Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “hypervariable regions”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources
PubMed1985

The VK gene expressed by BALB/c ABPC48 cross-reactive idiotypes induced by anti-idiotypic immunization is identical to that of BALB/c anti-oxazolone and A/J anti-arsonate antibodies.

Anti-idiotypic immunization triggers the production of antibodies that are structurally related to the idiotype. We have shown that the heavy chain variable regions of antibodies produced after anti-ABPC48 (A48) anti-idiotypic immunization of BALB/c mice are homologous to that of A48, except for the third hypervariable region. We present here partial light chain sequences of A48 and of antibodies induced by anti-idiotypic immunization. Nearly perfect homology is found, suggesting that these chains are the products of genes derived from a unique VK germ-line gene. These observations indicate that the H and L hypervariable regions contribute to define the structure of A48 idiotopes. Remarkably, the VK sequence we identify is the same as that described for anti-arsonate and anti-oxazolone antibodies. We discuss the relative importance of particular amino acids for idiotype expression and antigen-binding activity.

Animals↗
PubMed1976

Studies on the structural localization of rabbit H chain allotypic determinants controlled by the a locus. Purification and immunological properties of an immunopeptide bearing a3 allotypic determinants.

An immunopeptide bearing a3 allotypic determinant(s) was isolated from the gamma chain of an a3 homozygous rabbit (G222-2) immunized with type III pneumococcal vaccine. Immunocogical properties of peptides were studied using a radioimmunoassay that involved inhibition by these peptides of a reaction between 125I-labeled anti-a3 antibody and Sepharose-bound a3 immunoglobulin G (IgG). The gamma chain was isolated from IgG of restricted heterogeneity and then citraconylated and digested with trypsin. The tryptic digest (TD1) was passed through an anti-a3 immunoabsorbent column either directly or after an intermediate step of Sephadex G-75 chromatography. The bound peptides (T1) were eluted with 0.1 M acetic acid and further digested with trypsin. The digest (TD2) was again run on the anti-a3 immunoabsorbent column to purify the bound immunopeptide T2. In the radioimmunossay this immunopeptide was found to have major a3 determinant(s). Its molecular weight was found to be approximately 6,000, which decreased to about 3,000 after reduction and alkylation. These data, together with NH2- and COOH-terminal analyses and cysteine peptide mapping, demonstrated that T2 is composed of two polypeptide chains linked by a disulfide bond, one from the cysteine 22 region having lysine at the COOH terminus and the other from the cysteine 92 region arginine at the COOH terminus. The lysine peptide was separated from the arginine peptide and its NH2-terminal sequence was found to be Gly-Asx-Glx-Ser-Thr-Cys. Since the cysteine is at position 22, the lysine peptide starts at position 17. It has approximately 22 residues. The framework sequence from 17 to 20 is different from those reported so far. In addition, the heavy chain used in these studies has some other unusual features including a histidine, probably in the first hypervariable region. The presence of histidine in the first hypervariable region of rabbit heavy chain has not been reported previously. The other peptide which is about 30 amino acids in length and ends with arginine 94, probably includes positions 67, 70, 71, 84, and 85 that are believed to have substitutions correlating with a allotypes. In a hypothetical three-deminsional model of the Fv portion of rabbit anti-SIII antibody BS-5, residues 17 to 33 of the lysine peptide and 67 to 79 and 84 to 85 which may be present in the arginine peptide are fully exposed on the surface and are far removed from the antibody combining site.

Amino Acids↗
PubMed1990

Sequence analysis of amphotropic and 10A1 murine leukemia viruses: close relationship to mink cell focus-inducing viruses.

