Monte Carlo simulations of a protein molecule with and without hydration energy calculated by the hydration-shell model

Abstract

Monte Carlo simulations of a small protein, carmbin, were carried out with and without hydration energy. The methodology presented here is characterized, as compared with the other similar simulations of proteins in solution, by two points: (1) protein conformations are treated in fixed geometry so that dihedral angles are independent variables rather than cartesian coordinates of atoms; and (2) instead of treating water molecules explicitly in the calculation, hydration energy is incorporated in the conformational energy function in the form of Σg _i A _i, whereA _i is the accessible surface area of an atomic groupi in a given conformation, andg _i is the free energy of hydration per unit surface area of the atomic group (i.e., hydration-shell model). Reality of this model was tested by carrying out Monte Carlo simulations for the two kinds of starting conformations, native and unfolded ones, and in the two kinds of systems,in vacuo and solution. In the simulations starting from the native conformation, the differences between the mean propertiesin vacuo and solution simulations are not very large, but their fluctuations around the mean conformation during the simulation are relatively smaller in solution thanin vacuo. On the other hand, in the simulations starting from the unfolded conformation, the molecule fluctuates much more largely in solution thanin vacuo, and the effects of taking into account the hydration energy are pronounced very much. The results suggest that the method presented in this paper is useful for the simulations of proteins in solution.