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PubMed1999

Proteoglycan receptor binding by Neisseria gonorrhoeae MS11 is determined by the HV-1 region of OpaA.

The interaction of the OpaA protein of Neisseria gonorrhoeae MS11mk with heparan sulphate-containing proteoglycan receptors on Chang conjunctiva epithelial cells was examined using isolated receptor binding and cell adherence/internalization assays. OpaA deletion proteins, in which the four surface-exposed regions of the protein were deleted individually, and chimeric OpaA/B proteins, in which the surface-exposed regions of the OpaA and OpaB proteins were exchanged, were expressed in N. gonorrhoeae. The recombinant deletion proteins and the chimeric OpaA/B proteins were surface exposed in the outer membrane of N. gonorrhoeae. Isolated receptor-binding assays and Chang cell infection assays with OpaA deletion variants indicated that hypervariable region 1 was essential for the interaction of N. gonorrhoeae with the proteoglycan receptor. Expression of chimeric OpaA/B proteins confirmed the central role of hypervariable region 1 in receptor binding and demonstrated that this domain alone confers the invasive biological phenotype in a non-heparan sulphate proteoglycan-binding Opa protein. The other variable regions of OpaA enhanced receptor binding in the presence of region 1, but did not constitute binding domains on their own. The results indicate that proteoglycan receptor binding results from a hierarchical interaction between the variable domains of the OpaA protein of MS11mk.

Amino Acid Sequence↗

PubMed1976

Variable region sequence of the light chain from a Waldenströms IgM with specificity for phosphorylcholine.

The variable region sequence of the light chain from the human IgM FR with binding activity for phosphorylcholine has been determined. Automated Edman degradation was used for the whole chain and for a large cyanogen bromide fragment comprising the third hypervariable region and the entire constant part. The rest of the sequence was established by means of the "Dansyl-Edman" technique with tryptic peptides. The sequence of light chain FR can be assigned to the subgroup II of human light chains with which it shares 92% homology within the nonhypervariable (frame-work) residues. There is no apparent sequence homology betweeen the variable region of the human light chain FR and the aminoterminal 41 residues of the light chains published so far from the mouse myeloma proteins TEPC 15, HOPC 8, S 107, and McPC 603 with phosphorylcholine binding activity. Recent data on the light chain of the phosphorylcholin binding mouse myeloma protein MOPC 167 (see Conclusion), however, indicate a considerable structural homology between the first hypervariable region of this murine protein and that of the human IgM FR, suggesting that both IgM FR and IgA MOPC 167 might have been selected by similar antigens.

Amino Acid Sequence↗

PubMed1988

Characterization of a silent pilin gene locus from Neisseria meningitidis strain FAM18.

We cloned and characterized a silent pilin locus (pilS) in the chromosome of Neisseria meningitidis strain FAM18. This locus represents the sole region of the FAM18 chromosome with strong homology to a gonococcal pilin gene. The FAM18 pilS locus encodes two tandem, in-frame, truncated pilin genes and shares many features with the previously described pilS locus of N. meningitidis strain C114. However, DNA sequence comparison shows that different information resides in the hypervariable region of one of the gene copies between the two strains. The conservation of reading frames within silent copies and the sequence diversity in hypervariable regions are reminiscent of gonococcal pilS loci and suggest that pilS loci may be of functional importance in the meningococcus.

Amino Acid Sequence↗

PubMed1997

Mapping of antigenic sites involved in neutralization on the capsid protein of feline calicivirus.

In order to locate amino acid residues involved in the formation of feline calicivirus (FCV) neutralizing epitopes, we analysed the capsid protein gene of monoclonal antibody neutralization-resistant variants of FCV. Amino acid substitutions in the variants were identified in the two hypervariable regions of the capsid protein. Four linear and two conformational epitopes were located in the regions from residues 426 to 460 and 490 to 520, respectively. The relative positions of individual epitopes agreed with our previous antigenic analysis. Two antigenic sites composed of the neutralizing epitopes were mapped in the hypervariable regions of the capsid protein, demonstrating that a relationship exists between the genetic variability and antigenic differences in the neutralization of FCV.

Animals↗

PubMed2003

Molecular cloning and sequence analysis of ussurin, a new metalloproteinases/disintegrin from Gloydius ussuriensis.

