The purpose of this project involves analysis of structure-function relationships in the enzymes of the mandelate pathway in P. putida and enzymes that are structurally homologous from other metabolic pathways. We have recently published a paper that presents evidence that one of these enzymes, mandelate racemase, is homologous to proteins with different overall functions and substrates. We call this set of related proteins the """"""""enolase superfamily"""""""". The common structures reflect a common fundamental chemical step that these enzymes all perform and provides a model system for studying how nature has conscripted the common architecture for a range of metabolic functions. The Computer Graphics Laboratory is essential to further development of this work: using models of the known homologs to design more general models of the scaffold are useful in helping us to understand how differences in sequence generate differences in function. This work seeks to utilize comparative study of homologous enzyme structures to learn more about general principles useful in re-engineering proteins. Other proteins in the mandelate pathway are being studied from similar perspectives. We expect to develop the computational aspect of the work in a new grant proposal that will be submitted to the NIH within the next year. Some of this work is also being developed with CGL staff under a joint grant held by Prof. Babbitt and CGL faculty Profs. Teri Klein, Conrad Huang, and Thomas Ferrin.
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