confirmed by a cleaved amplified polymorphism (CAP) marker and an allele-specific PCR. The sole amino acid substitution Ile-2041-Asn was not found in this population. It is likely this mutation evolved later among individuals already possessing the other substitutions. Three haplotypes were identified from the resistant population based on the six amino acid combinations, and two are linked with herbicide resistance in this population. The multiple amino acid substitutions including the Ile-2041-Asn form the molecular basis endowing a high degree of resistance to ACCase-inhibiting herbicides in this L. rigidum population. 相似文献
5.
Construction and expression of mutant cDNAs responsible for genetic polymorphism in aldehyde oxidase in Donryu strain rats 总被引:1,自引:0,他引:1
Adachi M Itoh K Masubuchi A Watanabe N Tanaka Y 《Journal of biochemistry and molecular biology》2007,40(6):1021-1027
We demonstrated the genetic polymorphism of aldehyde oxidase (AO) in Donryu strain rats: the ultrarapid metabolizer (UM) with nucleotide mutation of (377G, 2604C) coding for amino acid substitution of (110Gly, 852Val), extensive metabolizer (EM) with (377G/A, 2604C/T) coding for (110Gly/Ser, 852Val/Ala), and poor metabolizer (PM) with (377A, 2604T) coding for (110Ser, 852Ala), respectively. The results suggested that 377G > A and/or 2604C > T should be responsible for the genetic polymorphism. In this study, we constructed an E. coli expression system of four types of AO cDNA including Mut-1 with (377G, 2604T) and Mut-2 with (377A, 2604C) as well as naturally existing nucleotide sequences of UM and PM in order to clarify which one is responsible for the polymorphism. Mut-1 and Mut-2 showed almost the same high and low activity as that of the UM and PM groups, respectively. Thus, the expression study of mutant AO cDNA directly revealed that the nucleotide substitution of 377G > A, but not that of 2604C > T, will play a critical role in the genetic polymorphism of AO in Donryu strain rats. The reason amino acid substitution will cause genetic polymorphism in AO activity was discussed. 相似文献
6.
Genetic polymorphism of human plasma apolipoprotein A-IV is due to nucleotide substitutions in the apolipoprotein A-IV gene 总被引:3,自引:0,他引:3
P Lohse M R Kindt D J Rader H B Brewer 《The Journal of biological chemistry》1990,265(17):10061-10064
Genetic polymorphism of human plasma apolipoprotein A-IV has been detected by isoelectric focusing techniques followed by immunoblotting. The molecular basis for this apoA-IV polymorphism has been elucidated. Analysis of the protein coding sequences of the apoA-IV alleles 1 and 2 revealed a single G to T substitution in the apoA-IV-2 allele. The point mutation, occurring in a region highly conserved among the mouse, rat, and human A-IV apolipoproteins, converts the glutamine at position 360 of the mature protein to a histidine. This amino acid substitution adds one positive charge unit to the apoA-IV-1 isoprotein (pI 4.97) thus creating the more basic apoA-IV-2 isoprotein (pI 5.02). Computer analysis of the apoA-IV-2 allele revealed that the single G to T substitution results in the loss of a BbvI and a Fnu4HI restriction enzyme site and in the formation of a new restriction site for the enzyme SfaNI. Protein primary and secondary structure predictions were largely unaffected by this amino acid exchange. These results on the structure of the apoA-IV-1 and apoA-IV-2 alleles suggest that the three other rare isoproteins (apoA-IV-0, apoA-IV-3, and apoA-IV-4) are also due to nucleotide and subsequent amino acid substitutions in the apoA-IV sequence. 相似文献
7.
A single nucleotide polymorphism of CYP2b6 found in Japanese enhances catalytic activity by autoactivation 总被引:4,自引:0,他引:4
Ariyoshi N Miyazaki M Toide K Sawamura Yi Kamataki T 《Biochemical and biophysical research communications》2001,281(5):1256-1260
A single nucleotide polymorphism (SNP) resulting in a substitution from Gln to His was found in exon 4 of the CYP2B6 gene in Japanese. The frequency of the variant allele was found to be 19.9%. The mutant- and the wild-type enzymes were expressed in Escherichia coli, and the effects of the single amino acid substitution on the catalytic activity were examined by investigating the kinetic profiles of 7-ethoxycoumarin O-deethylase activity. The wild-type enzyme showed typical Michaelis-Menten kinetics, while the mutant-type enzyme represented the sigmoidal kinetics with a higher V(max) value compared to that of the wild-type enzyme. Eadie-Hofstee plots further revealed an existence of allosteric effects for the reaction catalyzed by the variant. This is the first evidence demonstrating that only one amino acid substitution, Gln172His, caused by natural SNP enhances the catalytic activity of CYP by obtaining the character of homotropic cooperativity. 相似文献
8.