Viral interference studies have demonstrated the existence of four distinct murine leukemia virus (MuLV) receptors on NIH 3T3 mouse cells. The four viral interference groups are ecotropic MuLV; mink cell focus inducing virus (MCF); amphotropic MuLV; and 10A1, a recombinant derivative of amphotropic MuLV that uses a unique receptor but also retains affinity for the amphotropic MuLV receptor. We report here that 10A1 infects rat and hamster cells, unlike its amphotropic parent. We isolated an infectious molecular clone of 10A1 and present here the sequences of the env genes and enhancer regions of amphotropic MuLV and 10A1. The deduced amino acid sequences of amphotropic MuLV and 10A1 gp70su are remarkably similar to those of MCF and xenotropic MuLV (for which mouse cells lack receptors), with 64% amino acids identical in the four groups. We generated a consensus from these comparisons. Further, the differences are largely localized to a few discrete regions: (i) amphotropic MuLV has two short insertions relative to MCF, at residues 87 to 92 and 163 to 169, and (ii) amphotropic MuLV and MCF are totally different in a hypervariable region, which is greater than 30% proline, at residues approximately 253 to 304. 10A1 closely resembles amphotropic MuLV in its N terminus but contains an MCF-type hypervariable region. These results suggest the possibility that receptor specificity is localized in these short variable regions and further that the unique receptor specificity of 10A1 is due to the novel combination of amphotropic MuLV and MCF sequences rather than to the presence of any novel sequences. The Env proteins of ecotropic MuLV are far more distantly related to those of the other four groups than the latter are to each other. We also found that the enhancer regions of amphotropic MuLV and 10A1 are nearly identical, although 10A1 is far more leukemogenic than amphotropic MuLV.

Amino Acid Sequence↗
PubMed1994

Sequence variability in the env-coding region of hepatitis C virus isolated from patients infected during a single source outbreak.

The variability of the hepatitis C virus genome was investigated in a group of German patients who developed chronic hepatitis C after parenteral administration of contaminated immunoglobulin to prevent Rh sensitization after pregnancy. The nucleotide and deduced amino acid sequence alterations of the E1 and the first hypervariable region of the E2 gene of the hepatitis C virus (HCV) genome from sera of two randomly selected patients were studied by comparison of HCV sequences obtained from the original inoculum (anti Rh immunoglobulin) and from patient sera collected in 1979 and 1989. All isolates were classified as subtype 1b but showed nucleotide insertions of up to 12 nucleotides at the cleavage site of E1/E2. Microheterogeneity of HCV genomes was found in the immunoglobulin supporting the quasispecies model of HCV distribution. Remarkable nucleotide exchanges over the 10 year period in the E1 region (0.9-5.2 x 10(-3) base substitutions per genome site per year) and especially in the first hypervariable region of the E2 gene (about 1.5 x 10(-2)) occurred. The HCV genome undergoes a selection of variants, though it is not known if this derives from mutation or selection of pre-existing rare variants.

Amino Acid Sequence↗
PubMed1994

The affinity-selection of a minibody polypeptide inhibitor of human interleukin-6.

A major challenge in basic and applied biological research is the engineering of small proteins with pre-determined structures and novel functions. In a limited number of cases, this has been achieved by de novo design. An alternative combinatorial approach is based on the construction of large libraries of random peptides and on methods for the selection of the desired molecules. Here we describe a successful combination of both the rational design and the combinatorial approaches for developing proteins with useful biological functions, in this case the construction of a specific inhibitor of the cytokine human interleukin-6. In previous work, the 'minibody', a 61 residue polypeptide consisting of a beta-pleated framework and two hypervariable regions, was designed, synthesized and expressed on f1 phage surface. We report the construction of a repertoire of 50 million minibodies displayed on phage in which the hypervariable regions have been randomized. One polypeptide which binds tightly and specifically to human interleukin-6 was isolated from this collection of minibody mutants. This particular minibody is an effective inhibitor of the cytokine's biological activity. The approach described here could in principle be applied to other molecular targets.

Amino Acid Sequence↗
PubMed1992

An X chromosome inactivation assay based on differential methylation of a CpG island coupled to a VNTR polymorphism at the 5' end of the monoamine oxidase A gene.

A CpG island has been identified just upstream of the first exon of the human monoamine oxidase A (MAOA) gene, localized to Xp11.4-Xp11.23. Southern blotting following digestion with the methylation sensitive restriction endonucleases SmaI, HpaII and HhaI, indicated that CpG dinucleotides within the CpG island were unmethylated on the active X chromosome and extensively methylated on the inactive X chromosome. These sites of differential methylation were close to a polymorphic GT-dinucleotide/VNTR region, which is located 1 kb 3' of the first exon and has a heterozygosity value of 75%. PCR primers were designed for amplification of 1.2-1.3 kb DNA fragments, encompassing both the hypervariable region and a cluster of six HpaII sites within the CpG-rich region. Cleavage of HpaII sites was found to be restricted to active X chromosomes. Therefore, following HpaII digestion, DNA fragments were exclusively amplified from inactive X chromosomes. The resulting PCR products were digested with SacI, which reduced the size of the DNA fragments containing the hypervariable region to 230-330 bp, and were subsequently analyzed on denaturating polyacrylamide gels. Because amplified fragments were exclusively derived from the inactive X chromosome, the relative densities of the two allelic fragments should reflect the proportions of cells that have either of the two X chromosome inactivated. The results of this PCR-based X chromosome inactivation assay were fully concordant with Southern blotting methylation analyses at the PGK locus. It therefore provides a rapid and informative method in tumour clonality analysis and carrier detection in X-linked diseases.

