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Water and Oxygen Diffusion Pathways Within Photosystem II. Computational Studies of Controlled Substrate Access and Product Release

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The Biophysics of Photosynthesis

Part of the book series: Biophysics for the Life Sciences ((BIOPHYS,volume 11))

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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.

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Authors and Affiliations

  1. Department of Biology, Brock University, 500 Glenridge Ave., St. Catharines, ON, Canada, L2S 3A1

    Serguei Vassiliev Ph.D. & Doug Bruce Ph.D.

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  1. Serguei Vassiliev Ph.D.
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  2. Doug Bruce Ph.D.
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Correspondence to Serguei Vassiliev Ph.D. .

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Editors and Affiliations

  1. Dept of Biochemistry & Molecular Biology, Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA

    John Golbeck

  2. Dept of Chemistry, Brock University, St. Catharines, Ontario, Canada

    Art van der Est

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Vassiliev, S., Bruce, D. (2014). Water and Oxygen Diffusion Pathways Within Photosystem II. Computational Studies of Controlled Substrate Access and Product Release. In: Golbeck, J., van der Est, A. (eds) The Biophysics of Photosynthesis. Biophysics for the Life Sciences, vol 11. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-1148-6_12

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