P-glycoprotein gene (MDR1) cDNA from human adrenal: normal P-glycoprotein carries Gly185 with an altered pattern of multidrug resistance 总被引:10,自引:0,他引:10
N Kioka J Tsubota Y Kakehi T Komano M M Gottesman I Pastan K Ueda 《Biochemical and biophysical research communications》1989,162(1):224-231
We isolated a full-length MDR1 cDNA from human adrenal where P-glycoprotein is expressed at high level. The deduced amino acid sequence shows two amino acid differences from the sequence of P-glycoprotein obtained from colchicine-selected multidrug resistant cultured cells. The amino acid substitution Gly----Val at codon 185 in P-glycoprotein from colchicine resistant cells occurred during selection of cells in colchicine. As previously reported, cells transfected with the MDR1 cDNA carrying Val185 acquire increased resistance to colchicine compared to other drugs. The other amino acid substitution Ser----Ala at codon 893 probably reflects genetic polymorphism. The MDR1 gene, the major member of the P-glycoprotein gene family expressed in human adrenal, is sufficient to confer multidrug-resistance on culture cells. 相似文献
9.
T. D. Volkova E. V. Askarova D. O. Koroev A. V. Kamynina M. P. Filatova I. Yu. Yakupov O. M. Volpina 《Russian Journal of Bioorganic Chemistry》2014,40(4):410-416
Survivin is an oncofetal protein involved in the inhibition of apoptosis and the regulation of cell division. The functions of survivin are determined by its structural state (monomer or dimer). Owing to the natural polymorphism, either the Glu or the Lys residue can be at position 129 of the amino acid sequence of survivin. Lys has the capability for acetylation, and only the protein containing the acetylated residue Lys129 tends to form a dimer. Thus, antibodies recognizing the amino acid substitution Glu129Lys can serve as a tool in the structural and functional investigations of survivin. For preparing the target antibodies, survivin fragments containing residue 129 were synthesized, rabbits were immunized with synthetic peptides, and the antibodies were purified by affinity chromatography on Sepharose conjugated with the corresponding peptides. It was shown by ELISA and immunoblotting that the affinity-purified antibodies are capable of recognizing the amino acid substitution Glu129Lys in the sequence of recombinant and endogenous survivin. 相似文献
10.
A DNA variation in the coding region of the human cystatin C gene has been detected by direct sequencing. The polymorphism, a G/A transition, leads to an Ala/Thr variation in the penultimate amino acid of the signal peptide. The base substitution results in the loss of a SstII restriction site, thus allowing the design of a rapid polymerase chain reaction assay for analysis of this polymorphism in the population. 相似文献
11.
H. Tenkanen P. Koskinene J. Metso M. Baumann M. Lukka R. Kauppinen-Mäkelin K. Kontula M-R. Taskinen M. Mänttäri V. Manninen C. Ehnholm 《生物化学与生物物理学报:疾病的分子基础》1992,1138(1):27-33
We have identified a hitherto genetic polymorphism of apolipoprotein A-IV (apo-IV). The molecular basis for this polymorphism is an A to G substitution at nucleotide 1687 resulting in an Asn to Ser change of amino acid 127. The frequencies of the two apoA-IV alleles (designated apoA-IV127Asn and apoA-IV127Ser), determined by Hinc II restriction analysis of PCR amplified exon three of the apoA-IV gene, were 0.788 and 0.212, respectively, in a Finnish population sample. Allele frequencies of another polymorphism due to a Thr to Ser substitution at amino acid 347 were determined using Hinf I restriction analysis. The allele frequencies were 0.823 for apoA-IV347Thr and 0.177 for apoA-IV247Ser. None of the apoA-IV polymorphisms (apoA-IV127:Asn→Ser, apoA-IV347:Thr→Ser and apoA-IV360:Gln→His) had any effect of plasma lipid and lipoprotein concentrations in cohorts of dyslipidemic men and in a population sample of normolipidemic controls. There was also no association between the history of previous myocardial infarction and any of the apoA-IV alleles. 相似文献
12.
