- Ph.D. Chemistry, Duke University
- M.S. Chemistry, Southern Methodist University
- B.S. Chemistry, Texas Christian University
- Bioinorganic chemistry of mercury, sulfur and cobalt
- Enzyme mechanisms and biochemical pathways
Click herefor a list of confirmed and predicted mercury methylating bacteria and archaea.
- Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: Implications for engineering bioscavengersT. Wymore, M.J. Field, P. Langan, J.C. Smith and J.M. Parks, J. Phys. Chem. B, 2014, In press.
- Unexpected effects of gene deletion on mercury interactions with the methylation-deficient mutant ΔhgcABH. Lin, R.A. Hurt Jr., A. Johs, J.M. Parks, J.L. Morrell-Falvey, L. Liang, D.A. Elias and B. Gu, Environ. Sci. Technol. Lett., 2014, In press.
- Mercury methylation by HgcA: Theory supports carbanion transfer to Hg(II)J. Zhou, D. Riccardi, A. Beste, J.C. Smith and J.M. Parks, Inorg. Chem. 2014, 53, 772–777.
- Chemical factors that control lignin polymerization A.K. Sangha, B.H. Davison, R.F. Standaert, M.F. Davis, J.C. Smith and J.M. Parks, J. Phys. Chem. B., 2014, 118, 164–170.
- Why mercury prefers soft ligandsD. Riccardi, H.-B. Guo, J. M. Parks, B. Gu, A.O. Summers, S.M. Miller, L. Liang and J.C. Smith, J. Phys. Chem. Lett., 2013, 4, 2317-2322.
- 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, J. Proteome Res., 2013, 12, 3307-3316.
- 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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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, 2013, 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.
Understanding enzyme catalysis using computer simulationJ. M. Parks, P. Imhof, and J. C. Smith. Encyclopedia of Catalysis, 2nd Edition, 2010.