The metalloproteinases/disintegrins in the snake venom act as platelet aggregation inhibitor by an antagonism against integrin on platelet through its RGD sequence and may play other important role in cell-cell fusion, cell matrix interaction and other cellular function. Ussurin is a new metalloproteinase/disintegrin that was cloned from Gloydius ussuriensis. Poly (A+) RNA was purified from the total RNA preparation from venom gland of a single G. ussuriensis using the poly (A+) tract-mRNA isolation system. A cDNA library was constructed with the SMART PCR cDNA library construction kit. The cDNA library was screened and the positive clones were selected. The full-length cDNA of Ussurin was obtained. The cDNA encoding the Ussurin precursor has a 51bp 5'-UTR, the open reading frame of Ussurin and a 490 bp 3'-UTR, the open reading frame of Ussurin cDNA nucleotide sequence is 1434 bp and codes for 478 amino acids with a predicted molecular mass of 53.2 kD and an isoelectric point of 5.37. There is no potential N-glycosylation site in the deduced sequence region. Its deduced amino acid sequence consists of four region, a signal sequence of 18 amino acid residues, a zymogen pro-peptide of 171 amino acid residues with a cysteine switch motif (PK-MCGVT) in it, a central metalloproteinase domain of 201 amino acid residues containing a conserved zinc-chelating sequence (HEXXHXXGXXH) and a methionine-turn CIM involving zinc banding also, a space sequence between metalloproteinase domain and disintegrin domain of 15 amino acid residues with a conserved T392, T397, S400, which is specific residues of the P-II snake venom metalloproteinases, a disintegrin domain of 73 amino acid residues with a characteristic RGD region and six-disulfide bonds. Ussurin belongs to P-II class. The cDNA sequence and deduced amino acid sequence of Ussurin precursor were compared with homologous sequence in the GenBank database, the result reveals high degree of homology in sequence and organization pattern of domain with metalloproteinase/disintegrin gene family of other snake species. Compared with the alignment of amino acid sequence of metalloproteinase/disintegrin member, hypervariable regions of this member were revealed, besides they share higher homologous in the zymogen domain. It suggests that the hypervariable regions are the counterparts directly suitable for interacting with different domain of receptors, different receptors or substrates.

Amino Acid Sequence↗

PubMed2006

A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA.

We established a genotyping system for a panel of 150 SNPs in the coding regions of mitochondrial DNA based on multiplex tag-array minisequencing. We show the feasibility of this system for simultaneous identification of individuals and prediction of the geographical origin of the mitochondrial DNA population lineage of the sample donors by genotyping the panel of SNPs in 265 samples representing nine different populations from Africa, Europe, and Asia. Nearly 40,000 genotypes were produced in the study, with an overall genotyping success rate of 95% and accuracy close to 100%. The gene diversity value of the panel of 150 SNPs was 0.991, compared to 0.995 for sequencing 500 nucleotides of the hypervariable regions I and II of mtDNA. For 17 individuals with identical sequences in the hypervariable regions of mtDNA, our panel of SNPs increased the power of discrimination. We observed 144 haplotypes that correspond to previously determined mitochondrial "haplogroups," and they allowed prediction of the origin of the maternal population lineage of 97% of the analyzed samples.

Asian People↗

PubMed1989

Human immune responsiveness to Lolium perenne pollen allergen Lol p III (rye III) is associated with HLA-DR3 and DR5.

A well-characterized allergen of Lolium perenne (perennial rye grass) pollen, Lol p III, has been used as a model antigen to study the genetic control of the human immune response. Associations between HLA type and IgE or IgG antibody (Ab) responsiveness to Lol p III were studied in two groups of skin-test-positive Caucasoid adults (N = 135 and 67). We found by nonparametric and parametric analyses that immune responsiveness to Lol p III was significantly associated with HLA-DR3 and DR5. No association was found between any DQ type and immune responsiveness to Lol p III. Geometric mean IgE or IgG Ab levels to Lol p III were not different between B8+, DR3+ subjects and B8-, DR3+ subjects, showing that HLA-B8 had no influence on the association. Lol p III IgG Ab data obtained on subjects after grass antigen immunotherapy showed that 100% of DR3 subjects and 100% of DR5 subjects were Ab+. A comparison of all the available protein sequences of DRB gene products showed that the first hypervariable region of DR3 and DR5 (and DRw6), and no other region, contains the sequence Glu9-Tyr-Ser-Thr-Ser13. Our observations are consistent with the possibility that immune responsiveness to the allergen Lol p III is associated with this amino acid sequence in the first hypervariable region of the DR beta 1 polypeptide chain.

