A monoclonal antibody that defines an idiotope with two subsites in galactan-binding myeloma proteins

RNase H activity of HIV reverse transcriptases is confined exclusively to the dimeric forms

A method for the rapid preparation of a defined substrate to monitor RNase H activity has been developed. Using this substrate, we have investigated the RNase H activities of the different forms of recombinant HIV-1 and HIV-2 reverse transcriptase (RT) in detail. As we report here, RNase H activity is associated only with the dimeric forms (p51/p66 or p66/p66) of the enzymes.

The cell surface receptor is a major determinant restricting the host range of the B-lymphotropic papovavirus

The B-lymphotropic papovavirus (LPV) productively infects only a subset of human B-lymphoma-derived cell lines while transfection of the viral genome yields infectious viral particles in a much wider variety of human hematopoietic cell lines. We have analyzed the contribution of a putative LPV receptor on the cell surface of B-cell lines in restricting the virus host range. In order to establish a quantitative virus binding assay for LPV, infectious virus particles were highly purified by metrizamide equilibrium density centrifugation and used as immunogens to raise seven mouse monoclonal antibodies specific for LPV VP1. Virus particle binding was quantitated in an indirect, nonradioactive assay with an LPV VP1-specific enzyme-linked immunosorbent assay. Binding of LPV particles to permissive human B-lymphoma cell line BJA-B occurred within minutes. Kinetics and capacity of binding were similar at 4 and 37 degrees C. A BJA-B cell was estimated to bind approximately 600 virus particles at conditions under which 50% of the administered virus was bound. The sialidase and trypsin sensitivities of the cellular virus binding moiety show that sialylated and proteinaceous components are necessary components of the LPV receptor on BJA-B cells. Despite a high binding capacity of BJA-B cells for simian virus 40, LPV binding was not significantly affected by a 20-fold excess of simian virus 40 particles, indicating that these related polyomaviruses do not bind to the same receptor on BJA-B cells. Reduction of LPV binding to sialidase-pretreated BJA-B cells was accompanied by a similar reduction of infection, indicating that virus binding may be a limiting factor in the LPV replicative cycle. The two highly LPV-permissive human B-lymphoma cell lines BJA-B and Namalwa displayed high virus binding whereas low and nonpermissive hematopoietic cell lines showed reduced or undetectable virus binding. We conclude that the inability of LPV particles to productively infect the nonpermissive human hematopoietic cell lines analyzed is probably due to the absence or insufficient expression of a functional cell surface receptor.

Modeling the anti-CEA antibody combining site by homology and conformational search

A model for an antibody specific for the carcinoembryonic antigen (CEA) has been constructed using a method which combines the concept of canonical structures with conformational search. A conformational search technique is introduced which couples random generation of backbone loop conformations to a simulated annealing method for assigning side chain conformations. This technique was used both to verify conformations selected from the set of known canonical structures and to explore conformations available to the H3 loop in CEA ab initio. Canonical structures are not available for H3 due to its variability in length, sequence, and observed conformation in known antibody structures. Analysis of the results of conformational search resulted in three equally probable conformations for H3 loop in CEA. Force field energies, solvation free energies, exposure of charged residues and burial of hydrophobic residues, and packing of hydrophobic residues at the base of the loop were used as selection criteria. The existence of three equally plausible structures may reflect the high degree of flexibility expected for an exposed loop of this length. The nature of the combining site and features which could be important to interaction with antigen are discussed.

Immunochemical studies on pneumococcal type 37 capsular polysaccharide

Pneumococcal type 37 capsular polysaccharide was obtained free of contaminants by affinity chromatography on Con-A, wheat germ agglutinin, Maclura pomifera lectin and HOPC-8 mouse myeloma protein affinity columns. The immunochemical reactivity of native and periodate oxidized borohydride reduced type 37 polysaccharide antigen with polyclonal rabbit and monoclonal mouse anti-Pn37 hybridoma antibodies was studied by quantitative precipitation. Quantitative hapten inhibition studies, employing the isomeric series of alpha- and beta-(1----2), (1----3), (1----4) and (1----6)-linked glucobioses as competitive inhibitors of antibody precipitation establish a specificity for anti-Pn37 antibody directed at least in part, against the Glc beta(1----2) Glc (sophorosyl) unit. A high mol. wt, D-glucose containing polysaccharide antigen, cross-reactive with rabbit anti-Pn37 is reported which was found to occur in the culture medium of 7 of 19 strains of Actinomyces examined.

