Amino Acid Sequence Of Variable Region Research Articles

Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning.

MotivationKnowing the sensitivity of a viral strain versus a monoclonal antibody is of interest for HIV vaccine development and therapy. The HIV strains vary in their resistance to antibodies, and the accurate prediction of virus-antibody sensitivity can be used to find potent antibody combinations that broadly neutralize multiple and diverse HIV strains. Sensitivity prediction can be combined with other methods such as generative algorithms to design novel antibodies in silico or with feature selection to uncover the sites of interest in the sequence. However, these tools are limited in the absence of in silico accurate prediction methods.ResultsOur method leverages the CATNAP dataset, probably the most comprehensive collection of HIV-antibodies assays, and predicts the antibody-virus sensitivity in the form of binary classification. The methods proposed by others focus primarily on analyzing the virus sequences. However, our article demonstrates the advantages gained by modeling the antibody-virus sensitivity as a function of both virus and antibody sequences. The input is formed by the virus envelope and the antibody variable region aminoacid sequences. No structural features are required, which makes our system very practical, given that sequence data is more common than structures. We compare with two other state-of-the-art methods that leverage the same dataset and use sequence data only. Our approach, based on neuronal networks and transfer learning, measures increased predictive performance as measured on a set of 31 specific broadly neutralizing antibodies.Availability and implementation https://github.com/vlad-danaila/deep_hiv_ab_pred/tree/fc-att-fix

Display of somatostatin-related peptides in the complementarity determining regions of an antibody light chain

Peptide display in antibody complementarity determining regions (CDRs) offers several advantages over other peptide display systems including the potential to graft heterologous peptide sequences into multiple positions in the same backbone molecule. Despite the presence of six CDRs in an antibody variable domain, the majority of insertions reported have been made in heavy chain CDR3 (h-CDR3) which may be explained in part by the highly variable length and sequence diversity found in h-CDR3 in native antibodies. The ability to graft peptide sequences into CDRs is restricted by amino acids in these loops that make structural contacts to framework regions or are oriented towards the hydrophobic interior and are important for the proper folding of the antibody. To identify such positions in human κ-light chain CDR1 (κ-CDR1) and CDR2 (κ-CDR2), we performed alignments of 1330 κ-light chain variable region amino acid sequences and 19 variable region X-ray crystal structures. From analyses of these alignments, we predict insertion points where sequences can be grafted into κ-CDR1 and κ-CDR2 to prepare synthetic antibody molecules. We then tested these predictions by inserting somatostatin and somatostatin-related sequences into κ-CDR1 and κ-CDR2, and analyzing the expression and ability of the modified antibodies to bind to membranes containing somatostatin receptor 5. These results expand the repertoire of CDRs that can be used for the display of heterologous peptides in the CDRs of antibodies.

Sequences of cDNAs encoding immunoglobulin heavy- and light-chain variable regions from two anti-dioxin monoclonal antibodies

We report the cDNA cloning of the γ- and κ-chain-encoding genes for two mouse monoclonal antibodies (mAb) which recognize dioxins. The nucleotide sequences encoding the variable regions of these mAb were also determined. Although the mAb have similar dioxin-binding characteristics, their deduced variable region amino-acid sequences are very different.

Cryoglobulinemia induced by a murine IgG3 rheumatoid factor: skin vasculitis and glomerulonephritis arise from distinct pathogenic mechanisms.

MRL-lpr/lpr mice spontaneously develop a lupus-like syndrome characterized by immunopathological manifestations such as necrotizing vascular lesions of ear tips and severe glomerulonephritis. Similar skin vascular and glomerular lesions associated with cryoglobulinemia can be induced in normal mice by injection of a monoclonal antibody (mAb)--6-19 (gamma 3 heavy chain and kappa light chain), exhibiting both cryoglobulin and anti-IgG2a rheumatoid factor (RF) activities--derived from the MRL-lpr/lpr autoimmune mouse. To determine the role of RF and/or IgG3 Fc fragment-associated cryoglobulin activities in 6-19 mAb-induced tissue lesions, a 6-19-J558L hybrid mAb (gamma 3 heavy chain and lambda 1 light chain) was produced by fusion between the 6-19 hybridoma and the J558L myeloma. Here we report that the 6-19-J558L hybrid mAb, which loses the RF activity but retains the cryoglobulin activity, fails to induce skin vascular lesions. However, it is still able to provoke glomerular lesions identical to those caused by the 6-19 mAb. Further, we have observed that the depletion of the corresponding autoantigen, IgG2a, in mice by treatment with anti-IgM antisera from birth also prevents the development of skin but not glomerular lesions. Our results indicate that both RF and cryoglobulin activities of the 6-19 mAb are required for the development of skin vasculitis, but its cryoglobulin activity alone is sufficient to cause glomerular lesions. In addition, cDNA cloning and sequencing of the 6-19 mAb has revealed that the 6-19 kappa light chain variable region amino acid sequence is encoded in a germ-line configuration, suggesting that immunoglobulin variable region germ-line genes could contribute to the generation of pathogenic autoantibodies.

