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Simulation of protein conformational freedom as a function of pH: constant‐pH molecular dynamics using implicit titration
Author(s) -
Baptista António M.,
Martel Paulo J.,
Petersen Steffen B.
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199704)27:4<523::aid-prot6>3.0.co;2-b
Subject(s) - molecular dynamics , chemistry , titration , titration curve , computational chemistry , function (biology) , stability (learning theory) , chemical physics , thermodynamics , physics , computer science , evolutionary biology , machine learning , biology
Solution pH is a determinant parameter on protein function and stability, and its inclusion in molecular dynamics simulations is attractive for studies at the molecular level. Current molecular dynamics simulations can consider pH only in a very limited way, through a somewhat arbitrary choice of a set of fixed charges on the titrable sites. Conversely, continuum electrostatic methods that explicitly treat pH effects assume a single protein conformation whose choice is not clearly defined. In this paper we describe a general method that combines both titration 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 correctly sampling both charges and conformation, can become a valuable help in the understanding of the dependence of protein function and stability on pH. © 1997 Wiley‐Liss Inc.