Paper Citing NAMD - Abstract
Zaraiskaya, Tatiana; Vassiliev, Sergey; Bruce, Doug
Discovering oxygen channel topology in photosystem II using implicit ligand sampling and wavefront propagation
JOURNAL OF COMPUTATIONAL SCIENCE, 5:549-555, MAY 2014
Photosystem II (PSII) of photosynthesis uses water as substrate for its photochemical reaction. Molecular oxygen is one of the products of this complex reaction which uses the energy of light to oxidize water and reduce plastoquinone. The active site of PSII is buried deep within the protein, which raises the question of whether there are specific access channels guiding substrate water to the site of catalysis and product oxygen away from it. Substrate/product channels have been proposed to exist and serve various functions in PSI!, however the preferred paths have not been unambiguously identified. We investigated oxygen transport between the active site of PSII and the solvent. For this purpose, we have applied molecular dynamics simulations followed by implicit ligand sampling. We then found minimal cost pathways for the oxygen through the protein and obtained topology maps of the oxygen-accessible part of a chemical labyrinth. Application of this new strategy led to identification of two oxygen channels in the protein. Both channels connect the protein surface with region of high oxygen affinity near the active site. (c) 2013 Elsevier B.V. All rights reserved.