Base Sequence↗
PubMedDate not supplied

The HLA association with rheumatoid arthritis.

Rheumatoid arthritis (RA) is primarily associated with HLA-DR4 in a wide range of ethnic groups. DNA analysis of HLA-DRB1 sequences shows that a limited set of alleles are positively associated with the disease. Third hypervariable region sequences QRRAA, QKRAA and RRRAA are found in up to 85% of RA patients and may constitute the basic unit of association. Risk estimates for alleles and hypervariable regions differ between ethnic groups and subsets of patients. Severe RA and Felty's syndrome are significantly associated with DR4 Dw4 and, to a lesser extent, with DR4 Dw14. In patients the latter allele is almost exclusively found in combination with Dw4, suggesting that complementation is occurring. Critical substitutions in the peptide binding groove correlate with the presence of RA, suggesting that the disease may be driven by the presentation of specifically bound peptide and/or may be influenced by differential selection of the T cell repertoire.

Arthritis, Rheumatoid↗
PubMed1974

Specificity of antibodies: primary structural basis of hapten binding.

The primiary structure of the 83 residues of the NH(2)-terminus of the V(II), region was determined for each of three different antibodies to hapten which were produced in inbred guinea pigs. Each antibody had a different and distinctive primary structure within each of the two "hypervariable" regions (Hv1 and Hv2) included in the analyzed part of the variable region of the heavy chain. The sequences of Hvl and Hv2 in the three antibodies were either unique or of restricted variability compared with those of "normnal" immunoglobulin G2. Further implication of Hv1 and Hv2 in contributing to ligand-binding specificity of antibodies came from the placement of residues modified by affinity labeling reagents in these hypervariable regions.

Amino Acid Sequence↗
PubMed1976

Demonstration of an idiotypic antigen on a monoclonal cold agglutinin and on its isolated heavy and light chains.

A potent anti-idiotype serum produced in a rabbit immunized with the isolated heavy chains of an IgM cold agglutinin "Col" was rendered specific by solid-state adsorptions. The anit-Col idiotype was shown to bind specifically to both isolated Col heavy (mu) and light (kappa) chains as well as to intact Col IgM by three methods: (i) reversal of anti-idiotype inhibition of Col cold agglutinin in an automated hemagglutination-inhibition assay system; (ii) adsorption of the anti-idiotype by affinity gels consisting of Col IgM, mu, or kappa chains covalently coupled to Sepharose 2B; (iii) binding of Col IgM and its isolated chains by an anti-idiotype affinity gel. Fragments of Col light chain lacking constant region determinants but still capable of inhibiting anti-idiotype were produced by limited pepsin digestion of the light chains. The finding of shared idiotypic determinants on isolated heavy and light chains of a monoclonal antibody suggests that these chains share a common sequence in a hypervariable region. As an extension of the gene insertion theory of Wu and Kabat, we postulate that genes coding for hypervariable regions may be available for insertion into the DNA for both heavy and light chains.

Agglutinins↗
PubMedDate not supplied

The amino acid sequence of the variable regions of the light chains from two idiotypically cross reactive IgM anti-gamma globulins.

Amino acid sequence analysis of the light chains of two IgM rheumatoid factors is presented. The parent molecules of these chains are human IgM proteins with specificity for human IgG and sharing idiotypic cross reactivity. The heavy chains had previously been shown to have extremely similar hypervariable regions. This communication presents data indicating that the light chains, even though representing two different kappa subgroups, also share identities in their hypervariable regions. These data can be most easily interpreted in terms of a gene interaction model for immunoglobulin V region assembly.

Amino Acid Sequence↗
PubMed1993

A hypothesis for the HLA-B27 immune dysregulation in spondyloarthropathy: contributions from enteric organisms, B27 structure, peptides bound by B27, and convergent evolution.

