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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.

SUBMITTER: Perrin BS 

PROVIDER: S-EPMC4110074 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.

Perrin B Scott BS   Miller Benjamin T BT   Schalk Vinushka V   Woodcock H Lee HL   Brooks Bernard R BR   Ichiye Toshiko T  

PLoS computational biology 20140724 7


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  ...[more]

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