The specificities of polyclonal and monoclonal anti-idiotypes to anti-alpha(1----6)dextrans; possible correlations of idiotype with amino acid sequence

The specificities of polyclonal and monoclonal anti-idiotypes to three anti-alpha(1----6)dextrans-10.16.1, QUPC52, and W3129--were examined by competition ELISA. A major idiotype was defined by two polyclonal and two monoclonal anti-idiotypes to 10.16.1, and a polyclonal anti-idiotype to QUPC52. Another monoclonal anti-idiotype to 10.16.1 defines a non-overlapping determinant. One monoclonal anti-idiotype to 10.16.1 and one to W3129 were hapten inhibitable. By comparing amino acid sequences of Id+ and Id- anti-alpha(1----6)dextrans, the major idiotype was assigned to residues in VH CDR3, with a possible contribution from VH CDR2, a conclusion supported by the hapten inhibition results. Both a monoclonal and a previously described polyclonal anti-idiotype to W3129 define a determinant found on only W3129, among the anti-alpha(1----6)dextrans tested.

Topographic analysis with monoclonal anti-idiotopes: probing the functional anatomy of immunoglobulin variable domains

Attempts to correlate immunoglobulin variable domain functional properties with variable domain primary structure have been valuable, but these efforts have suggested that to more fully account for variable domain function in terms of structure will require knowledge of molecular relationships in three dimensions. In this review we describe generally applicable methods, using monoclonal anti-idiotopes, for the determination of spatial relationships of idiotopes relative to one another and relative to two orienting structural markers of variable domains: 1) the hapten-binding site and 2) the junction of the variable and constant domains. Using these methods it has been possible to construct an oriented idiotope map which spans the variable domain along an axis connecting the paratope and the variable domain-constant domain junction. In addition, it has been possible to correlate idiotope position with other properties of idiotope expression. This approach may contribute to the development of predictive principles of idiotope expression.

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin et al. [submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon beta replicate the conformation of the crystal structure closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows significant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low-energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimization and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.

Location of antigenic epitopes on antibody molecules

Using X-ray crystallographic co-ordinates of immunoglobulins, surface regions accessible to a large spherical probe, comparable in size to an antibody domain, were computed. Locations of these exposed regions were compared with those of experimentally determined antigenic sites, i.e. idiotypic, allotypic and isotypic serological markers. In all cases, an excellent agreement was found. The most prominent computed epitopes correspond to convex parts of antibody surface made by reverse turn segments of the polypeptide chain. The computed epitopes occur in homologous positions in all the immunoglobulin domains, and most of the beta-sheet surfaces on the domains are poorly antigenic. The CH2 domain (Fc fragment) has many more antigenic sites than the Fab fragments (antigen-binding fragments). Variable domain epitopes (idiotypes) involve both hypervariable and framework residues, and only about 25% of the hypervariable residues are strongly antigenic. The results indicate that, in a vertebrate body, each antibody molecule may be recognized, and its concentration regulated, by at least 40 complementary anti-immunoglobulin antibodies; therefore, a possibility of an "immune network" with much higher connectivity than is generally assumed should be seriously contemplated.

Production and characterization of a monoclonal antibody to bovine beta-crystallin

A monoclonal antibody to a bovine lens 27K beta-crystallin polypeptide has been produced from a rat x mouse hybridoma. The antibody reacts with the 27K polypeptide of bovine, mouse, rat, and human lenses, but does not react to the 27K polypeptide of monkey lens nor does it react with any component in the Philly mouse lens which is missing the 27K polypeptide. The antibody does not recognize any of the other major bovine beta-crystallin polypeptides but does recognize a large number of native beta-crystallin proteins. The antigenic specificity and species cross-reactivity of this antibody provides an excellent opportunity to study many aspects of lens development and cataractogenesis.

