Microfolding: Study of Protein Conformation Change by Molecular Dynamics Calculations

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Dr. Hermans proposes molecular dynamics studies to investigate equilibria and kinetics of conformation change of peptides and proteins. Calculations will be done for systems which are explicitly solvated with several layers of solvent molecules. (1) Conformational free energy surfaces will be calculated in a 4-step process: conformation space will be explored by dynamics simulations in vacuo; probability distributions near each free energy minimum will be computed by free dynamics; free energy differences between conformations will be determined by restrained free-energy simulations with applied torques, and by free-energy simulations with molecular substitution; barriers between minima will be explored separately. These results will be used in conjunction with different approaches (free dynamics; a stochastic model; transition state dynamics) in order to determine the rates of barrier crossings, i.e.kinetic parameters of conformation changes. (2) He plans to develop a method for determining a priori the effect of amino acid replacement on the stability of folded peptide structures and of native, folded conformations of proteins. This will have as aims both to develop techniques that consistently reproduce available experimentally measured free energy changes, and to use the details about structure and thermodynamics that the dynamics simulations are uniquely suited to provide, and thereby quantitate the differences in terms of underlying physical effects. (3) He plans to study conformational flexibility in enzyme active sites in two examples: side chain flexibility in serine protease, and its possible relation to specificity for different substrates; inhibitor flexibility in dihydrofolate reductase and its relation to specificity for enzymes from different species. (4) Finally, he will attempt to distinguish alternate conformations of parts of protein molecules, namely, small surface loops and peptide groups, according to free energy, in order to develop a tool applicable in structure determinations where experimental data provide insufficient detail.***//