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Jerry M. Parks
Research Scientist
Oak Ridge National LaboratoryP.O. Box 2008
1 Bethel Valley Road
Building 6011, MS-6309
Oak Ridge , TN 37831-6309
Education:
- Ph.D. Chemistry, Duke University
- M.S. Chemistry, Southern Methodist University
- B.S. Chemistry, Texas Christian University
Biography:
Research Interests
- Bioinorganic chemistry of mercury
- Enzyme mechanisms and biochemical pathways
- Bioenergy
- Nerve agent detoxification by catalytic bioscavengers
Click herefor a list of confirmed and predicted mercury methylating bacteria and archaea.
Journal Publications
- Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC-MS/MS Data, C. McClintock, J. M. Parks, M. Bern, P. K. Ghattyvenkatakrishna, R. L. Hettich, In revision.
- The genetic basis for bacterial mercury methylationJ.M. Parks, A. Johs, M. Podar, R. Bridou, R.A. Hurt Jr., S.D. Smith, S.J. Tomanicek, Y. Qian, S.D. Brown, C.C. Brandt, A.V. Palumbo, J.C. Smith, J.D. Wall, D.A. Elias and L. Liang, Science, 2013, 339, 1332-1335.
- Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogsR. Chaudret, J. M. Parks and W. T. Yang, J. Chem. Phys., 2013, 138, 045102.
- Cluster-continuum calculations of hydration free energies of anions and group 12 divalent cationsD. Riccardi, H.-B. Guo, J. M. Parks, B. Gu, L. Liang, and J. C. Smith, J. Chem. Theory Comput. 2013, 9, 555–569.
- Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog T. Tschaplinski et al., Biotechnol. Biofuels, 2012, 5:71.
- Radical coupling reactions in lignin synthesis: A density functional theory studyA. K. Sangha, J. M. Parks, R. F. Standaert, A. Ziebell, M. Davis, and J. C. Smith, J. Phys. Chem. B, 2012, 116, 4760–4768
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Benchmark interaction energies for biologically relevant non-covalent complexes containing divalent sulfurB. J. Mintz and J. M. Parks, J. Phys. Chem. A, 2012, 116, 1086-1092.
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Structural characterization of intramolecular Hg2+ transfer between flexibly-linked domains of mercuric ion reductaseA. Johs, I. M. Harwood, J. M. Parks, R. Nauss, J. C. Smith, L. Liang, and S. M. Miller, J. Mol. Biol. 2011, 413, 639-656.
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Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellumS. D. Brown, A. D. Guss, T. V. Karpinets, J. M. Parks, N. Smolin, S. Yang, M. L. Land, D. M. Klingeman, A. Bhandiwad, M. Rodriguez Jr., B. Raman, X. Shao, J. R. Mielenz, J. C. Smith, M. Keller and L. R. Lynd., Proc. Nat. Acad. Sci., 2011, 108, 13752-13757.
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Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II)H.-B. Guo, A. Johs, J. M. Parks, L. Olliff, S. M. Miller, A. O. Summers, L. Liang, and J. C. Smith. J. Mol. Biol. 2010, 398, 555-568.
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Mechanism of Hg-C protonolysis in the bacterial organomercurial lyase MerBJ. M. Parks, H. Guo, C. Momany, L. Liang, S. M. Miller, A. O. Summers, and J. C. Smith, J. Am. Chem. Soc., 2009, 131, 13278-13285.
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Mechanism of Cdc25b phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculationsJ. M. Parks, H. Hu, J. Rudolph, and W.T. Yang, J. Phys. Chem. B, 2009, 113 (15), 5217-5224.
- A pseudobond parameterization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymesJ. M. Parks, H. Hu, A. J. Cohen and W.T. Yang, J. Chem. Phys., 2008, 129, 154106.
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Hepatitis C virus NS5b polymerase: QM/MM calculations show the important roles of the internal energy in ligand bindingJ. M. Parks, R. K. Kondru, H. Hu, D. N. Beratan, and W.T. Yang, J. Phys. Chem. B, 2008, 112 (10), 3168-3176.
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QM/MM Minimum Free Energy Path for accurate reaction energetics in solution and enzymes: Iterative optimization on the potential of mean force surfaceH. Hu, Z.Y. Lu, J. M. Parks, S. K. Burger, W.T. Yang, J. Chem. Phys., 2008, 128, 034105.
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Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrateJ. Sohn, J. M. Parks, G. Buhrman, P. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, W.T. Yang, and J. Rudolph, Biochem., 2005, 44, 16563-16573.
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Quantum chemical characterization of the reactions of the phenylnitrenium ion with guanineJ. M. Parks, G. P. Ford and C. J. Cramer, J. Org. Chem., 2001, 66, 8997-9004.
- Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on ConversionB. H. Davison, J. M. Parks, M. F. Davis and B. S. Donohoe, 2013, in Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, ed. C. Wyman John Wiley & Sons, Ltd.
- Molecular simulation as a tool for studying ligninA. K. Sangha, L. Petridis, J. C. Smith, A. Ziebell and J. M. Parks, Environmental Progress and Sustainable Energy, 2012, 31, 47-54.
- Mercury detoxification by bacteria: Simulations of transcription
activation and mercury-carbon bond cleavageH.-B. Guo, J.M. Parks, A.
Johs, and J.C. Smith, 2011, in Modeling of Molecular Properties (ed. P. Comba, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
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Understanding enzyme catalysis using computer simulationJ. M. Parks, P. Imhof, and J. C. Smith. Encyclopedia of Catalysis, 2nd Edition, 2010.
