title: Investigating the mechanisms of photosynthetic proteins using continuum electrostatics.
abstract: Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.
authors.affiliation: Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, Bayreuth 95447, Germany. Matthias.Ullmann@uni-bayreuth.de
authors.forename: G Matthias
authors.initials: GM
authors.lastname: Ullmann
authors.forename: Edda
authors.initials: E
authors.lastname: Kloppmann
authors.forename: Timm
authors.initials: T
authors.lastname: Essigke
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Krammer
authors.forename: Astrid R
authors.initials: AR
authors.lastname: Klingen
authors.forename: Torsten
authors.initials: T
authors.lastname: Becker
authors.forename: Elisa
authors.initials: E
authors.lastname: Bombarda
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D008958:Models, Molecular; D010788:Photosynthesis; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D011506:Proteins