Analysis of the structural diversity of monoclonal antibodies to cyclosporine

Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity

Three antibodies, HyHEL-8 (HH8), HyHEL-10 (HH10), and HyHEL-26 (HH26) are specific for the same epitope on hen egg white lysozyme (HEL), and share >90% sequence homology. Their affinities vary by several orders of magnitude, and among the three antibodies, HH8 is the most cross-reactive with kinetics of binding that are relatively invariable compared to HH26, which is highly specific and has quite variable kinetics. To investigate structural correlates of these functional variations, the Fv regions of HH8 and HH26 were homology-modeled using the x-ray structure of the well-characterized HH10-HEL complex as template. The binding site of HH26 is most charged, least hydrophobic, and has the greatest number of intramolecular salt bridges, whereas that of HH8 is the least charged, most hydrophobic and has the fewest intramolecular salt bridges. The modeled HH26-HEL structure predicts the recently determined x-ray structure of HH26, (Li et al., 2003, Nat. Struct. Biol. 10:482-488) with a root-mean-square deviation of 1.03 A. It is likely that the binding site of HH26 is rendered rigid by a network of intramolecular salt bridges whereas that of HH8 is flexible due to their absence. HH26 also has the most intermolecular contacts with the antigen whereas HH8 has the least. HH10 has these properties intermediate to HH8 and HH26. The structurally rigid binding site with numerous specific contacts bestows specificity on HH26 whereas the flexible binding site with correspondingly fewer contacts enables HH8 to be cross-reactive. Results suggest that affinity maturation may select for high affinity antibodies with either "lock-and-key" preconfigured binding sites, or "preconfigured flexibility" by modulating combining site flexibility.

Cyclosporin A as a model antigen: immunochemical and structural studies

The immunosuppressant drug cyclosporin (Cs) A is a cyclic undecapeptide which has been used as a model antigen because structural information and a large number of analogs, modified at each of its 11 positions, were available. This review summarizes immunochemical and crystallographic studies of the interaction between the Fab of monoclonal antibody R45-45-11 and Cs. Three points are discussed: (1) the different conformations of CsA and the question of its biologically active form; (2) the Fab-CsA recognition mechanism; and (3) the relationship between structure and binding properties of CsA analogs.

Insight into odorant perception: the crystal structure and binding characteristics of antibody fragments directed against the musk odorant traseolide

Monoclonal antibodies were elicited against the small hydrophobic hapten traseolide, a commercially available musk fragrance. Antibody variable region sequences were found to belong to different sequence groups, and the binding characteristics of the corresponding antibody fragments were investigated. The antibodies M02/01/01 and M02/05/01 are highly homologous and differ in the binding pocket only at position H93. M02/05/01 (H93 Val) binds the hapten traseolide about 75-fold better than M02/01/01 (H93 Ala). A traseolide analog, missing only one methyl group, does not have the characteristic musk odorant fragrance. The antibody M02/05/01 binds this hapten analog about tenfold less tightly than the original traseolide hapten, and mimics the odorant receptor in this respect, while the antibody M02/01/01 does not distinguish between the analog and traseolide. To elucidate the structural basis for the fine specificity of binding, we determined the crystal structure of the Fab fragment of M02/05/01 complexed with the hapten at 2.6 A resolution. The crystal structure showed that only van der Waals interactions are involved in binding. The somatic Ala H93 Val mutation in M02/05/01 fills up an empty cavity in the binding pocket. This leads to an increase in binding energy and to the ability to discriminate between the hapten traseolide and its derivatives. The structural understanding of odorant specificity in an antibody gives insight in the physical principles on how specificity for such hydrophobic molecules may be achieved.

Structural diversity of monoclonal CD4 antibodies and their capacity to block the HIV gp120/CD4 interaction

A number of monoclonal antibodies have been raised against CD4, the receptor on T cells for the HIV envelope glycoprotein gp120. In the present paper we describe biological activities and sequence analysis of seven CD4 MAb. Five of these MAb preparations compete with HIV/gp120 for CD4 binding. The sequences of the variable regions for these MAb were determined in order to ascertain any correlation with selective V gene usage. A relationship was found between the expressed variable region genes and the CD4 recognition pattern. The VH genes that are used can be subdivided into two major groups expressing either a VH gene belonging to the J558 family or to the VGam family. The usage of the VL genes varies, indicating that the epitope specificity is predominantly determined by the rearranged VH genes. The distinct cross-reactivity pattern of these MAb also correlates with their capacity to block binding of recombinant gp120 to CD4 in vitro. Although five of these MAb were able to block gp120 binding none of the CDR sequences shows a relevant homology to the gp120 sequence. This indicates a steric hinderence mechanism for blocking gp120 binding and not a direct interaction with the receptor binding site on CD4. The data also confirm the failure of these MAb as a potential target for receptor mimicry.

