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Continuum Electrostatic Analysis of Proteins

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Protein Modelling

Abstract

Electrostatic interactions play an important role in many biochemical processes. The continuum electrostatics model, which originates from the Poisson-Boltzmann equation, provides a framework to represent the electrostatics properties of proteins together with their ligands and how these properties are influenced by the solvent; all this with limited computational costs. Therefore, methods based on continuum electrostatics are ideal to analyze bio-molecular processes in their own environment. In this review, first we illustrate the physical basis of the Poisson-Boltzmann equation, then we discuss the strategy to obtain its solution, i.e. the electrostatic potential, and which information can be deducted from it. Afterwards, we report how methods based on continuum electrostatics can be applied to analyze the interactions of proteins, in particular electron transfer proteins, and to calculate the probabilities of protonation and redox states of proteins. Furthermore, we outline how continuum electrostatics allows to access also the non-equilibrium behavior of bio-molecular systems.

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Acknowledgments

This work was supported by the DFG Grants UL 174/8 and BO 3578/1.

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Authors and Affiliations

  1. Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, NW I, 95447, Bayreuth, Germany

    G. Matthias Ullmann

  2. Experimental Physics IV, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany

    Elisa Bombarda

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  1. G. Matthias Ullmann
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  2. Elisa Bombarda
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Correspondence to G. Matthias Ullmann .

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Editors and Affiliations

  1. Chemistry Department, Eotvos Lorand University, Budapest, Hungary

    Gábor Náray-Szabó

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Ullmann, G.M., Bombarda, E. (2014). Continuum Electrostatic Analysis of Proteins. In: Náray-Szabó, G. (eds) Protein Modelling. Springer, Cham. https://doi.org/10.1007/978-3-319-09976-7_6

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