Okazaki A Shoji-Hosaka E Nakamura K Wakitani M Uchida K Kakita S Tsumoto K Kumagai I Shitara K 《Journal of molecular biology》2004,336(5):1239-1249
Depletion of fucose from human IgG1 oligosaccharide improves its affinity for Fcgamma receptor IIIa (FcgammaRIIIa). This is the first case where a glycoform modification is shown to improve glycoprotein affinity for the receptors without carbohydrate-binding capacity, suggesting a novel glyco-engineering strategy to improve ligand-receptor binding. To address the mechanisms of affinity improvement by the fucose depletion, we used isothermal titration calorimetry (ITC) and biosensor analysis with surface plasmon resonance. ITC demonstrated that IgG1-FcgammaRIIIa binding was driven by favorable binding enthalpy (DeltaH) but opposed by unfavorable binding entropy change (DeltaS). Fucose depletion from IgG1 enhanced the favorable DeltaH, leading to the increase in the binding constant of IgG1 for the receptor by a factor of 20-30. The increase in the affinity was mainly attributed to an enhanced association rate. A triple amino acid substitution in IgG1, S298A/E333A/K334A, is also known to improve IgG1 affinity for FcgammaRIIIa. ITC demonstrated that the amino acid substitution attenuated the unfavorable DeltaS resulting in a three- to fourfold increase in the binding constant. The affinity enhancement by the amino acid substitution was due to a reduced dissociation rate. These results indicate that the mechanism of affinity improvement by the fucose depletion is quite distinct from that by the amino acid substitution. Defucosylated IgG1 exhibited higher antibody-dependent cellular cytotoxicity (ADCC) than S298A/E333A/K334A-IgG1, showing a correlation between IgG1 affinity for FcgammaRIIIa and ADCC. We also examined the effect of FcgammaRIIIa polymorphism (Val158/Phe158) on IgG1-FcgammaRIIIa binding. The Phe to Val substitution increased FcgammaRIIIa affinity for IgG1 in an enthalpy-driven manner with the reduced dissociation rate. These results together highlight the distinctive functional improvement of affinity by IgG1 defucosylation and suggest that engineering of non-interfacial monosaccharides can improve glycoprotein affinity for receptors via an enthalpy-driven and association rate-assisted mechanism. 相似文献
13.
The porcine hormone-sensitive lipase gene: sequence, structure, polymorphisms and linkage mapping 总被引:7,自引:0,他引:7
The porcine hormone-sensitive lipase gene and its cDNA have been isolated and sequenced. Several putative regulatory sequences have been detected in the promotor region. The deduced amino acid sequence is 85% identical to the corresponding human, mouse and rat sequence. A search for polymorphisms revealed one intronic and one exonic polymorphism, the latter resulting in a conservative amino acid substitution. Linkage mapping located the LIPE gene close to the calcium release channel (CRC) locus on chromosome 6. 相似文献
14.
Keisuke Sasaki Akihiro Yoneda Akinori Ninomiya Manabu Kawahara Tomomasa Watanabe 《Biochemical and biophysical research communications》2013,430(1):161-166
The Mx protein is known to inhibit the multiplication of several RNA viruses. In chickens, a polymorphism at amino acid position 631 (631 aa) of Mx protein has been suggested to be involved in the antiviral ability against vesicular stomatitis virus (VSV) and influenza virus, indicating that a Ser-to-Asn substitution at 631 aa is the source of this antiviral ability. However, how the substitution at 631 aa contributes to the antiviral activity remains to be clarified. In this study, we investigated differences in antiviral activity against VSV and intracellular localization between Ser and Asn types at 631 aa of the chicken Mx protein. The results showed that chicken Mx protein with an Asn at 631 aa inhibited VSV multiplication and Mx distribution in a granular-like pattern in the cytoplasm. However, Mx carrying the Ser type did not inhibit viral growth and homogenous spread throughout the cytoplasm. Furthermore, we found that replacing Ser with Asn at 631 aa provided Mx with antiviral activity against VSV, with Mx showing granular-like distribution in the cytoplasm. These results demonstrated that a single amino acid polymorphism at 631 aa of the chicken Mx protein altered both the antiviral activity and intracellular localization. 相似文献
15.
Nuno Ferrand 《Biochemical genetics》1989,27(11-12):673-678
A genetic polymorphism of beta-chain rabbit (Oryctolagus cuniculus) hemoglobin is demonstrated by means of acid starch gel electrophoresis. The biochemical evidence presented suggests that a previously reported substitution of a neutral amino acid for a histidine is responsible for the detected genetic variation. Segregation analysis was performed in a sample of 15 matings with 49 offspring and confirmed the genetic hypothesis: two common alleles at an autosomal locus. The calculated gene frequencies in a random sample of 125 individuals are HBB*1 = 0.48 and HBB*2 = 0.52. 相似文献
16.
