Paper Citing NAMD - Abstract
Vassiliev, Serguei; Comte, Pascal; Mahboob, Abdullah; Bruce, Doug
Tracking the Flow of Water through Photosystem II Using Molecular Dynamics and Streamline Tracing
BIOCHEMISTRY, 49:1873-1881, MAR 9 2010
The CaMn(4) Cluster or 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 CaMn(4) cluster by Moving through protein. Channels for water entrance, and proton and oxygen exit, have previously been proposed following the analysis Of cavities found within X-ray structures Of PSII. However, these analyses do not account for the dynamic motion of proteins and cannot track the movement of water within PSII. To study water dynamics in PSII, WC performed molecular dynamics simulations and developed it novel approach for the Visualization of water diffusion within protein based oil it streamline tracing algorithm used in fluid dynamics and diffusion tensor Imaging. We identified it system of branching pathways of water diffusion in PSII leading to the OEC that connect to it number of distinct entrance points oil the lumenal surface. We observed transient changes in the connections between channels and entrance points that Served to moderate both the now of water near the OEC and the exchange of water inside and outside of the protein. Water flow was significantly altered In simulations lacking the OEC which were characterized by I simpler and wider channel with only two openings, consistent with the creation of an ion channel that allows entry of Mn(2+), Ca(2+), and Cl(-) as required for construction of the CaMn(4) Cluster.