Adult↗

PubMed1987

Atypical glycosylation of an IgG monoclonal cryoimmunoglobulin.

The NH2-terminal amino acid sequence of the heavy chain of the IgG monoclonal cryoimmunoglobulin Ger was determined. Evidence for the glycosylation of the first heavy chain hypervariable region of this protein was found. The inability of the deglycosylated Fab fragment of Ger to inhibit cryoprecipitation provides direct evidence that the presence of an additional sialic acid residue in a heavy chain's first hypervariable region can account for the cryo properties of this protein. This is the first convincing description of a molecular defect that explains the atypical low temperature solubility of a monoclonal cryoimmunoglobulin.

Amino Acid Sequence↗

PubMedDate not supplied

[The apoB genotype and the efficacy of hypolipidemic therapy].

Several men were examined for association between restriction fragment length polymorphism (RELP) Xba I (exon 26) number of tandem repeats in 3'-hypervariable region of the apolipoprotein-B gene and serum levels of cholesterol and triglyceride. These two types of polymorphism were studied. An association of the Xba I site and alleles containing more repeats in the 3'-hypervariable region with higher cholesterol and triglyceride was observed. 32 patients with CHD aged 24-56 years were examined. All the patients are males with clinical picture of CHD (stable angina pectoris of II-III functional classes) and dyslipoproteinemia of II a, II b and IV types by D. S. Fredrickson. Xba-I polymorphism of apo-B gene was detected by DNA polymerase reaction method. The following Xba-I genotypes were distinguished: X1X1 (absence of Xba I site); X1X2 (heterozygosity on Xba I site) and X2X2 (homozygosity on Xba-I site). Lipantil (fenofibratte) was prescribed in a dose of 300 mg daily after meals (100 mg three times a day). Data obtained show that DNA polymorphism of apo-B gene not only influences plasma lipids concentration but also determines effectiveness of hypolipidemic therapy. Hypolipidemic effect of lipantil depends on Xba-I site presents in apo-B gene and is significantly expressed in homozygous patients with X1X1 genotype.

Adult↗

PubMed1977

Structural studies on induced antibodies with defined idiotypic specificities. V. The complete amino acid sequence of the light chain variable regions of anti-p-azophenylarsonate antibodies from A/J mice bearing a cross-reactive idiotype.

The complete amino acid sequence of the variable regions of light chains derived from anti-p-azophenylarsonate antibodies from A/J mice bearing a cross-reactive idiotype is reported. At least two and probably more than three distinct light chains are associated with this idiotypically characterized antibody. The antibodies have several differences in their "framework" structures but evidence is presented indicating that all three light chain hypervariable regions have a homogeneous sequence. The data are discussed in relation to the various theories of antibody diversity. In addition, the findings support the view that hypervariable regions, idiotypic determinants, and the antibody-combining site involve, to a large extent, the same molecular structures.

Amino Acid Sequence↗

PubMedDate not supplied

Sequence of precursor polyprotein gene (segment A) of infectious bursal disease viruses isolated in Korea.

The coding regions of segment A of two recent Korean very virulent (vv) infectious bursal disease virus (IBDV) isolates (KK1 and KSH) and one atypical IBDV isolate (K310) were amplified by reverse transcriptase-polymerase chain reaction, sequenced, and compared with published sequences for IBDV. The overall amino acid sequence similarity of the KK1 and KSH strains compared with foreign vvIBDV strains was between 97.43% and 98.02%. The KK1 and KSH strains, like vvIBDV strains, share unique amino acid residues at positions 222(A), 256(I), 294(I), and 299(S). The sequence of K310 strain was markedly different from other IBDV strains. The K310 strain had 12, 2, and 1 unique amino acid substitutions in the VP2 hypervariable region, VP4, and VP3 gene, respectively, and 3 of 12 substitutions in a VP2 hypervariable region were found in two hydrophilic regions known to be involved in antigenic determination. Also, the K310 strain had 222(S) and 254(S), which were found in variant IBDV strains. The SWSASGS heptapeptide is conserved in all Korean IBDV isolates. By phylogenetic analysis, KK1 and KSH were categorized in one group with foreign vvIBDV isolates, but K310 isolate was categorized in a separate group that was differentiated from the other IBDV strains compared. The K310 strain seemed to be evolved from a separate lineage of IBDV strain.

Amino Acid Substitution↗

PubMed1991

Multiple sclerosis and HLA: is the susceptibility gene really HLA-DR or -DQ?

