CREATION OF MODEL BASE AMINO ACID LIBRARIES

University Of California, San Francisco, San Francisco CA

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Specific binding of proteins to DNA and RNA is important in regulation of biological processes and viral lifecycles. Hydrogen bonds often dominate specific interactions, and a modeling study of amino acid hydrogen bond compatibility with particular bases, base pairs, and base steps may help us understand and predict the basis of amino acid-nucleic acid specificity. We have written a program that systematically analyzes the hydrogen bonding possibilities between amino acids and single bases, and amino acids and base pairs. We are in the process of analyzing the resulting database for interesting insights into specificity. This program, in addition to requiring computational power, requires the visualization capabilities of the Computer Graphics Laboratory.