Photosynthesis Research

, 98:503

Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems

REVIEW

DOI: 10.1007/s11120-008-9358-2

Cite this article as:
Ho, F.M. Photosynth Res (2008) 98: 503. doi:10.1007/s11120-008-9358-2

Abstract

Even prior to the publication of the crystal structures for photosystem II (PSII), it had already been suggested that water, O2 and H+ channels exist in PSII to achieve directed transport of these molecules, and to avoid undesirable side reactions. Computational efforts to uncover these channels and investigate their properties are still at early stages, and have so far only been based on the static PSII structure. The rationale behind the proposals for such channels and the computer modelling studies thus far are reviewed here. The need to take the dynamic protein into account is then highlighted with reference to the specific issues and techniques applicable to the simulation of each of the three channels. In particular, lessons are drawn from simulation studies on other protein systems containing similar channels.

Keywords

Photosystem II Molecular dynamics Channels Substrate water access H+ exit pathway O2 exit pathway 

Abbreviations

ACh

Acetylcholine

AChE

Acetylcholinesterase

ASM

Adiabatic simulation method

ATP

Adenosine triphosphate

bR

Bacteriorhodopsin

CcO

Cytochrome c oxidase

DFT

Density functional theory

ESEEM

Electron spin echo modulation

EXAFS

Extended X-ray absorption fine structure; envelope

ILS

Implicit ligand sampling

LES

Locally enhanced sampling

MC

Monte Carlo

MD

Molecular dynamics

MM

Molecular mechanics

MS-EVB

Multi-state empirical valence band

PDB ID

Protein data bank identification code

PSII

Photosystem II

QM

Quantum mechanics

YZ

Tyrosine 161 on the D1 subunit of PSII

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of Photochemistry and Molecular Science, The Ångström LaboratoryUppsala UniversityUppsalaSweden

Personalised recommendations