Water and oxygen diffusion pathways within photosystem II. Computational studies of controlled substrate access and product release

Abstract

The problem of finding and characterizing channels responsible for controlling the movement of small molecules within protein complexes is addressed, using photosystem II (PSII) of photosynthesis as an example. The shortcomings of traditional methods of searching for channels in static crystallographic structures are discussed. Basic concepts and advantages of molecular dynamics (MD) simulations and existing computational approaches based on MD structures to finding water channels are introduced. The use of MD to observe water diffusion within proteins, visualize water flow, and localize water channels is described. This is followed by more detailed characterization and analysis of the found channels, with respect to their permitivity for water. The second part of the chapter focuses on oxygen channels within PSII. The experimental and computational techniques for characterization of oxygen channels in proteins are reviewed. A powerful computational technique, based on analysis of 3D energy maps, is introduced. The construction of oxygen 3D free energy maps for PSII and their analysis using a wavefront propagation technique is described to find oxygen diffusion pathways and characterize the rate of oxygen diffusion within PSII.