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

Miguel Machuqueiro; António M Baptista

doi:10.1021/jp056456q

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

Miguel Machuqueiro·António M Baptista

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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.

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Algorithms Computer Simulation Hydrogen-Ion Concentration Models, Molecular Osmolar Concentration Peptides Protein Structure, Secondary Protons Time Factors Titrimetry Journal Article Research Support, Non-U.S. Gov't

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Miguel Machuqueiro, António M Baptista. 2006-02-16. Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.. https://doi.org/10.1021/jp056456q

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