Document Type

Article

Publication Date

7-24-2014

Keywords

Computational Biology, Electron Transport, Internet, Oxidation-Reduction, Proteins, Thermodynamics

Digital Object Identifier (DOI)

http://dx.doi.org/10.1371/journal.pcbi.1003739

Abstract

A module for fast determination of reduction potentials, , of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to , is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of . In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent is identified, and the of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of for mutagenesis.

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This work is licensed under a Creative Commons Attribution 3.0 License.

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Citation / Publisher Attribution

PLoS Computational Biology, v. 10, issue 7, art. e1003739

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