Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM

• Published in: Journal of molecular recognition 2001-05, Vol.14 (3), p.172-184
• Main Authors: Yuriev, Elizabeth, Ramsland, Paul A., Edmundson, Allen B.
• Format: Article
• Language: English
• Subjects: Antibodies, Monoclonal - chemistry; Antibodies, Monoclonal - immunology; antibody; Antibody Affinity; Antibody Specificity; antibody-peptide complex; Binding Sites, Antibody - immunology; combinatorial library; Cross Reactions - immunology; cross-reactivity; Databases, Factual; docking; Humans; Immunoglobulin Heavy Chains - chemistry; Immunoglobulin Heavy Chains - immunology; Immunoglobulin Light Chains - chemistry; Immunoglobulin Light Chains - immunology; Immunoglobulin M - chemistry; Immunoglobulin M - immunology; Ligands; Models, Molecular; peptide; Peptide Library; peptide recognition; Peptides - chemical synthesis; Peptides - chemistry; Peptides - immunology; Protein Binding; Protein Conformation; Software; Waldenstrom Macroglobulinemia - immunology
• ISSN: 0952-3499; 1099-1352
• DOI: 10.1002/jmr.533

A monoclonal IgM cryoglobulin with diverse binding behavior was isolated from a patient (Mez) with Waldenström's macroglobulinemia. It gave very high titers in the binding of combinatorially synthesized libraries of peptides ranging in size from two to eight residues. The crystal structure of Mez Fv revealed that the binding site was divided into two cavities of unequal volumes with dimensions and chemical properties that were compatible with the binding of peptides. Access to this unique combination of structural information and peptide binding data led us to carry out Mez‐peptide docking simulations to gain insight into the Mez binding propensities. In the present article, the results for docking of five peptide libraries are combined with discussions of the methods and approximations involved in the docking process. We analyze the origins of peptide binding affinity for Mez IgM in terms of its cross‐reactivity and its structural preferences. Copyright © 2001 John Wiley & Sons, Ltd. Abbreviations used: 3‐D three‐dimensional Ab antibody A absorbance C constant CDR complementarity‐determining region CH constant domain of the heavy chain ELISA enzyme‐linked immunosorbent assay Fv fragment variable H heavy HB hydrogen bond L light PDB Protein Data Bank V variable VH variable region of the heavy chain VL variable region of the light chain vdW van der Waals