Education

Ph.D. Chemistry, Duke University

M.S. Chemistry, Southern Methodist University

B.S. Chemistry, Texas Christian University

Group Members

-UT/ORNL Postdoc

-Zhongyu Mou

-ORNL Postdoc

-Connor Cooper

-NSF GRFP Fellow

-Ph.D. students, UTK

Publications

• • Environmental mercury chemistry – In silico. A.M. Asaduzzaman, D. Riccardi, A.T. Afaneh, J.C. Smith, F. Wang, J.M. Parks and G. Schreckenbach. Acc. Chem. Res., 2019, In press.
  • Identification of Binding Sites for Efflux Pump Inhibitors of the Escherichia coli AcrAB-TolC component AcrA. Darzynkiewicz, Z.M., Abdali, N., Green, A.T., Hazel, A.T., Fulton, R.L., Gryczynski, Z., Gumbart, J.C., Parks, J.M., Smith, J.C., and Zgurskaya, H.I. Biophys. J. 2019, In press.
  • Quantum chemical approaches for calculating stability constants of mercury complexes. ACS Earth Space Chem., 2018, 2, 1168-1178.
  • Distribution of mechanical stress in the Escherichia coli cell envelope. H. Hwang, N. Paracini, J.M. Parks, J.H. Lakey and J.C. Gumbart. Biochim. Biophys. Acta Biomembr., 2018, 1860, 2566-2575.
  • Quantitative proteomic analysis of biological processes and responses of the bacterium Desulfovibrio desulfuricans ND132 upon deletion of its mercury methylation genes. Proteomics, 2018, 18, 1700479.
  • Molecular properties that define the activities of antibiotics in Escherichia coli and Pseudomonas aeruginosa. S.J. Cooper, G. Krishnamoorthy, D. Wolloscheck, J. Nguyen, J.K. Walker, V. Rybenkov, J.M. Parks, and H.I. Zgurskaya. ACS Infect. Dis. 2018, 4, 1223-1234.
  • Hyperconjugation promotes catalysis in a pyridoxal 5′-phosphate-dependent enzyme. S. Dajnowicz, J.M. Parks, X. Hu, R.C. Johnston, A. Kovalevsky, and T.C. Mueser. ACS Catal. 2018, 8, 6733-6737.
  • Quantum chemical calculation of pKas of environmentally relevant functional groups: Carboxylic acids, amines, and thiols in aqueous solution. P. Lian, R.C. Johnston, J.M. Parks and J.C. Smith.  J. Phys. Chem. A. 2018, 122, 4366–4374.
  • Methylmercury speciation and dimethylmercury production in sulfidic solutions C.R. Kanzler, P. Lian, E.L. Trainer, X. Yang, N. Govind, J.M. Parks and A.M. Graham. Environ. Sci. Processes Impacts, 2018, 20, 584-594.
  • Impact of hydration and temperature history on the structure and dynamics of lignin. D. Vural, C. Gainaru, H. O’Neill, Y. Pu, M.D. Smith, J.M. Parks, S.V. Pingali, E. Mamontov, B. Davison, A. Sokolov, A. Ragauskas, J.C. Smith and L. Petridis. Green Chem. 2018. 20, 1602-1611.
  • Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis. C.M. Goins, S. Dajnowicz, M.D. Smith, J.M. Parks and D.R. Ronning. J. Biol. Chem. 2018. 293, 3651-3662.
  • Substrate binding induces conformational changes in a class A beta-lactamase that prime it for catalysis. P.S. Langan, V.G. Vandavasi, S.J. Cooper, K.L. Weiss, S.L. Ginell, J.M. Parks and L. Coates. ACS Catal. 2018, 8, 2428-2437.
  • Development of CHARMM-compatible force field parameters for cobalamin and related cofactors from quantum mechanical calculations. A. Pavlova, J.M. Parks and J.C. Gumbart. J. Chem. Theory Comput. 2018, 14, 784-798.
  • Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme. S. Dajnowicz, R.C. Johnston, J.M. Parks, M.P. Blakeley, D.A. Keen, K.L. Weiss, O. Gerlits, A. Kovalevsky and T.C. Mueser. Nat. Commun. 2017, 8, 955.
  • Toward the rational design of macrolide antibiotics to combat resistance. A. Pavlova, J.M. Parks, A. Oyelere and J.C. Gumbart, Chem. Biol. Drug Des. 2017, 90, 641-652.