M. A. Kovalyova L. I. Kovalyov L. S. Eryomina A. A. Makarov M. V. Burakova I. Yu. Toropygin M. V. Serebryakova S. S. Shishkin A. I. Archakov 《Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry》2008,2(4):325-334
Proteomic studies of some human tissues and organs (skeletal muscles, myometrium, motor zone of the brain, prostate), and also cultivated myoblasts revealed 41 proteins, in which the presence of certain variants of amino acids (“conflicts”) was recognized at several “conflict” positions. Among the 93 registered “amino acid conflicts”, seven cases represented the results of the protein polymorphisms caused by corresponding substitution of individual amino acid. Proteomic analysis of prostate proteins revealed two isoforms of a prostate-specific antigen, formed due to alternative splicing. Thus, our results have shown that employment of the proteomic technologies may characterize various types of biochemical polymorphism in many human proteins. 相似文献
17.
In this paper, a new algorithm is presented, which makes possible multilevel comparison of BLOSUM protein substitution matrices based on data from different groups of organisms. As an example, a comparison between substitution matrices based on data from two groups of bacterial genomes with different GC content is presented. Our approach includes evaluating the number of amino acid pairs in BLOCKS databases created separately for the two groups of bacteria using protein sequences deposited in the COG database. Differences of distributions of amino acid pair counts are tested using the chi-squared based G-test. Different analysis levels make it possible to distinguish different patterns of amino acid substitution. Application of the algorithm reveals statistically significant differences in amino acid substitution patterns between AT-rich and GC-rich groups of bacterial organisms. The differences are particularly visible in the overall substitution pattern, amino acid conservation pattern and in comparison of substitution patterns for single amino acids. The algorithm presented in this paper can be considered a novel method for multi-level comparison of amino acid substitution patterns. The presented approach is not limited to bacterial organisms and BLOSUM substitution matrices. Statistically significant differences between substitution patterns in the two groups of bacterial organisms with respect to amino acid conservation pattern can be the evidence of different rate of evolutionary change between AT-rich and GC-rich bacterial organisms. 相似文献
18.
19.
Zuo B Xiong YZ Deng CY Su YH Wang J Lei MG Li FE Jiang SW Zheng R 《Animal genetics》2004,35(3):230-233
LIM domain proteins are important regulators of the growth, determination and differentiation of cells. Four-and-a-half LIM-only protein 3 (FHL3) is a type of LIM-only protein that contains four tandemly repeated LIM motifs with an N-terminal single zinc finger (half LIM motif). In this study, we have determined the complete coding sequence of pig FHL3 which encodes a 280 amino acid protein. The coding region of the pig FHL3 gene is organized in five exons and spans an approximately 2.1-kb genomic region. Comparative sequencing of six pig breeds revealed three single nucleotide polymorphisms (SNPs) within exon 2 of which an A-->G substitution at position 313 changes a codon for arginine into a codon for glycine. The substitution was situated within a PstI recognition site and developed as a PCR-RFLP marker for further use in population variation investigations and association analysis. The A/G polymorphism was segregating only in Landrace pigs. Association studies of the FHL3 polymorphism with carcass traits provided preliminary evidence that the PstI PCR-restriction fragment length polymorphism (RFLP) genotype may be associated with variation in several carcass traits of interest for pig breeding. Further investigations in more Landrace pigs are needed to confirm this. 相似文献
20.
Loss of function of a lupus-associated FcgammaRIIb polymorphism through exclusion from lipid rafts 总被引:2,自引:0,他引:2
Floto RA Clatworthy MR Heilbronn KR Rosner DR MacAry PA Rankin A Lehner PJ Ouwehand WH Allen JM Watkins NA Smith KG 《Nature medicine》2005,11(10):1056-1058
Dysfunction of receptors for IgG (FcgammaRs) has been thought to be involved in the pathogenesis of systemic lupus erythematosus (SLE). We show that a recently described SLE-associated polymorphism of FcgammaRIIb (FcgammaRIIbT(232)), encoding a single transmembrane amino acid substitution, is functionally impaired. FcgammaRIIbT(232) is unable to inhibit activatory receptors because it is excluded from sphingolipid rafts, resulting in the unopposed proinflammatory signaling thought to promote SLE. 相似文献