Paper Citing NAMD - Abstract
Dal Peraro, M. D.; Spiegel, Katrin; Lamoureux, Guillaume; De Vivo, Marco; DeGrado, William F.; Klein, Michael L.
Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:444-453, MAR 2007
Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the intrinsic difficulty of handling polarization and charge transfer contributions. In order to improve the description of metalloproteins, a simple reparameterization strategy is proposed herein that does not involve artificial constraints. Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. The present approach is demonstrated to provide enough accuracy to maintain the integrity of the metal pocket for a variety of metalloproteins during extended (multi-nano second) molecular dynamics simulations. The method enables the sampling of small conformational changes and the relaxation of local frustrations in NMR structures. (c) 2006 Elsevier Inc. All rights reserved.
