Paper Citing NAMD - Abstract
Vassiliev, Sergey; Zaraiskaya, Tatiana; Bruce, Doug
Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:1671-1678, SEP 2012
The Mn4Ca cluster of the oxygen-evolving complex (OEC) of photosynthesis catalyzes the light-driven splitting of water into molecular oxygen, protons, and electrons. The OEC is buried within photosystem II (PSII), a multisubunit integral membrane protein complex, and water must find its way to the Mn4Ca cluster by moving through protein. Molecular dynamics simulations were used to determine the energetic barriers for water permeation though PSII extrinsic proteins. Potentials of mean force (PMFs) for water were derived by using the technique of multiple steered molecular dynamics (MSMD). Calculation of free energy profiles for water permeation allowed us to characterize previously identified water channels, and discover new pathways for water movement toward the Mn4Ca cluster. Our results identify the main constriction sites in these pathways which may serve as selectivity filters that restrict both the access of solutes detrimental to the water oxidation reaction and loss of Ca2+ and Cl- from the active site. (C) 2012 Elsevier B.V. All rights reserved.
