Unique features of the variable regions of Bence Jones proteins and their possible relation to antibody complementarity

Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic

Dystroglycanopathies are diseases characterized by progressive muscular degeneration and impairment of patient's quality of life. They are associated with altered glycosylation of the dystrophin-glycoprotein (DGC) complex components, such as α-dystroglycan (α-DG), fundamental in the structural and functional stability of the muscle fiber. The diagnosis of dystroglycanopathies is currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic hypoglycosylated muscle condition. Thus, modified α-DG mucins have been considered potential targets for the development of new diagnostic strategies toward these diseases. In this context, this work describes the synthesis of the hypoglycosylated α-DG mimetic glycopeptide NHAc-Gly-Pro-Thr-Val-Thr[αMan]-Ile-Arg-Gly-BSA (1) as a potential tool for the development of novel antibodies applicable to dystroglycanopathies diagnosis. Glycopeptide 1 was used for the development of polyclonal antibodies and recombinant monoclonal antibodies by Phage Display technology. Accordingly, polyclonal antibodies were reactive to glycopeptide 1, which enables the application of anti-glycopeptide 1 antibodies in immune reactive assays targeting hypoglycosylated α-DG. Regarding monoclonal antibodies, for the first time variable heavy (VH) and variable light (VL) immunoglobulin domains were selected by Phage Display, identified by NGS and described by in silico analysis. The best-characterized VH and VL domains were cloned, expressed in E. coli Shuffle T7 cells, and used to construct a single chain fragment variable that recognized the Glycopeptide 1 (GpαDG1 scFv). Molecular modelling of glycopeptide 1 and GpαDG1 scFv suggested that their interaction occurs through hydrogen bonds and hydrophobic contacts involving amino acids from scFv (I51, Y33, S229, Y235, and P233) and R8 and α-mannose from Glycopeptide 1.

Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies

The antibody repertoire of Bos taurus is characterized by a subset of variable heavy (VH) chain regions with ultralong third complementarity determining regions (CDR3) which, compared to other species, can provide a potent response to challenging antigens like HIV env. These unusual CDR3 can range to over seventy highly diverse amino acids in length and form unique β-ribbon 'stalk' and disulfide bonded 'knob' structures, far from the typical antigen binding site. The genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well understood. Here we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene, IGHV1-7 (VHBUL) rearranged to the longest diversity gene, IGHD8-2. An eight nucleotide duplication at the 3' end of IGHV1-7 encodes a longer V-region producing an extended F β-strand that contributes to the stalk in a rearranged CDR3. A low amino acid variability was observed in CDR1 and CDR2, suggesting that antigen binding for this subset most likely only depends on the CDR3. Importantly a novel, potentially AID mediated, deletional diversification mechanism of the B. taurus VH ultralong CDR3 knob was discovered, in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in place. These deletions serve to further diversify cysteine positions, and thus disulfide bonded loops. Hence, both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.

From esoteric theory to therapeutic antibodies

Theoretical analyses of amino acid and nucleotide sequences of immunoglobulins have provided a unique approach to the understanding of structure and function of antibodies. Variability plots unambiguously identified that the antibody-combining site is formed by six short complementarity determining regions (CDRs), three each from light and heavy chains. Since three-dimensional (3-D) foldings of framework regions (FRs) are similar among different antibodies, the 3-D configurations of CDRs from a specific antibody can be predicted based on their amino acid sequences. The resulting structure forms a compact surface that fits the antigen molecule tightly. The third CDR of the heavy chain (CDRH3), which is coded by the D-minigene together with the N- and/or P-segments, appears to play a unique role in fine fitting between antibody and antigen molecules. In order to maintain biological activities, the grafting of mouse CDRs onto human FRs should closely match the human FR amino acid sequences with the original mouse antibody. Similarities between human and mouse FR sequences that have been preserved for over 20 million years of evolution can be a useful tool in humanizing mouse antibodies.