Idiotypic analysis of monoclonal anti-fluorescyl antibodies: localization and characterization of idiotypic determinants

Nine monoclonal IgG anti-fluorescyl antibodies, which exhibit diverse affinities for fluorescein (Fl) (Ka values ranging from 5 X 10(6) to 10(10) M-1) were analyzed idiotypically. Each of the BALB/c hybridoma proteins (gamma, kappa) exhibited unique idiotypic determinants although two clones (6-10-6 and 20-19-1) were partially (15-20%) cross-reactive. Of two other clones (4-6-9 and 4-6-10) derived from the same cell line, 4-6-9 contained gamma 1 heavy (H) chains and 4-6-10 contained both gamma 1 and gamma 2b H-chains. In addition, 4-6-9 shared idiotypic determinants with 4-6-10 although the latter also displayed unique idiotypic specificities. Collectively, the nine clones demonstrated structural diversity analogous to previous studies which defined binding mechanism diversity. The location of determinants recognized by anti-idiotype reagents directed against each of the monoclonal antibodies was examined by binding inhibition with free Fl and fluorescein-BSA (Fl-BSA). All clones contained determinants both within the active site (Fl-inhibitable) and in close proximity to it (Fl-BSA-inhibitable), although the relative proportions of these determinants varied among the clones. Inhibitor concns required for 50% inhibition varied independently of ligand binding affinity, and therefore were more likely influenced by the heterogeneous nature and affinity of the anti-idiotype reagents toward the individual determinants. Idiotypic analysis of H- and light (L) chains derived from five monoclonal antibodies of diverse affinities was performed. Fl binding and expression of idiotypic determinants by all clones required both H- and L-chains. Restoration of the idiotype by reassociated H- and L-chains was found to be highly restricted to homologous H- and L-chain pairs, as heterologous combinations did not result in the expression of either parental idiotype. The latter was true whether the heterologous pairs were derived from clones of the same isotype or the heterologous combination associated to form an intact molecule with greater affinity than the parental H- and L-chain combination. Heterologous recombinants from the two clones (6-10-6 and 20-19-1) exhibiting partial idiotypic cross-reactivity were able to restore a fraction (approximately 25%) of their idiotypic determinants. Results demonstrated the extensive conformational requirements of ligand binding and idiotype expression and indicated that a high degree of specificity in the VH- and VL-chain interaction must exist for the expression of these idiotypes.

Monoclonal antibodies reveal the structural basis of antibody diversity

Hybridoma technology has made it possible to introduce into continuous culture normal antibody-forming cells and to obtain large amounts of the immunoglobulin produced by each of these cells. Examination of the structure of a number of monoclonal antibodies that react with a single antigen has provided new information on the structural basis of the specificity and affinity of antibodies. Comparisons of families of monoclonal antibodies derived from a single germ line gene revealed the importance of somatic mutation in generating antibody diversity. Monoclonal antibodies that react with variable regions of other monoclonals allow the further dissection and modulation of the immune response. Finally, the continued somatic instability of immunoglobulin genes in cultured antibody-forming cells makes it possible to determine the rate of somatic mutation and to generate mutant monoclonal antibodies that may be more effective serological reagents.

Galactan-binding antibodies. Diversity and structure of idiotypes

A group of eight IgM hybridoma proteins induced with beta(1,6)-D-galactan-containing antigens has been characterized in terms of primary amino acid sequence and idiotype expression. The H chain amino acid sequences reveal very strong homology in the VH segment although several substitutions are seen that suggest the occurrence of somatic mutation in these IgM molecules. Significant sequence variation was observed in CDR-3, the region generated by the D segment, and the two recombination events, VH-D and D-JH. The number of amino acids in this region contributed by the D segment was found to vary from two to six, yet the overall length of CDR-3 was precisely maintained by the addition of amino acids on either side of D during the recombination processes. These additional amino acids are suggested to result from nucleotide addition by repair enzymes. Idiotypic analysis of these proteins, in conjunction with an assessment of the H chain sequences, has permitted an identification of the molecular basis of both cross-reacting and unique idiotypic determinants expressed by these molecules.

