A Structure-Based Database of Antibody Variable Domain Diversity

• Published in: Journal of molecular biology Vol. 348; no. 3; pp. 699 - 709
• Main Authors: Bond, Christopher J., Wiesmann, Christian, Marsters, James C., Sidhu, Sachdev S.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 06.05.2005
• Subjects: Amino Acid Sequence; Animals; antibody; Antibody Diversity; combinatorial mutagenesis; Complementarity Determining Regions - chemistry; Complementarity Determining Regions - genetics; Crystallography, X-Ray; Humans; Immunoglobulin Heavy Chains - chemistry; Immunoglobulin Heavy Chains - genetics; Models, Molecular; Molecular Sequence Data; Peptide Library; phage display; protein engineering; Protein Structure, Tertiary; variable domain; CDR; protein engineering; combinatorial mutagenesis; antibody; phage display; α-HCG; V HH; variable domain; V H
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.02.063

The diversity of natural antibodies is limited by the genetic mechanisms that engender diversity and the functional requirements of antigen binding. Using an in vitro-evolved autonomous heavy chain variable domain (V HH-RIG), we have investigated the limits of structurally-tolerated diversity in the three complementarity-determining regions and a fourth loop within the third framework region. We determined the X-ray crystal structure of the V HH-RIG domain at 1.9 Å resolution and used it to guide the design of phage-displayed libraries encompassing the four loops. The libraries were subjected to selections for structural stability, and a database of structurally-tolerated sequences was compiled from the sequences of approximately 1000 unique clones. The results reveal that all four loops accommodate significantly greater diversity than is observed in nature. Thus, it appears that most sequence biases in the natural immune repertoire arise from factors other than structural constraints and, consequently, it should be possible to enhance the functions of antibodies significantly through in vitro evolution.