ICBS: a database of interactions between protein chains mediated by beta-sheet formation.
BACKGROUND
Interchain beta-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 beta-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 beta-strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions, the majority of which involve the formation of antiparallel beta-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 beta-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 beta-sheet interactions and that the database will help identify new protein interactions and targets for these agents.


BACKGROUND
The database is available at: http://www.igb.uci.edu/servers/icbs/
Dou
Yimeng
Y
School of Information and Computer Science, University of California, Irvine, CA 92697, USA.
Baisnée
Pierre-François
PF
Pollastri
Gianluca
G
Pécout
Yann
Y
Nowick
James
J
Baldi
Pierre
P
D001665:Binding Sites; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008956:Models, Chemical; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D014584:User-Computer Interface
D011506:Proteins