Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins

Authors

• B. Scott Perrin Jr., Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health
• Benjamin T Miller, Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health
• Vinushka Schalk, New College of Florida
• H. Lee Woodcock III, University of South FloridaFollow
• Bernard R. Brooks, Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health
• Toshiko Ichiye, Georgetown University

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, 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.

Rights Information

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

Was this content written or created while at USF?

Yes

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.
https://digitalcommons.usf.edu/chm_facpub/12