  • Modeling of the passive permeability of mercury and methylmercury complexes through a bacterial cytoplasmic membrane. J. Zhou, M.D. Smith, S.J. Cooper, X. Cheng, J.C. Smith and J.M. Parks. Environ. Sci. Technol. 2017, 51, 10595–10604.
  • Identification and structure-activity relationships of novel compounds that potentiate the effects of novobiocin in Escherichia coli. K.M. Haynes, N. Abdali, V. Jhawar, H.I. Zgurskaya, J.M. Parks, A.T. Green, J. Baudry, V. Rybenkov, J.C. Smith and J.K. Walker. J. Med. Chem. 2017, 60, 6205-6219.
  • Exploring covalent allosteric inhibition of antigen 85C from Mycobacterium tuberculosis by ebselen derivatives. C. Goins, S. Dajnowicz, S. Thanna, S.J. Sucheck, J.M. Parks and D.R. Ronning, ACS Infect. Dis. 2017, 3, 378-387.
  • Direct evidence that an extended hydrogen bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase. S. Dajnowicz, J.M. Parks, X. Hu, K. Gesler, A.Y. Kovalevsky and T.C. Mueser, J. Biol. Chem. 2017, 292, 5970-5980.
  • Identification of mercury and dissolved organic matter complexes using ultrahigh-resolution mass spectrometry. H. Chen, R.C. Johnston, B.F. Mann, R.K. Chu, N. Tolic, J.M. Parks and B. Gu., Environ. Sci. Technol. Lett. 2017, 4, 59-65.
  • Reviving antibiotics: Efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump. N. Abdali, J.M. Parks, K.M. Haynes, J.L. Chaney, A.T. Green, D. Wolloscheck, J.K. Walker, V.V. Rybenkov, J. Baudry, J.C. Smith and H.I. Zgurskaya. ACS Infect. Dis. 2017, 3, 89-98.
• • Active-site protonation states in an acyl-enzyme intermediate of a Class A beta-lactamase with a monobactam substrate. V. Vandavasi, K. Weiss, J.M. Parks, J.B. Cooper, S.B. Ginell and L. Coates, Antimicrob. Agents Chemother. 2017, 61, e01636-16.
  • Toward quantitatively accurate calculation of the redox-associated acid-base and ligand-binding equilibria of aquacobalamin. R.C. Johnston, J. Zhou, J.C. Smith and J.M. Parks, J. Phys. Chem. B. 2016, 120, 7307-7318.
  • Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site. O. Gerlits, T. Wymore, A. Das, C.-H. Shen, J.M. Parks, J.C. Smith, K. Weiss, D.A. Keen, M.P. Blakeley, J.M. Louis, P. Langan, I. Weber and A. Kovalevsky, Angew. Chem. Int. Ed. 2016, 218, 5008-5011.
  • Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation. A. Das, O. Gerlits, J.M. Parks, P. Langan, A. Kovalevsky and W.T. Heller, Structure. 2015, 23, 2331-2340.
  • Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Q. Wan, J.M. Parks, B.L. Hanson, Z. Fisher, A. Ostermann, T.E. Schrader, D.E. Graham, L. Coates, P. Langan and A. Kovalevsky, Proc. Nat. Acad. Sci., 2015, 112, 12384-12389.
  • HackaMol: An object-oriented Modern Perl library for molecular hacking on multiple scales. D. Riccardi, J.M. Parks, A. Johs and J.C. Smith, J. Chem. Inf. Model. 2015, 55, 721-726.
  • Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation. S. D. Smith, R. Bridou, A. Johs, J. M. Parks, D. A. Elias, R. A. Hurt Jr., S. D. Brown, M. Podar and J. D. Wall., Appl. Environ. Microbiol. 2015, 81, 3205-3217.
  • X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and QM/MM study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. P. Lian, H.-B. Guo, D. Riccardi, A. Dong, J.M. Parks, Q. Xu, E. Pai,  S.M. Miller, D.-Q. Wei, J.C. Smith and H. Guo, Biochemistry 2014, 53, 7211-7222.
