Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine

J Phys Chem B. 2006 Feb 16;110(6):2927-33. doi: 10.1021/jp056456q.

Abstract

A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Simulation*
  • Hydrogen-Ion Concentration
  • Models, Molecular
  • Osmolar Concentration
  • Peptides / chemistry*
  • Protein Structure, Secondary
  • Protons*
  • Time Factors
  • Titrimetry

Substances

  • Peptides
  • Protons