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Molecular Dynamics Simulations of Trichomonas vaginalis Ferredoxin Show a Loop-Cap Transition

Tiffany E. Weksberg ^*, Gillian C. Lynch , Kurt L. Krause    and B. Montgomery Pettitt ^* 

^* Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030; Department of Chemistry and Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77004; and Department of Biochemistry, University of Otago, Dunedin, New Zealand 9001

Correspondence: Address reprint requests to B. Montgomery Pettitt, E-mail: pettitt{at}uh.edu.

The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2 Å. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.