Critical Assessment of Common Force Fields for Molecular Dynamics Simulations of Potassium Channels

Simone Furini, Carmen Domene

Research output: Contribution to journalArticle

Abstract

For the last two decades, the KcsA K+ channel has served as a case study to understand how potassium channels operate at the atomic scale, and molecular dynamics simulations have contributed significantly to the current knowledge of the atomic mechanisms of conduction, inactivation, and gating in this family of membrane proteins. Currently, microsecond trajectories are becoming the new standard in the field, and consequently, it is critical to assess and compare the performance of the classical force fields ordinarily used in simulations of biological systems as well as to quantitatively assess the agreement with experimental data for trajectories of this order of magnitude. To that extent, we performed classical molecular dynamics simulations with CHARMM36 and AMBER-ff14sb force fields using atomic models based on the experimental structure of the KcsA channel in the open/conductive state, at conditions of ionic concentrations and membrane potentials resembling the ones adopted in experiments. In simulations using the CHARMM force field, the experimental open/conductive structure of the channel exhibited high conformational plasticity and fast collapse toward an occluded state. In contrast, in an identical set of simulations using the AMBER force field, no major deviations from the experimental structure were recorded. Force field development is a complex process in which many approximations are typically required and adopted. The results presented here provide additional motivation to further improve the existing models and, crucially, alert practitioners about limitations.

Original languageEnglish
JournalJournal of Chemical Theory and Computation
Early online date15 Oct 2020
DOIs
Publication statusE-pub ahead of print - 15 Oct 2020

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