Structure-activity relationships for the interaction between cyclosporin A derivatives and the Fab fragment of a monoclonal antibody

The crystallographic structure of a complex between cyclosporin A and the Fab fragment of monoclonal antibody R45-45-11 has been solved to 2.65 A resolution (Altschuh et al., 1992a, Science 256, 92; Vix et al., 1993, Proteins 15, 339), yielding a precise three-dimensional picture of interacting surfaces. In order to evaluate the contribution of observed contacts to the energy of interaction, we have measured the effect on binding affinity of minor chemical modifications of CS. The equilibrium binding constant of the Fab fragment for a set of cyclosporin analogs was obtained by measuring in a biosensor instrument the dependence of complex formation on Fab concentration, at constant analog concentrations. Data were analysed using Scatchard plots. Differences in binding energy resulting from cyclosporin modifications discriminated between two types of contact areas. The first type displays adaptability to structural modifications of cyclosporin at the cost of a small decrease in binding energy, and contacting residues in the antibody form the periphery of the combining site. The second type does not accommodate structural changes and corresponds in cyclosporin to three residues whose modifications drastically decrease binding energy with the antibody. The corresponding contact residues in the antibody form the core of the antibody combining site.

Differences in heavy chain amino acid sequences affecting the specificity of antibodies for variants of cytochrome c

In a previous study [Goshorn et al. (1991) J. biol. Chem. 266, 2134-2142], several mAb specific for the same region on different cytochromes c were shown to have similar H or L chains. To determine the effect of differences in individual chains on antigenic variant specificity in the present study, chimeric mAb were prepared by recombining the H and L chains of mAb having the same or a different cytochrome c specificity. The H and L chains of two mAb to the region around residue 60 on horse cytochrome c (1F5.D1 and 2E5.G10) were functionally interchangeable even though the H chain differed by 11 amino acid residues in the complementarity-determining regions (CDR) and 15 amino acids overall in the variable regions. The L chains only differed by four amino acid residues in the CDR (five residues overall). Neither the H nor L chain of a mAb binding the same region of rat cytochrome c (6H2.B4) was functionally interchangeable with the chains of the two horse cytochrome c-specific mAb. The L chain of this mAb is very different from the other L chains which were derived from a different V kappa family, but the H chain is nearly as similar to the horse cytochrome c-specific H chains as they are to each other. Most of the differences occur in CDR3 and result from the use of a distinct DH segment. The results indicate that, in some cases, the specificity of a mAb for a particular variant of a protein Ag, at least in regard to the H chain, is determined by only a few amino acid differences. The differences in the sequences of the H chains of the three mAb in this study and in the structures of their specific Ag provide insight into a possible molecular basis for the specificity of these mAb.

Interaction of cyclosporin A with an Fab fragment or cyclophilin. Affinity measurements and time-dependent changes in binding

Different conformers of the immunosuppressant cyclosporin A have been observed in structural studies of the isolated molecule and of its complex with cyclophilin or with an Fab fragment. The factors that control this conformational change are not well understood. Variations in the amount of complex formed with cyclophilin or with the antibody were measured as a function of time after adding cyclosporin to the proteins, using the Pharmacia BIAcore biosensor instrument. Up to 1 hour was needed to reach maximum complex formation in solution, which is likely to reflect the time needed for a conformational transition of cyclosporin. The equilibrium affinity constant of both proteins for cyclosporin has been measured.

Crystallographic analysis of the interaction between cyclosporin A and the Fab fragment of a monoclonal antibody

The structure of the complex between cyclosporin A and the Fab fragment of a monoclonal antibody has been established by crystallographic analysis to 2.65 A resolution. The structure has been solved by molecular replacement using a composite Fab model. The current R-factor after refinement is 0.179 between 8 and 2.65 A resolution. The antibody is one among three known structures with long H3 loops. This loop conformation is observed for the first time in the presence of the antigen. Residues from all six hypervariable loops interact with cyclosporin A. However, the 17 residues long loop H3 is the main contributor to the buried combining site area and to the van der Waals contacts made with cyclosporin A, with 52 and 63%, respectively, of the total contribution.

A conformation of cyclosporin A in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex

The conformation of the immunosuppressive drug cyclosporin A (CsA) in a complex with a Fab molecule has been established by crystallographic analysis to 2.65 angstrom resolution. This conformation of CsA is similar to that recently observed in the complex with the rotamase cyclophilin, its binding protein in vivo, and totally different from its conformation in an isolated form as determined from x-ray and nuclear magnetic resonance analysis. Because the surfaces of CsA interacting with cyclophilin or with the Fab are not identical, these results suggest that the conformation of CsA observed in the bound form preexists in aqueous solution and is not produced by interaction with the proteins.

Anti-cyclosporine monoclonal antibodies and their anti-idiotopic counterpart: structure and biological activity

In order to study the structural and functional mimicry of an antigen by anti-idiotypic antibodies, we generated anti-idiotopic monoclonal antibodies (anti-Id mAbs) against a mAb (R45-45-11) with specificity for the immunosuppressive cyclic undecapeptide cyclosporine (Cs; Sandimmune). Three out of five anti-Id mAbs inhibited the binding of Cs to the anti-Cs mAb R45-45-11. All anti-Id mAbs cross-reacted only with one (anti-Cs mAb V45-271-10) out of 19 anti-Cs mAbs. The anti-Cs mAb V45-271-10 recognizes an epitope on the Cs molecule which is very similar to that recognized by R45-45-11. R45-45-11 and V45-271-10 differ only by one amino acid in the variable region. The anti-Id mAbs which recognize combining site-associated idiotopes (Ids) reverse the blocking effect of the anti-Cs mAb R45-45-11 on Cs immunosuppression in vitro. The sequences of the variable regions of heavy and light chain of one anti-Id mAb were determined. X-ray analysis of the corresponding Fab fragment, either alone or complexed with the Fab fragment of the Id, is currently in progress.