SIMULATION OF PROTEIN CONFORMATIONAL FREEDOM AS A FUNCTION OF PH - CONSTANT-PH MOLECULAR-DYNAMICS USING IMPLICIT TITRATION

Solution pH is a determinant parameter on protein function and stabili ty, and its inclusion in molecular dynamics simulations is attractive for studies at the molecular level, Current molecular dynamics simulat ions can consider pH only in a very limited way, through a somewhat ar bitrary choice of a set of fixed charges on the titrable sites, Conver sely, continuum electrostatic methods that explicitly treat pH effects assume a single protein conformation whose choice is not clearly defi ned, In this paper we describe a general method that combines both tit ration and conformational freedom. The method is based on a potential of mean force for implicit titration and combines both usual molecular dynamics and pH-dependent calculations based on continuum methods, A simple implementation of the method, using a mean field approximation, is presented and applied to the bovine pancreatic trypsin inhibitor. We believe that this constant-pH molecular dynamics method, by correct ly sampling both charges and conformation, can become a valuable help in the understanding of the dependence of protein function and stabili ty on pH. (C) 1997 Wiley-Liss, Inc.