Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins.

TLDR: A powerful Monte Carlo method is described to simulate thermal conformational fluctuations in native proteins by using an empirical conformational energy function in which bond lengths and bond angles are kept fixed and only dihedral angles are independent variables.

Abstract: A powerful Monte Carlo method is described to simulate thermal conformational fluctuations in native proteins by using an empirical conformational energy function in which bond lengths and bond angles are kept fixed and only dihedral angles are independent variables. In this method, collective variables corresponding to eigenvectors of the second-derivative matrix of the energy function at its minimum point are scaled according to corresponding eigenvalues in such a way that the energy function in terms of the scaled collective variables is isotropic at the minimum point. Simulation is carried out with an isotropic step size in the space of these scaled collective variables. This simulation method is applied to a small protein, bovine pancreatic trypsin inhibitor (BPTI), and its model harmonic system defined by a quadratic energy function with the same second-derivative matrix as that of BPTI at its minimum point. Efficiency of the simulation method with an isotropic step size in the space of the scaled collective variables is found to be about 500–50 times greater than the conventional method with with an isotropic step in the space of the usual nonscaled variables. One step of this new method generates conformational changes that occur in the real-time range of 0.05 ps. In a record of 5 × 105 step simulation, the BPTI molecule is observed to migrate beyond a single minimum-energy region.