Resolution of hypervariable regions in T-cell receptor beta chains by a modified Wu-Kabat index of amino acid diversity

The Wu-Kabat variability coefficient is a well-established descriptor of the susceptibility of an amino acid position to evolutionary replacements. It conveniently highlights stretches of accentuated amino acid variation that, for example, in an antibody molecule account for most of the antigen contacts (complementarity-determining regions). Diverse opinion are held as to why the index yields unclear results when applied instead to the polypeptide sequences of the T-cell antigen receptor. We show that a simple modification enhances the resolving power of the index by increasing the weight on the frequency distribution of the amino acids in the formula. Application of the improved index to T-cell receptor beta chains highlights four unambiguous hypervariable regions, three of which are positioned similar to immunoglobulin complementarity-determining regions along the chain. In a Fab-like three-dimensional model of the T-cell receptor, the four hypervariable regions coincide with the four loops on the surface of the domain and form a contiguous area available for binding.

Variable region genes for the immunoglobulin framework are assembled from small segments of DNA--a hypothesis

Sequences of each of the four framework segments FR1, FR2, FR3, and FR4 of the variable regions (V-regions) of light and heavy chains of immunoglobulins were grouped into sets with identical sequences. Sets contained from 1 to 18 members. When each V-region was traced from one FR to the next, it was seen that members of the same set in FR1 could be associated with different sets in FR2, FR3, and FR4. This suggests that the framework for the light and heavy chain V-regions is assembled during embryonic development from sets of minigenes for each FR segment. FR4 from three sets of human V(k)I chains also contained members of V(k)II, V(k)III, and V(k)IV subgroups; one FR2 set contained eight rabbit V(k), one human V(k)IV, and four mouse V(k) and an FR4 set contained two human V(H)III and one mouse V(H)III, indicating substantial evolutionary preservation of these sequences and suggesting that the sets of minigenes are highly conserved in the germ line. The clone of Tonegawa et al. [Tonegawa, S., Maxam, A. M., Tizard, R., Bernard, O. & Gilbert, W. (1978) Proc. Natl. Acad. Sci. USA 75, 1485-1489] could be a hybrid FR1 and FR3 coming from minigenes of MOPC 315 (a V(lambda)II) whereas FR2 would come from MOPC 104E (a V(lambda)I). That FR4 is not joined to the rest of the V-region in 12-day-old mouse embryo DNA is also in accord with this hypothesis. Mouse sperm DNA should be examined to establish whether the hypothesized minigenes are separated by intervening sequences and whether the complementarity-determining (hypervariable) regions or segments of the V-region are separated from the framework in genomic DNA. Sperm DNA from rabbits or other species could be used to search for minigene segments whose sequences are identical in several species.

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.

Localization of two additional hypervariable regions in immunoglobulin heavy chains

Cyanogen bromide fragments were isolated from the heavy chains of three human IgG myeloma proteins of the V(H)III subgroup, sequenced by an automated method, and localized to the variable region. Inspection of these sequences, together with corresponding stretches from both human and animal proteins (studied in other laboratories) led to the detection of two additional hypervariable regions characteristic of the V(H) segment of immunoglobulin heavy chains. These areas of hypervariability, involving heavy-chain residues 86-91 and 101-109, were separated by a region of relative constancy. The close relationship of these two hypervariable regions, and the previously described first heavy-chain hypervariable region (residues 31-37), to the first heavy-chain disulphide bridge implies that the three hypervariable areas might be in close steric approximation in native immunoglobulin molecules. Examination of the sequences of the terminal portion of V(H) of all these proteins (the segment from residue 95 to the beginning of homology region C(H)l) revealed that no subgroup-specific residues could be identified in this area. Thus, heavy-chain subgroup distinctions may not extend through the entire variable region.

The amino acid sequence of a human kappa light chain

The amino acid sequence of the light chain of the myeloma protein Dee was studied. The light chain is of the kappa type and of subgroup I. The variable part contains some substitutions that are unique and also some that have been observed already in other kappaI chains (repeated variants). Based on these repeated variants a subdivision of the kappaI subgroup is proposed.

