Computational Biology, Electron Transport, Internet, Oxidation-Reduction, Proteins, Thermodynamics
Digital Object Identifier (DOI)
A module for fast determination of reduction potentials, E°, 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 E°, 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 E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° 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 E° for mutagenesis.
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Citation / Publisher Attribution
PLoS Computational Biology, v. 10, issue 7, art. e1003739
Scholar Commons Citation
Perrin, B. Scott Jr.; Miller, Benjamin T; Schalk, Vinushka; Woodcock, H. Lee III; Brooks, Bernard R.; and Ichiye, Toshiko, "Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins" (2014). Chemistry Faculty Publications. 12.