Seventy-one patients with multiple sclerosis (MS) were classified into four subgroups according to the clinical pattern of their disease; their HLA-DR and DQ polymorphisms were defined by serological methods and analysis of Taq1 digestion fragments hybridizing with DRB, DQA, and DQB cDNA probes. The frequencies of the polymorphisms in the patients were compared with those of 100 control subjects. The frequencies of a 3.25-kb fragment from Mspl digests of genomic DNA which hybridized to DQA were also defined in the same groups of patients and control subjects. HLA-DR2 (DRw 15 subtype) and the associated HLA-DQw6 were observed in significant excess in the patients compared with the normal subjects (63% vs. 32% for DRw15; 65% vs. 42% for DQw6). There were no significant differences in the distribution of the DR or DQ alleles between the groups of patients showing different clinical patterns of disease, nor was there an excess in the patients of DQw8 and DQw9 which share hypervariable region sequences of the DQB chain in common with DQw6. The results argue against two recently proposed hypotheses of MS. First, they are not consistent with the proposal that susceptibility to MS is associated with expression of a hypervariable region of DQB shared by DQw6, 8, and 9. Second, they do not support the concept that primarily chronic progressive and relapsing/remitting MS are two immunogenetically distinct disease entities. Our evidence is consistent with the hypothesis that one of the true disease susceptibility genes for MS lies elsewhere within the HLA region and in Northern European populations is found in significant association with DRw15 and DQw6.

Adult↗

PubMed2002

DNA vaccination of ferrets with chimeric influenza A virus hemagglutinin (H3) genes.

Recently a technology was established based on homologous recombination that allowed the rapid generation of chimeric HA genes of influenza viruses, containing the antigenic determinants obtained from various influenza virus A (H3N2) viruses. In the present report plasmids were generated using a H3 HA vector handle and the hypervariable regions of two genetically distinct influenza A H3N2 viruses, A/Stockholm/7/97 and A/Netherlands/18/94. In a ferret model it was shown that immunisation with plasmid DNA encoding chimeric HA indeed elicited antibody responses specific for the virus from which the hypervariable region with the antigenic determinants were obtained. After DNA-immunisation of the ferrets, protective immunity against infection with influenza virus A/Netherlands/18/94 was evaluated.

Animals↗

PubMed1999

Amino acid polymorphism at residue 71 in HLA-DR beta chain plays a critical role in susceptibility to ulcerative colitis.

The association of ulcerative colitis with distinct HLA-DRB1 alleles has not been easy to ascertain. Recent studies show that among HLA-DR2 alleles, DRB1*15 but not DRB1*16, is associated with the disease. Similarly, in the HLA-DR1 group, only DRB1*0103 is increased in ulcerative colitis patients. The aim of our study was to identify critical DRB1 residues that might account for these differences. We typed 121 patients with ulcerative colitis and 275 controls using gene amplification and sequence-specific oligonucleotide probing for HLA-DRB1 and DRB3. We observed a strong negative association between HLA-DRB1 alleles that encode lysine at position 71 in their beta-chain and susceptibility to ulcerative colitis. Differences in the prevalence among other alleles differing only in the third hypervariable region suggested a hierarchy of susceptible and protective class II alleles related to the presence of an acidic, neutral, or basic amino acid residue at position 71. These data implicate most strongly the amino acid residues in the third hypervariable region of the DRbeta chain, especially DRbeta71, in the association between ulcerative colitis and HLA. However, this does not exclude the contribution of other parts of the molecule and other immunoregulatory genes.

Adult↗

PubMed1972

Construction of a three-dimensional model of the polypeptide backbone of the variable region of kappa immunoglobulin light chains.

From (varphi,Psi) data for the middle amino acid, n, in the series of tripeptides (n - 1)(n)(n + 1) in six proteins whose three-dimensional structure is known from x-ray studies, (varphi,Psi) values for the residues 2-107 of kappa Bence Jones proteins and immunoglobulin light chains were computed. It was assumed that all residues except those in the hypervariable regions 24-34, 50-56, and 89-97, were involved essentially in three-dimensional structure, and hence, their (varphi,Psi) angles would mostly be those best satisfying all kappa tri- and constituent di-peptides that occur at those positions. A set of criteria for selecting and averaging (varphi,Psi) angles is given. In the hypervariable regions, which are presumed to be involved in site complementarity, the (varphi,Psi) angles were selected for a single Bence Jones protein Ag. The three-dimensional models, constructed from the computed (varphi,Psi) values by hand and by display computer were very similar, and residues 23 and 88 were sufficiently close for the disulfide bond to form.