Several human rheumatic diseases occur predominantly in persons who carry the histocompatibility (HLA) class I allele B27. They have also been related to Gram-negative enteric microorganisms. In addition, the recent recovery of peptides bound to B27 has allowed an understanding of the structural requirements for their binding. Using the accumulated data base of protein sequences, we have tested a series of hypotheses. First, we have asked whether the primary amino acid sequence of the hypervariable regions of HLA-B27 shares short sequences with the proteins of Gram-negative enteric bacteria. The data demonstrate that, unique among the HLA-B molecules, the hypervariable regions of HLA-B27 unexpectedly share short peptide sequences with proteins from these bacteria. Second, we have asked whether the enteric proteins tend to satisfy the structural requirements for peptide binding to B27 in those regions of the sequence shared with B27. This hypothesis also tends to be true, especially in an allelically variable part of the B27 sequence which is predicted to bind B27 if it were to be presented as a free peptide. We conclude that HLA-B27 and enteric Gram-negative bacteria have undergone a previously unappreciated form of convergent evolution which may be important in the process leading to these rheumatic diseases. Moreover, the regions of the enteric bacterial proteins which are contiguous with the short sequences shared with B27 tend to have structures which are also predicted to bind B27. These observations suggest a mechanism for autoimmunity and lead to the prediction that the B27-associated diseases are mediated by a subset of T-cell receptors, B27, and the peptides bound by B27.

Amino Acid Sequence↗
PubMed1987

Characterization of a human 'midisatellite' sequence.

We have examined the structure and DNA sequence of a human genomic locus that consists of a large hypervariable region made up of repeats of a simple sequence. With several restriction enzymes, the locus shows many restriction fragments that vary quantitatively as well as qualitatively. Other restriction enzymes produce only a single, high-molecular-weight fragment at this locus. Almost all of the fragments are revealed with a simple sequence probe. Southern transfers of the high-molecular-weight restriction fragments produced by the restriction enzymes NotI and SfiI, resolved by pulsed-field gel electrophoresis, gave at most two fragments, demonstrated to be allelic, showing that the majority of the restriction fragments seen in the complex patterns are at a single locus. The estimated size of the region homologous to the probe varied from 250 to 500 kilobases. DNA sequencing indicated that the region consists of tandem repeats of a 40-base-pair sequence. Some homology was detected to the tandem repeating units of the insulin gene and the zetaglobin pseudogene hypervariable regions, and to the "minisatellite" DNA at the myoglobin locus.

Base Sequence↗
PubMed1991

Additional complexity within the HLA-D region: sequence analysis of two new DRw13-DQw7 haplotypes.

HLA-DRB1 is by far the most polymorphic locus within the HLA-D region with now well over 40 alleles. Nearly one fourth of these alleles are subtypes of DRw6, and these are in most cases undetectable by routine typing procedures. In this paper we present the molecular characterization of two new Caucasian DRw13-DQw7 haplotypes by DNA sequencing of the polymorphic first domain exons of DRB1 and DRB3 loci. The first haplotype, DRB1*1301-DRB3*0101-DQB1*0301, has arisen by a recombination between locus DRB1 from a DRw13-DQw6 haplotype and DQA1 from a DR4-DQw7 haplotype, as determined by DNA sequencing, DQ oligotyping, and restriction fragment length polymorphism typing. The second haplotype, DRB1*1305-DQB1*0301, is characterized by the novel DRB1*1305 allele differing from DRB1*1301 by three amino acids. It probably arose by a gene conversion event between a DRw13-DQw6 allele and DRB1*1101. This allele represents a DRw11/DRw13 hybrid DR molecule with a DRw13 serological epitope in the second hypervariable region and a Dw5 cellular epitope in the third hypervariable region. As determined by sequencing of locus DRB3, this allele is associated with DRw52b. Our molecular analysis of the complex HLA-DRw13 group now allows unambiguous DNA typing of all five DRw13 alleles with seven oligonucleotides, a significant improvement in the context of organ transplantation.

Amino Acid Sequence↗
PubMed1990

Glycosylation governs the binding of antipeptide antibodies to regions of hypervariable amino acid sequence within recombinant gp120 of human immunodeficiency virus type 1.

