A free energy calculation study on the thermal stability and denatured state structure of RNaseHII

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The thermal stability of proteins is determined by the delicate balance between the free energy of the native state and that of the denatured state. Structures of the native state have been obtained at high resolutions for many proteins. However, structures of the denatured state have not yet obtained for any proteins in spite of their importance in clarifying the stability mechanisms of proteins. In this study, we obtained reliable model structures of RNaseHII in the denatured state from high temperature MD simulations. The model structures successfully gave almost the same stability free energy as experimental values for all Ile and Leu mutants. The stability free energies of the mutants were calculated by the free energy perturbation method based on MD simulations. The software used in this study, COSMOS90 for MD simulations, PERTURB for amino-acid substitutions, and FENE for free energy estimations, were developed by the author.