Amino acid sequence of the heavy chain variable region from the A/J mouse anti-arsonate monoclonal antibody 36-60 bearing a minor idiotype.

In addition to the predominant idiotype family (IdCR) associated with the murine A/J anti-azophenylarsonate response, a second idiotype family (Id36-60) was defined on the basis of serologic cross-reactivity and amino acid sequence homology among monoclonal antibodies [Marshak-Rothstein, A., Margolies, M.N., Benedetto, J.D., & Gefter, M.L. (1981) Eur. J. Immunol. 11, 565-572]. The complete variable region amino acid sequence of the A/J IgG2a hybridoma protein 36-60 heavy chain was obtained by automated Edman degradation of the intact chain and fragments generated by cleavage with CNBr and by tryptic digestion of a succinylated CNBr peptide. A comparison of the Id36-60 heavy chain sequence to that of the IdCR heavy chain variable region reveals only 45% homology between them. The structural data indicate that different genes encode the VH, D, and JH gene-encoded sequences in the two idiotypes.

Immunoglobulin idiotype and anti-anti-idiotype utilize the same variable region genes irrespective of antigen specificity.

Idiotypic determinants characterizing certain antibody specificities have been proven valuable structural and genetic markers in studies of antibody diversity and regulation. The heritable predominant idiotype associated with the response to p-azophenylarsonate in A/J mice consists of a set of highly homologous (greater than 95%) heavy and light chain variable region amino acid sequences probably arising by somatic mutation from one or a few V region genes. We examined a peculiar set of monoclonal antibodies that have been defined as CRI by serologic analysis, but that have no affinity for the hapten Ars. These antibodies were elicited by immunization with anti-CRI rather than by the conventional immunization with antigen. The amino acid sequences of the amino terminal half of the V regions of these anti-(anti-CRI) antibodies are indistinguishable from those of conventional Ars-binding CRI antibodies. Thus, Ars-binding CRI and Ars-nonbinding anti-(anti-CRI) are derived from similar or identical VH and VL genes.

Immunoglobulin heavy chains from anti-inulin myeloma proteins: evidence for a new heavy chain joining segment.

Immunoglobulin heavy chains have been shown to be encoded by at least 3 widely separated genetic elements, designated variable (V), diversity (D), and joining (J), which undergo rearrangement during somatic differentiation to produce the active gene form. The D segment codes for a portion of the 3rd hypervariable region and thus potentially contributes significantly to structural diversity in this portion of the molecule. Heavy chains from anti-inulin proteins are unusual in that they essentially lack a 3rd hypervariable region. Thus, if a D segment exists in these proteins, it is extremely short, possibly 1 to 2 amino acids, and more likely serves a framework function rather than introduces structural diversity in the 3rd hypervariable region. We have completed the heavy chain variable region amino acid sequence from proteins AMPC1 and T957 bringing to 6 the number of complete sequences from this group. All of these proteins lack a 3rd hypervariable region. In addition, substitutions are found within the J segments of AMPC1 and T957, which are unlikely to be generated by the recombination event. The occurrence of Pro at position 105 in both of these J segments in contrast to the Gln found in all other heavy chains using this J segment suggests the possible existence of a previously unidentified J segment gene.

Preliminary crystallographic data on the human λIII Bence Jones protein dimer Cle

A complete human λ Bence Jones protein dimer (Cle) has been isolated and crystallized. Protein Cle was characterized immunochemically and chemically as having a variable region amino acid sequence associated with light chains of the λ chain subgroup, λIII, and a constant region sequence characteristic of “non-Mcg” type λ chains. Bence Jones protein Cle contains two covalently bound intact monomers, each having a molecular weight of ~23,000. Crystals of Bence Jones protein Cle, obtained from ammonium sulfate solutions, diffract to 2.6 Å resolution and have the orthorhombic space group P2 12 12 1 with cell dimensions a = 113.0 A ̊ , b = 72.3 A ̊ , and c = 48.9 A ̊ . The asymmetric unit consists of a dimer with a molecular weight of ~ 46,000.

Genetic control of variable and constant regions of immunoglobulin heavy chains.

IMMUNOGLOBULIN polypeptide chains consist of two well defined regions designated the “variable region” and the “constant region”. Whereas great diversity exists in amino-acid sequences of variable regions, the constant regions of a given subclass of heavy chains (CH)* are essentially invariant in sequence1, 2. Exceptions are the allelic forms, such as the rabbit allotypes A14 and A153, 4, where a threonine-alanine interchange occurs in the constant region of γ chains (Appella, Chersi, R. G. M. and Dubiski, in preparation). The markers unique to a chains (for example, A14-A15) are closely linked to allotypic markers at the a locus (a1, a2, a3)3, 4 which seem to be present on four different Ig heavy chain classes (α, γ, e, µ)5–7. These puzzling observations can be explained if the a locus determinants are variable region markers which reflect genetically controlled differences in some relatively constant residues within the VH region sequences7.