Amino Acid Sequence↗

PubMed2006

Comparison of PCR-based methods for typing Staphylococcus aureus isolates.

In this study, we compared the potentials of (i) a multiplex PCR-based multilocus variable-number tandem repeat (VNTR) assay; (ii) a triplex PCR coamplifying fragments of spa, coa, and the hypervariable region adjacent to the mecA gene; (iii) restriction profile analysis of the STAR repetitive element; (iv) randomly amplified polymorphic DNA analysis; (v) inter-IS256 PCR; and (vi) rep-MP3 PCR. Multilocus VNTR typing and triplex PCR (coa, spa, and hypervariable region) approaches showed excellent reproducibility and high discriminatory power; however, only multilocus VNTR typing could distinguish all pulsed-field gel electrophoresis and spa types. Multilocus VNTR typing appears to be the most useful PCR-based method for the rapid genotyping of Staphylococcus aureus strains.

Bacterial Typing Techniques↗

PubMedDate not supplied

Genetic characterization of 2 novel feline caliciviruses isolated from cats with idiopathic lower urinary tract disease.

Feline caliciviruses (FCVs) are potential etiologic agents in feline idiopathic lower urinary tract disease (I-LUTD). By means of a modified virus isolation method, we examined urine obtained from 28 male and female cats with nonobstructive I-LUTD, 12 male cats with obstructive I-LUTD, and 18 clinically healthy male and female cats. All cats had been routinely vaccinated for FCV. Two FCVs were isolated; I (FCV-U1) from a female cat with nonobstructive I-LUTD, and another (FCV-U2) from a male cat with obstructive I-LUTD. To determine the genetic relationship of FCV-U1 and FCV-U2 to other FCVs. capsid protein gene RNA was reverse transcribed into cDNA, amplified, and sequenced. Multiple amino acid sequence alignments and phylogenetic trees were constructed for the entire capsid protein, hypervariable region E, and the more conserved (nonhypervariable) regions A, B, D, and F. When compared to 23 other FCV isolates with known biotypes, the overall amino acid sequence identity of the capsid protein of FCV-U1 and FCV-U2 ranged from 83 to 96%; identity of hypervariable regions C and E ranged from 58 to 85%. Phylogenetically, FCV-U1 clearly separated from other FCV strains in phenograms based on nonhypervariable regions. In contrast, FCV-U2 consistently segregated with the Urbana strain in all phenograms. Clustering of isolates by geographic origin was most apparent in phenograms based on nonhypervariable regions. No clustering of isolates by biotype was apparent in any phenograms. Our results indicate that FCV-UI and FCV-U2 are genetically distinct from other known vaccine and field strains of FCV.

Animals↗

PubMed1990

HLA-DR alleles with naturally occurring amino acid substitutions and risk for development of rheumatoid arthritis.

To determine the HLA-DR4 subtypes associated with rheumatoid arthritis (RA), we performed amplification of DR4 DRB1 genes by the polymerase chain reaction and dot-blots with oligonucleotide probes. In 52 HLA-DR4+ RA patients, Dw4 was the predominant subtype. This subtype was found in 45 of 52 patients (86.5%) compared with 33 of 59 DR4+ controls (55.9%; P less than 0.001). In the whole population, Dw4 also gave the highest relative risk for RA (RR = 5.31). Relative risk was also associated with DR1.1, the common white DR1 (Dw1) type, which has a third hypervariable region amino acid sequence similar to some forms of DR4 and has glycine at position 86. Variants of DR1 (DR1.2) or DR4 (Dw13.1, Dw14.1) with valine at position 86 appeared less able to confer risk for RA. Substitution of residues in the third hypervariable region of the first domain of DRB1 appeared to correlate with relative risk for RA. Among subjects having 0-1 amino acid substitutions, RA developed in 53%, whereas in subjects with 2-4 amino acid changes, RA was present in only 17.4% (P less than 0.00001). DQw7 (formerly DQw3.1) was slightly increased in DR4+ RA patients compared with controls, but a striking excess of Dw4,DQw7 homozygous patients was observed. The results suggest that DQw7 may have an additional effect, possibly with a recessive mechanism, since it was observed only in DR4 homozygous patients.

Alleles↗