Title |
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins
|
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Published in |
PLoS Computational Biology, July 2014
|
DOI | 10.1371/journal.pcbi.1003739 |
Pubmed ID | |
Authors |
B. Scott Perrin, Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock, Bernard R. Brooks, Toshiko Ichiye |
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. |
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United States | 1 | 33% |
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Demographic breakdown
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Members of the public | 1 | 33% |
Mendeley readers
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Unknown | 5 | 9% |
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Medicine and Dentistry | 2 | 4% |
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