Sean Sun

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We present a methodology for obtaining the elastic properties of protein motifs. We combine the use of interpolated structures (IS), molecular dynamics (MD) and collective coordinates to deduce the elastic properties of the beta-sheet in F(1) ATPase. We find that about 3.5 kcal/mol (6 k(B) T at room temperature) of elastic energy is stored in the beta-sheet(More)
The conformational equilibria of Mg.ATP in solution is studied using molecular dynamics (MD) augmented with umbrella sampling methods. Free energy comparisons show that the Mg(2+) ion is equally likely to coordinate the oxygens of the two end phosphates, or of all three phosphates. The MD trajectories reveal two major degrees of freedom of the Mg.ATP(More)
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