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

Miguel Machuqueiro, António M. Baptista

Research output: Contribution to journalArticlepeer-review

96 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2927-2933
Number of pages7
JournalJournal of Physical Chemistry B
Volume110
Issue number6
DOIs
Publication statusPublished - 16 Feb 2006

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