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ICBS: a database of interactions between protein chains mediated by beta-sheet formation
Yimeng Dou1, Pierre-François Baisnée, Gianluca Pollastri
1School of Information and Computer Science, University of California, Irvine, CA 92697, USA.
Bioinformatics (Oxford, England)
|May 29, 2004
Summary
Interchain beta-sheet (ICBS) interactions are crucial in protein structure and disease. A new database quantifies these interactions, revealing insights into amino acid preferences and guiding the development of therapeutic agents.
Area of Science:
- Structural Biology
- Biochemistry
- Computational Biology
Background:
- Interchain beta-sheet (ICBS) interactions are fundamental to protein quaternary structures and aggregation.
- These interactions are implicated in various biological processes and diseases, including AIDS, cancer, anthrax, and Alzheimer's.
Purpose of the Study:
- To create a comprehensive, searchable database of ICBS interactions.
- To analyze amino acid composition and pairing statistics within ICBS interfaces.
- To provide insights for developing agents targeting ICBS interactions.
Main Methods:
- Development of a regularly updated, web-accessible database for ICBS interactions.
- Derivation of an ICBS index to quantify beta-ladder contributions.
- Statistical analysis of amino acid composition and pairing in beta-strands.
Main Results:
- A database of ICBS interactions is now available, updated weekly.
- Significant ICBS interactions occur in 15.8% of cases, often involving antiparallel beta-sheets and dimer/oligomer formation.
- Amino acid frequencies in ICBS interfaces resemble those in intrachain beta-sheets, with specific polar/non-polar pairing preferences observed.
Conclusions:
- The database provides valuable statistics and insights into ICBS interactions.
- Findings can guide the development of agents to modulate ICBS interactions.
- The database can aid in identifying novel protein interactions and therapeutic targets.