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Calculations of Electrostatic Energies in Proteins Using Microscopic, Semimicroscopic and Macroscopic Models and Free-Energy Perturbation Approaches

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Book cover Biophysical Techniques in Photosynthesis

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 26))

This chapter discusses computer models for evaluating electrostatic interactions in proteins, with emphasis on calculations of the free energies of electron-transfer states in photosynthetic bacterial reaction centers. We describe the microscopic Protein Dipoles Langevin Dipoles (PDLD) method, semimicroscopic approaches including the Poisson-Boltzmann, PDLD/S and Generalized Born models, a macroscopic model with a homogeneous dielectric medium, and microscopic free-energy-perturbation methods based on molecular dynamics simulations. We also describe the use of molecular dynamics simulations to obtain free energy surfaces of the reactant and product states as functions of the reaction coordinate for electron transfer.

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Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Washington, 357350, 98195-7350, Seattle, WA, USA

    William W. Parson

  2. Department of Chemistry, University of Southern California, 90007, Los Angeles, CA, USA

    Arieh Warshel

Authors
  1. William W. Parson
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  2. Arieh Warshel
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Editors and Affiliations

  1. Leiden University, 9504, 2300 RA, Leiden, Netherlands

    Thijs J. Aartsma  & Jörg Matysik  & 

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Parson, W.W., Warshel, A. (2008). Calculations of Electrostatic Energies in Proteins Using Microscopic, Semimicroscopic and Macroscopic Models and Free-Energy Perturbation Approaches. In: Aartsma, T.J., Matysik, J. (eds) Biophysical Techniques in Photosynthesis. Advances in Photosynthesis and Respiration, vol 26. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8250-4_20

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