Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2004 20(16):2767-2777; doi:10.1093/bioinformatics/bth326
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.
ICBS: a database of interactions between protein chains mediated by ß-sheet formation
1 School of Information and Computer Science, 2 Institute for Genomics and Bioinformatics, 3 Department of Chemistry and 4 Department of Biological Chemistry, University of California, Irvine, CA 92697, USA and 5 IUP Génie Physiologique et Informatique, University of Poitiers, 86000 Poitiers, France
Received on January 1, 2004; revised on March 4, 2004; accepted on May 5, 2004
Advance Access Publication May 27, 2004
Motivation: Interchain ß-sheet (ICBS) interactions occur widely in protein quaternary structures, interactions between proteins and protein aggregation. These interactions play a central role in many biological processes and in diseases ranging from AIDS and cancer to anthrax and Alzheimer's.
Results: We have created a comprehensive database of ICBS interactions that is updated on a weekly basis and allows entries to be sorted and searched by relevance and other criteria through a simple Web interface. We derive a simple ICBS index to quantify the relative contributions of the ß-ladders in the overall interchain interaction and compute first- and second-order statistics regarding amino acid composition and pairing at different relative positions in the ß-strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions, the majority of which involve the formation of antiparallel ß-sheets and many of which involve the formation of dimers and oligomers. The frequencies of amino acids in ICBS interfaces are similar to those in intrachain ß-sheet interfaces. A full range of non-covalent interactions between side chains complement the hydrogen-bonding interactions between the main chains. Polar amino acids pair preferentially with polar amino acids and non-polar amino acids pair preferentially with non-polar amino acids among antiparallel (i, j) pairs. We anticipate that the statistics and insights gained from the database will guide the development of agents that control interchain ß-sheet interactions and that the database will help identify new protein interactions and targets for these agents.
Availability: The database is available at: http://www.igb.uci.edu/servers/icbs/
Supplementary Information: http://www.igb.uci.edu/servers/icbs/
Contact: pfbaldi{at}ics.uci.edu
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Present address: Department of Computer Science, University College Dublin, Ireland.
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