Popular Molecular Mechanics Force Research Articles

Developing Improved Charge Sets for the Modeling of the KcsA K(+) Channel Using QM/MM Electrostatic Potentials.

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside the selectivity filter of the KcsA potassium channel. A comparison is made with the result of classical electrostatic calculations with nonpolarizable MM force fields (AMBER, CHARMM, and GROMOS). An effective procedure is proposed to improve force field charges by performing a fit on the electrostatic potential computed along QM/MM simulations, using a dynamical electrostatic potential derived charge set. The optimized charge set is able to reproduce the QM/MM electrostatic potentials along the channel axis within 1-2 kcal/mol, which represents an improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. By providing quantum mechanical benchmark charges and energies for the KcsA selectivity filter, we hope to facilitate developments toward the modeling of ion channels by providing an objective test as to whether a given implementation of a new, polarizable, model represents a real improvement over existing fixed point charge models.

A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials.

This paper introduces a self-consistent computational protocol for modeling protein electrostatic potentials according to static point-charge model distributions. The protocol involves a simple space-domain decomposition scheme where individual molecular domains are modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) protein environment. ElectroStatic-Potential (ESP) atomic charges of the constituent molecular domains are computed, to account for mutual polarization effects, and iterated until obtaining a self-consistent point-charge model of the protein electrostatic potential. The novel protocol achieves quantitative agreement with full QM calculations in the description of electrostatic potentials of small polypeptides where polarization effects are significant, showing a remarkable improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. The capabilities of the method are demonstrated in several applications, including calculations of the electrostatic potential in the potassium channel protein and the description of protein-protein electrostatic interactions.