An attempt to locate the non-helical and permissively helical sequences of proteins: application to the variable regions of immunoglobulin light and heavy chains

From a consideration of (varphi, Psi) values of the amino acids of myoglobin, lysozyme, the alpha and beta chains of horse oxyhemoglobin, tosyl-alpha-chymotrypsin, and carboxypeptidase A, an empirical procedure of predicting whether amino-acid residues in proteins are in a non-helical or may be in a helical conformation has been developed. The conformation of an amino acid at any position n is considered to be influenced by its nearest neighbors (the amino acids at positions n + 1 and n - 1), and the (varphi, Psi) values of the middle amino acid n for the various tripeptide sequences in the known proteins are tabulated. If helical, the (varphi, Psi) values are plotted to define a helical (varphi, Psi) domain. A 20 x 20 table for all tripeptides (n - 1)-(n)-(n + 1) taken sequentially for the entire chain was constructed; it lists the number of instances in which helical and non-helical conformations for the amino acids at position n were found. Certain sequences are found to be associated exclusively with non-helical and others exclusively with helical conformations, whereas many sequences may be either helical or non-helical. The distribution of non-helical residues serves to limit stretches of permissively helical regions; these are then further examined by the helical wheel method. As applied to cytochrome c from 18 species, the only permissively helical segment found was the stretch 91-101 near the C-terminus. For the variable regions of three light and three heavy chains of immunoglobulins, upper limits of 12 and 17% alpha-helix, respectively, were obtained.

An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity

In an attempt to account for antibody specificity and complementarity in terms of structure, human kappa-, human lambda-, and mouse kappa-Bence Jones proteins and light chains are considered as a single population and the variable and constant regions are compared using the sequence data available. Statistical criteria are used in evaluating each position in the sequence as to whether it is essentially invariant or group-specific, subgroup-specific, species-specific, etc. Examination of the invariant residues of the variable and constant regions confirms the existence of a large number of invariant glycines, no invariant valine, lysine, and histidine, and only one invariant leucine and alanine in the variable region, as compared with the absence of invariant glycines and presence of three each of invariant alanine, leucine, and valine and two each of invariant lysine and histidine in the constant region. The unique role of glycine in the variable region is emphasized. Hydrophobicity of the invariant residues of the two regions is also evaluated. A parameter termed variability is defined and plotted against the position for the 107 residues of the variable region. Three stretches of unusually high variability are noted at residues 24-34, 50-56, and 89-97; variations in length have been found in the first and third of these. It is hypothesized that positions 24-34 and 89-97 contain the complementarity-determining residues of the light chain-those which make contact with the antigenic determinant. The heavy chain also has been reported to have a similar region of very high variability which would also participate in forming the antibody-combining site. It is postulated that the information for site complementarity is contained in some extrachromosomal DNA such as an episome and is incorporated by insertion into the DNA of the structural genes for the variable region of short linear sequences of nucleotides. The advantages and disadvantages of this hypothesis are discussed.

Distribution of antibody-forming cells of different specificities in the lymph nodes and spleens of guinea pigs

The distribution of antibody-forming cells of different specificities in the lymph nodes and spleens of guinea pigs immunized with two separate antigens or with antigens bearing two determinants was studied. When animals were immunized with two soluble protein antigens or antigens in which the two antigenic determinants were on the same molecule, antibody-forming cells of different specificities were always randomly intermixed. However, when animals were immunized with two heat-aggregated particulate protein antigens and then boosted with soluble protein antigens, cells of different specificities were often seen to occur in groups. These results suggest that antibody-forming cells may not arise by the antigen-stimulated proliferation of precommitted antibody-forming cells, but rather antibody-forming cells arise by a transformation of uncommitted precursor cells as the result of their interactions with a locally produced material derived from the processing of antigen.