Antibodies raised to an overlapping series of peptides following the amino acid sequence of the external envelope glycoprotein (gp 120) of human immunodeficiency virus type 1 (HIV-1) recognize eight regions in recombinant gp 120 molecules. If the recombinant molecules are glycosylated, three of these regions show a reduced capacity to bind antibody. Of the other five regions, two are strain-specific and carbohydrate restricts antibody binding to their N-terminal flanks, and three can be recognized by antibodies in recombinant gp 120 from an unrelated strain of HIV-1. Antibodies in sera from HIV-1-infected patients bind at high levels to peptides from five regions of gp 120. Of these regions, two coincide with those recognized by antibodies raised to peptides. Four of the five epitopes recognized by the rat antipeptide sera whose ability to bind antibody is influenced most by glycosylation, and three of the five regions which induce high levels of antibodies in patients' sera, contain putative glycosylation sites which are variable between strains of HIV-1. Such sites flank the putative neutralization and CD4-binding regions of gp 120. It is suggested that changes in the number and position of carbohydrate moieties following mutation can alternately mask and reveal epitopes. Masking an epitope can render a virus resistant to neutralization, whereas virus which binds antibody without being neutralized is able to gain entry to cells bearing antibody and complement receptors. Changes in the glycosylation pattern of gp 120 may therefore contribute to the control of HIV-1 spread within its host.

Amino Acid Sequence↗
PubMed1992

Amplification of three hypervariable DNA regions by polymerase chain reaction for paternity determinations: comparison with conventional methods and DNA fingerprinting.

The present study evaluates the usefulness of a PCR-based method for routine paternity testing in 35 paternity cases. This identification method which is based on amplification of three hypervariable genetic loci, apoB, D1S80 and HLA-DQ alpha, is compared, with regard to reliability and technical feasibility, to the conventional identification methods based on protein polymorphisms and to Southern blot hybridizations with multi- and single locus probes. Data obtained by PCR-amplification of these three loci resulted in paternity indices (56.1, geometric mean value) which are at the same level as the corresponding values derived from standard genetic blood group markers (42.7). The geometric mean value of the paternity indices obtained by Southern blot hybridization using three single locus probes (190.6) was more informative, and the most informative analysis proved to be Southern blot hybridization with multilocus probes. The technical feasibility and the reproducibility of the PCR-based analysis is, however, overwhelming, and if several highly polymorphic loci are amplified, the resolving power of PCR-analysis is similar to that obtained using multilocus probes.

Blood Grouping and Crossmatching↗
PubMed1994

Hepatitis C virus (HCV) genotype distribution in German isolates: studies on the sequence variability in the E2 and NS5 region.

We report on molecular characterization of hepatitis C virus (HCV) isolates in intravenous drug abusers, as compared to non-drug using patients with posttransfusion hepatitis or sporadic hepatitis of unknown origin. Virus typing was performed by RFLP analysis of PCR products in the 5' NCR. Subtyping was done by hybridization with subtype specific probes or by sequencing in the NS4 and NS5 region, respectively. HCV subtype 1b was found most commonly among all the isolates. However, the subtype 3a had a high prevalence (about 46%) in the group of drug addicts. In these subtype 3a isolates the N-terminal part of the E2 protein was highly variable. This confirms the presence of a hypervariable region (HVR1) in this envelope protein found in all hepatitis C viruses. Each subtype 3a isolate examined had a characteristic unique hypervariable region in the E2 protein. It is noteworthy that there are four amino acids in this region which were highly conserved between all HCV sequences published. It can be assumed that such conserved amino acids are significant for structure and function of this viral protein. In our HCV subtype 3a isolates the NS5 sequences were highly conserved.

Amino Acid Sequence↗
PubMed1980

Structural correlates of cross-reactive and individual idiotypic determinants on murine antibodies to alpha-(1 leads to 3) dextran.

For the first time V-region amino acid sequence differences have been correlated with the expression of cross-reactive and individual idiotypes through an analysis of 12 dextran-binding proteins. This correlation has been possible because of the apparent sequence identity of the corresponding lambda chains. Expression of a cross-reactive idiotype was localized to two residues and/or a carbohydrate in the second hypervariable region of the heavy chain. Two individual idiotypes correlate with the two amino acids within the third hypervariable region that comprises the D segment of the dextran-binding proteins. These results demonstrate that idiotype reagents can recognize two amino acid differences within V and D segments of classical variable regions. In anti-dextran antibodies, cross-reactive idiotypes involve V-region determinants, whereas individual idiotype determinants correlate with D-segment variation.

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↗