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PEDS Advance Access originally published online on August 13, 2004
Protein Engineering Design and Selection 2004 17(5):463-472; doi:10.1093/protein/gzh058
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Protein Engineering, Design & Selection vol. 17 no. 5 © Oxford University Press 2004; all rights reserved

Conserved sequence and structure association motifs in antibody–protein and antibody–hapten complexes

Dennis R. Livesay1,2 and Shankar Subramaniam3,4

1Department of Chemistry and National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, Urbana, IL 61801 and 3Department of Bioengineering, Department of Chemistry and Biochemistry and San Diego Supercomputing Center, University of California at San Diego, La Jolla, CA 92037, USA

4 To whom correspondence should be addressed. E-mail: shankar{at}ucsd.edu

In this paper, we present the association requirements across a wide variety of antibody–antigen complexes. Phylogenetic analysis clearly indicates the representative nature of our structural dataset. Antigen molecules range from small-molecule haptens to complete protein structures. Common association motifs identified include five conserved tyrosine residues and a single conserved arginine residue from CDR-H3. Further, specificity is refined by a diverse array of antibody–antigen electrostatic interactions that maximize complex specificity. Through analysis of calculated pKa shifts on antigen binding, we find that these interactions are conserved at 23 alignment ‘hot-spot’ positions. Despite consistent roles in defining substrate specificity, 16 hot-spot positions are conserved less than 50% of the time. On the other hand, because of the conserved functional role of these positions, mutant screening at hot-spots is more likely to result in increased antigen specificity than elsewhere. Therefore, we believe these results should facilitate subsequent antibody design experimentation.

Received March 26, 2004; revised June 24, 2003; accepted July 8, 2004.

Edited by Anthony Rees


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