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Theoretical Investigations on Azotobacter vinelandii Ferredoxin I: Effects of Electron Transfer on Protein Dynamics

Markus Meuwly ^*  and Martin Karplus  

^* Department of Chemistry, University of Basel, Basel, Switzerland; Institut de Science et d'Ingénierie Supramoléculaires, Strasbourg, France; and Department of Chemistry and Biological Chemistry, Harvard University, Cambridge, Massachusetts

Correspondence: Address reprint requests to Markus Meuwly, Dept. of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland. Tel.: 41-61-267-3821; E-mail: m.meuwly{at}unibas.ch. or Martin Karplus, Dept. of Chemistry and Biological Chemistry, Harvard University, 2 Oxford St., Cambridge MA 02138. E-mail: marci{at}tammy.harvard.edu.

Structural, energetic, and dynamical studies of Azotobacter vinelandii ferredoxin I are presented for native and mutant forms. The protein contains two iron-sulfur clusters, one of which ([3Fe-4S]) is believed to play a central role in the electron-coupled proton transfer. Different charge sets for the [3Fe-4S] cluster in its reduced and oxidized state are calculated with broken symmetry ab initio density functional theory methods and used in molecular dynamics (MD) simulations. The validity of the ab initio calculations is assessed by comparing partially optimized structures of the [3Fe-4S] clusters with x-ray structures. Possible proton transfer pathways between the protein and the iron-sulfur cluster are examined by both MD simulations and ab initio calculations. The MD simulations identify three main-chain hydrogen atoms—HN(13), HN(14), and HN(16)—that are within H-bonding distance of the [3Fe-4S] cluster throughout the MD simulations. They could thus play a role in the proton transfer from the protein to the iron-sulfur cluster. By contrast, the HD2(15) atom of the Asp-15 is seldom close enough to the [3Fe-4S] cluster to transfer a proton. Poisson-Boltzmann calculations indicate that there is a low, but nonzero probability, that Asp-15 is protonated at pH 7; this is a requirement for it to serve as a proton donor. Ab initio calculations with a fragment model for the protein find similar behavior for the transfer of a proton from the OH of the protonated side chain and the main-chain NH of Asp-15. The existence of a stable salt bridge between Asp-15 and Lys-84 in the D15E mutant, versus its absence in the wild-type, has been suggested as the cause of the difference in the rate of proton transfer. Extensive MD simulations were done to test this idea; the results do not support the proposal. The present findings, together with the available data, serve as the basis for an alternative proposal for the mechanism of the coupled electron-proton transfer reaction in ferredoxin I.

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