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Bioinformatics Advance Access published online on November 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl563
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 11, 2006
Revised November 3, 2006
Accepted November 3, 2006

Article

In silico grouping of peptide/HLA class I complexes using structural interaction characteristics

Joo Chuan Tong 1, Tin Wee Tan 2, and Shoba Ranganathan 3 *

1 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597; Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613
2 Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597
3 Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, NSW 2109, Australia; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597


  Abstract

Motivation: Classification of human leukocyte antigen (HLA) proteins into supertypes underpins the development of epitope-based vaccines with wide population coverage. Current methods for HLA supertype definition, based on common structural features of HLA proteins and/or their functional binding specificities, leave structural interaction characteristics among different HLA supertypes with antigenic peptides unexplored.

Methods: We describe the use of structural interaction descriptors for the analysis of 68 peptide/HLA class I crystallographic structures. Interaction parameters computed include the number of intermolecular hydrogen bonds between each HLA protein and its corresponding bound peptide, solvent accessibility, gap volume, and gap index.

Results: The structural interaction patterns of peptide/HLA class I complexes investigated herein vary among individual alleles and may be grouped in a supertype dependent manner. Using the proposed methodology, eight HLA class I supertypes were defined based on existing experimental crystallographic structures which largely overlaps (77% consensus) with the definitions by binding motifs. This mode of classification, which considers conformational information of both peptide and HLA proteins, provides an alternative to the characterization of supertypes using either peptide or HLA protein information alone.

Associate Editor: Dmitrij Frishman
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