Structural correlates of immunoglobulin diversity

VL and VH domains, from different species and with widely different primary structures, interact with each other in the same way to create the globular FV region. Much of the FV is a highly conserved framework structure that is probably common to most, if not all, mammalian FV regions. The extensive contoured frontal surface of the FV is composed of highly variable polypeptide segments (Wu-Kabat complementarity-determining regions). These segments are derived from parts of VL, VH, JH gene products and most of the D gene product. This surface is currently considered to be the most likely location of the antigen-binding sites. The firm immunochemical data based on identification of contacting amino acids supporting this location are still, however, very fragmentary. VL and VH gene products form a large part of the potential antigen-reactive surface. Hence, combinations of different VL and VH gene products are the largest source of structural diversity. The JL and JH gene products have chiefly structural functions in maintaining domain architecture and controlling some interactions between VL and VH domains. The VL-J junction amino acid can provide unique structural properties in the deeper accesses of the potential antigen reaction surface. The VHD-JH junction is more superficial and could be, but has not yet been, directly implicated in antigen binding. The D gene product and the additional amino acids associated with the (VH-D-JH) rearrangement process do determine a substructural part of the potential antigen reactive surface. The D gene product (a connecting segment between two beta strands) can have many different secondary structures. Functionally, the D region product could interact with VL-CDR-1 amino acids to create a specific contour of the antigen reaction surface. Curiously, primary structural variations in H3 have not yet been directly implicated in antigen binding. Much remains to be learned about the role of VH-D-JH rearrangement in antibody diversity. The major genetic factors in creating structural diversity are the multiple VL and VH gene libraries. The gene rearrangement process provides a further amplification. Somatic mutations are yet another additional mechanism.

The complete amino acid sequence of the light chain variable region of two monoclonal anti-p-azobenzene-arsonate antibodies bearing the cross-reactive idiotype

Two monoclonal anti-p-azobenzene-arsonate antibodies produced by cell fusion of A/J spleen lymphocytes were selected. It had previously been shown that they both expressed the cross-reactive idiotype (CRI) and that the amino terminal sequence of their heavy chain variable region differed by only one amino acid substitution within the first 55 residues, at residue 41 in the second framework region. A novel, sensitive peptide-mapping method had indicated that the light chain of these two antibodies differed by at least three amino acid substitutions. Here, the complete amino acid sequence of the light chain variable region is presented. There are only 3 amino acid substitutions between the two antibodies, located in the first and second complementarity determining regions and the third framework region respectively. Although the variable region of the light chains of these two monoclonal antibodies show such a high degree of homology they differ by 26 and 27 substitutions from the reference sequence of the light chain of CRI+ anti-ABA serum antibodies. In addition, they are homologous to 4 other such CRI+ monoclonal antibody light chain sequences published so far, in which only 2 of the above 3 substitutions are not represented. The contribution of the light chain to the CRI is discussed.

Heterogeneity of cross-reactive idiotypes. Serological and structural analysis of monoclonal anti-p-azobenzene-arsonate antibodies expressing major and minor idiotypes

