NDLI: Protein Control of Electron Transfer Rates via Polarization: Molecular Dynamics Studies of Rubredoxin

Content Provider	PubMed Central
Author	Dolan, Elizabeth A. Yelle, Robert B. Beck, Brian W. Fischer, Justin T. Ichiye, Toshiko
Copyright Year	2004
Abstract	The protein matrix of an electron transfer protein creates an electrostatic environment for its redox site, which influences its electron transfer properties. Our studies of Fe-S proteins indicate that the protein is highly polarized around the redox site. Here, measures of deviations of the environmental electrostatic potential from a simple linear dielectric polarization response to the magnitude of the charge are proposed. In addition, a decomposition of the potential is proposed here to describe the apparent deviations from linearity, in which it is divided into a “permanent” component that is independent of the redox site charge and a dielectric component that linearly responds or polarizes to the charge. The nonlinearity measures and the decomposition were calculated for Clostridium pasteurianum rubredoxin from molecular dynamics simulations. The potential in rubredoxin is greater than expected from linear response theory, which implies it is a better electron acceptor than a redox site analog in a solvent with a dielectric constant equivalent to that of the protein. In addition, the potential in rubredoxin is described well by a permanent potential plus a linear response component. This permanent potential allows the protein matrix to create a favorable driving force with a low activation barrier for accepting electrons. The results here also suggest that the reduction potential of rubredoxin is determined mainly by the backbone and not the side chains, and that the redox site charge of rubredoxin may help to direct its folding.
Related Links	http://dx.doi.org/10.1016/s0006-3495(04)74264-2
Ending Page	2036
Page Count	7
Starting Page	2030
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	4
Volume Number	86
Language	English
Publisher	Biophysical Society
Publisher Date	2004-04-01
Access Restriction	Open
Rights Holder	Biophysical Society
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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