title: Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.
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.
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: B Scott
authors: BS
authors: Perrin
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: Benjamin T
authors: BT
authors: Miller
authors: Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America.
authors: Vinushka
authors: V
authors: Schalk
authors: Department of Chemistry, University of South Florida, Tampa, Florida, United States of America.
authors: H Lee
authors: HL
authors: Woodcock
authors: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
authors: Bernard R
authors: BR
authors: Brooks
authors: Department of Chemistry, Georgetown University, Washington, D.C., United States of America.
authors: Toshiko
authors: T
authors: Ichiye
mesh_terms: D019295:Computational Biology / Q000193:education* / Q000379:methods*; D004579:Electron Transport; D020407:Internet; D010084:Oxidation-Reduction; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins