SIMULATIONS OF BIOMOLECULES

Cornell University Ithaca, Ithaca NY

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Abstract

The aim of the proposed research is to use computation methods to increase the understanding of the dynamics and function of biomolecules. The essential conformational change in the control protein EFTu will be studied by normal mode analysis and molecular dynamics. All-atom explicit solvent simulations of lysozyme and of structurally related proteins will be performed to explore the origin of the differences in the native state dynamics and in the unfolding behavior. Discontinuous molecular dynamics simulations with simplified protein models will be used to examine the full potential energy surface and dynamics involoved in folding and unfolding. To obtain a deeper understanding of enzyme catalysis, the potential of mean force along the reaction path and the dynamics of the reaction will be calculated for lysozyme, xylose isomerase, hammerhead ribozyme and nitrogenase.