| Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition. | |
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MedLine Citation:
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PMID: 17325017 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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 A. 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. |
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Authors:
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Tiffany E Weksberg; Gillian C Lynch; Kurt L Krause; B Montgomery Pettitt |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. Date: 2007-02-26 |
Journal Detail:
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Title: Biophysical journal Volume: 92 ISSN: 0006-3495 ISO Abbreviation: Biophys. J. Publication Date: 2007 May |
Date Detail:
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Created Date: 2007-04-20 Completed Date: 2007-06-27 Revised Date: 2011-05-02 |
Medline Journal Info:
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Nlm Unique ID: 0370626 Medline TA: Biophys J Country: United States |
Other Details:
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Languages: eng Pagination: 3337-45 Citation Subset: IM |
Affiliation:
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Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Animals Computer Simulation Ferredoxins / chemistry* Metronidazole / chemistry* Models, Chemical* Models, Molecular* Molecular Conformation Oxidation-Reduction Porosity Solvents / chemistry Trichomonas vaginalis / metabolism* |
| Grant Support | |
ID/Acronym/Agency:
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5T15LM07093/LM/NLM NIH HHS; R01 GM037657-15/GM/NIGMS NIH HHS; R01 GM037657-15S1/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Ferredoxins; 0/Solvents; 443-48-1/Metronidazole |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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