%0 Journal Article
%T Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins
%A B. Scott Perrin Jr
%A Benjamin T. Miller
%A Bernard R. Brooks
%A H. Lee Woodcock
%A Toshiko Ichiye
%A Vinushka Schalk
%J -
%D 2014
%R 10.1371/journal.pcbi.1003739
%X A module for fast determination of reduction potentials, E¡ã, 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¡ã, 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¡ã. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E¡ã is identified, and the E¡ã 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¡ã for mutagenesis
%K Oxidation-reduction reactions
%K Point mutation
%K Protein structure
%K Free energy
%K Histidine
%K Density functional theory
%K Oxidation states
%K Protein structure databases
%U https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003739