Hybridoma-derived monoclonal anti-p-azobenzene-arsonate (ABA) antibodies were obtained from fusions of ABA-KLH primed A/J spleen cells with three different myeloma cell lines. Of the 156 antibody secreting hybridomas 24% carried the cross-reactive idiotype (CRI), which is known to be shared by 20-70% of anti-ABA serum antibodies in A/J mice. The isotypes, SDS-PAGE patterns and the partial amino acid sequences of the V-regions of one CRI negative and six CRI positive hybridoma proteins were determined. These antibodies were IgGl, kappa and IgG2b, kappa. Some idiotype carrying monoclonal antibodies appeared to be serologically identical. Although the partial VH amino acid sequences of these monoclonal antibodies showed great homology with each other and with serum antibody, several sequence variations in framework residues as well as in the first and second complementarily determining regions (CDRs) were found. The cross-reactive idiotype of the anti-ABA antibodies, therefore, exhibits structural microheterogeneity, i.e. it consists of a family of non-identical but closely related molecules as previously reported (Alkan et al., 1980; Estess et al., 1980; Marshak-Rothstein et al. 1980). Here the N-terminal sequence of the VH regions from 14 CRI+ and 8 CRI- antibodies as well as the VL regions from 11 CRI+ and 8 CRI- monoclonal antibodies are compared. Analysis of the available data demonstrated that there are pairs of hybridoma proteins (both CRI+ and CRI-) which have identical sequences for VH or VL. This suggests that there exist a minimum of 4 germ line genes coding for CRI+ VH, CRI+ VL, CRI- VH and CRI- VL respectively. In addition, CRI+ VL has always been found in association with a CRI+ VH.

Polymorphism in anti-phosphocholine antibodies reflecting evolution of immunoglobulin families

Complete variable (V) region amino acid sequences were determined for four heavy (H) and one light (L) chain from C57BL phosphocholine (PC)-binding monoclonal antibodies. Additional NH2-terminal sequences were obtained from H and L chains of C57BL and CBA/J origin. When these V regions were compared with previously reported anti-PC sequences, a number of observations could be made regarding the function and evolution of L and H chain segments used in these antibodies. (a) L and H chain V segments are remarkably conserved in these inbred strains, although there has been an accumulation of point mutations identifying apparently allelic forms of VK and VH. (b) Mice of each genotype use the same three VK segments in combination with a single VH segment to produce most anti-PC antibodies. An exception has been noted that indicates the occasional use of a second VH gene segment. (c) Multiple, different DH regions are used by mice of each strain, which suggests that the DH segment sequence plays no critical role in either antigen binding or VH-VL pairing. Furthermore, the DH segments and their corresponding gene families appear to be highly conserved in the inbred strains studied. (d) Most PC-binding antibodies use the JH1 joining segment. All JH1 sequences from C57BL mice differ from the BALB/c JH1 at position 105, which identifies allelic forms of the JH1 region. These studies are a first assessment of the nature of mutational events associated with the evolution of specific multigene immunoglobulin families and indicate that homologous VH, DH, JH, VK, and JK genes are similarly assembled and expressed in PC antibodies from three diverse genotypes.

Anti-immunoglobulin antibodies. III. Properties of sequential anti-idiotypic antibodies to heterologous anti-gamma globulins. Detection of reactivity of anti-idiotype antibodies with epitopes of Fc fragments (homobodies) and with epitopes and idiotopes (epibodies)

Murine anti-V region antibodies against a human monoclonal protein Gl with anti-gamma-globulin activity and bearing the Wa cross-reactive idiotype were prepared in several strains of mice. Antibodies were obtained that were specific for the Gl idiotype, the Wa cross-reactive idiotype, and for various framework antigenic determinants that were distinguished by a variety of procedures. Synthesis of such antibodies were found to be independent of MHC and Igh gene complexes. These anti-V region antibodies, produced by a majority of mouse strains investigated, also share a cross-reactive idiotype recognized by BALB/c anti-anti-V region Gl antibodies. A fraction of BALB/c anti-anti-V region Gl antibodies displayed human Fc gamma binding activity and, therefore, can be considered homobodies, as described in other systems. Two of the anti-idiotype antibodies obtained in this system exhibited a peculiar property: they interacted not only with their own antigen (IgM Gl), but also with the Fc fragment with which IgM Gl reacts. Thus, A/J anti-V region Gl antibodies bind to the human Fc gamma fragment in addition to IgM Gl. Similarly, a monoclonal CB6 F1 anti-anti-V region Gl antibody interacted with the V region of IgM Gl as well as with the syngeneic anti-V region antibodies. We called these anti-idiotypic antibodies epibodies because they interact with epitopes of the primary antigen. These homobodies and epibodies, obtained by immunization across heterologous barriers, represent new examples of recognition of the internal image of the antigen within the immune system.