Protein folding polarizing force fields in ECEPP2 and MM2

F. Torrens ( francisco-DOT-torrens-AT-uv-DOT-es.gif )
Inst. Ciencia Molecular, Universitat de Valencia, Dr. Moliner 50, E-46100 Burjassot (Valencia), Spain.

The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) are used for the simulation of the For-Gly-NH2 backbone. Two different methods are proposed for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID), which assumes scalar isotropic point polarizabilities, and the polarization scheme by interacting induced dipoles (ID), which calculates tensor effective anisotropic point polarizabilities (method of Applequist). A comparative study of the force fields ECEPP2 and MM2+polarization is presented. Molecular mechanics results are discussed, including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The global GAMMA and the local ALPHA, BETA and DELTA minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or overestimate the relative energy of some local minima, the ID polarization energy term represents a significant correction to the total relative energy.