  • L-arabinose binding, isomerization and epimerization by D-xylose isomerase: A combined X-ray/neutron crystallographic and molecular simulation study. P. Langan, A.K. Sangha, T. Wymore, J.M. Parks, Z.-K. Yang, B.L. Hanson, Z. Fisher, S. Mason, M.P. Blakeley, T. Forsyth, J.P. Glusker, H.L. Carroll, J.C. Smith, D.A. Keen, D.E. Graham and A. Kovalevsky, Structure 2014, 22, 1-14.
  • Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. L. Hong, M.A. Sharp, S. Poblete, R. Biehl, M. Zamponi, N. Szekely, M.-S. Appavou, R.G. Winkler, R. Nauss, A. Johs, J.M. Parks, Z. Yi, X. Cheng, L. Liang, M. Ohl, S.M. Miller, D. Richter, G. Gompper and J.C. Smith, Biophys. J. 2014, 107, 393-400.
  • Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: Implications for engineering bioscavengers. T. Wymore, M.J. Field, P. Langan, J.C. Smith and J.M. Parks, J. Phys. Chem. B, 2014, 118, 4479-4489.
  • Unexpected effects of gene deletion on mercury interactions with the methylation-deficient mutant ΔhgcAB. H. 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, 1, 271-276.
  • 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 ligands. D. 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 methylation J.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 analogs. R. 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 cations. D. 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 study. A. 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 sulfur. B. J. Mintz and J. M. Parks, J. Phys. Chem. A, 2012, 116, 1086-1092.
  • Molecular simulation as a tool for studying lignin. A. K. Sangha, L. Petridis, J. C. Smith, A. Ziebell and J. M. Parks, Environmental Progress and Sustainable Energy, 2012, 31, 47-54.
  • Structural characterization of intramolecular Hg2+ transfer between flexibly linked domains of mercuric ion reductase. A. 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 thermocellum. S. 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 MerB. J. 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 calculations. J. 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 enzymes. J. 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 binding. J. 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 surface. H. 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 substrate J. Sohn, J. M. Parks, G. Buhrman, P. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, W.T. Yang, and J. Rudolph, Biochemistry, 2005, 44, 16563-16573.
  • Quantum chemical characterization of the reactions of the phenylnitrenium ion with guanine. J. M. Parks, G. P. Ford and C. J. Cramer, J. Org. Chem., 2001, 66, 8997-9004.

  Book Chapters

  • Modeling Mercury in Proteins. J.M. Parks and J.C. Smith, Methods in Enzymology, Vol. 578, Computational Approaches for Studying Enzyme Mechanism, 2016, 103-122. G.A. Voth, Editor, Elsevier, B.V. 
  • Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion. B. H. Davison, J. M. Parks, M. F. Davis and B. S. Donohoe, in Aqueous Pretreatment of Plant Biomass for Biological and Chemical Conversion to Fuels and Chemicals, 2013, ed. C. Wyman, John Wiley & Sons, Ltd.

  • Mercury detoxification by bacteria: Simulations of transcription activation and mercury-carbon bond cleavage. H.-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 simulation. J. M. Parks, P. Imhof, and J. C. Smith. Encyclopedia of Catalysis, 2nd Edition, 2010.