Jerry M Parks

Jerry M Parks

R & D Staff Scientist

Bio

Education

Ph.D. Chemistry, Duke University

M.S. Chemistry, Southern Methodist University

B.S. Chemistry, Texas Christian University

Awards

2013     ORNL Director’s Award for Outstanding Team Accomplishment

2013     UT-Battelle Team Award for Scientific Research

2013     ORNL Significant Event Award

Publications

P.S. Langan, V.G. Vandavasi, S.J. Cooper, K.L. Weiss, S.L. Ginell, J.M. Parks, and L. Coates. Substrate Binding Induces Conformational Changes in a Class A β-lactamase that Prime it for Catalysis. ACS Catal. 2018. In press.

Goins, C.M., Dajnowicz, S., Parks, J.M. and Ronning, D.R. Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into Antigen 85 catalysis. J. Biol. Chem. 2018. In press.

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. In press.

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. In press.

Pavlova, A., Parks, J.M., Oyelere, A.K. and Gumbart, J.C. Toward the Rational Design of Macrolide Antibiotics to Combat Resistance. Chem. Biol. Drug Des. 2017, 90, 641-652.

Dajnowicz, S., Johnston, R.C., Parks, J.M., Blakeley, M.P., Keen, D.A., Weiss, K.L., Gerlits, O., Kovalevsky, A. and Mueser, T.C. Direct Visualization of Critical Hydrogen Atoms in a Pyridoxal 5’-Phosphate Enzyme. Nat. Commun. 2017, 8, 955.

Zhou, J., Smith, M.D., Cooper, S.J., Cheng, X., Smith, J.C. and Parks, J.M. Passive Permeability of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane. Environ. Sci. Technol. 2017, 51, 10595–10604.

Haynes, K.M., Abdali, N., Jhawar, V., Zgurskaya, H.I., Parks, J.M., Green, A.T., Baudry, J., Rybenkov, V., Smith, J.C. and Walker, J.K. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. J. Med. Chem. 2017, 60, 6205−6219.

Goins, C.M., Dajnowicz, S., Thanna, S., Sucheck, S.J., Parks, J.M. and Ronning, D.R. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives. ACS Infect. Dis. 2017, 3, 378–387.

Dajnowicz, S., Parks, J.M., Hu, X., Gesler, K., Kovalevsky, A.Y. and Mueser, T.C. Direct Evidence That an Extended Hydrogen Bonding Network Influences Activation of Pyridoxal 5'-Phosphate in Aspartate Aminotransferase. J. Biol. Chem. 2017, 292, 5970-5980.

Chen, H., Johnston, R.C., Mann, B.F., Chu, R.K., Tolic, N., Parks, J.M. and Gu, B. Identification of Mercury and Dissolved Organic Matter Complexes Using Ultra-high Resolution Mass Spectrometry. Environ. Sci. Technol. Lett. 20174, 59–65.

Vandavasi, V., Weiss, K., Parks, J.M. Cooper, J.B., Ginell, S.B. and Coates, L. Direct Observation of Active-site Protonation States in an Acyl-enzyme Intermediate of a Class A β-lactamase with a Monobactam Substrate. Antimicrob. Agents Chemother. 2017, 61, e01636-16.

Abdali, N., Parks, J.M., Haynes, K.M., Chaney, J.L., Green, A.T., Wolloscheck, D., Walker, J.K., Rybenkov, V.V., Baudry, J., Smith, J.C. and Zgurskaya, H.I. Reviving Antibiotics: Efflux Pump Inhibitors that Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump. ACS Infect. Dis. 2017, 3, 89–98.

Johnston, R.C., Zhou, J., Smith, J.C. and Parks, J.M. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand-Binding Equilibria of Aquacobalamin. J. Phys. Chem. B. 2016, 120, 7307−7318.

Gerlits, O., Wymore, T., Das, A., Shen, C.-H., Parks, J.M., Smith, J.C., Weiss, K., Keen, D.A., Blakeley, M.P., Louis, J.M., Langan, P., Weber, I. and Kovalevsky, A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angew. Chem. Int. Ed. 2016, 218, 5008-5011.

Das, A., Gerlits, O., Parks, J.M., Langan, P., Kovalevsky, A. and Heller, W.T. Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation. Structure, 2015, 23, 2331–2340.

Wan, Q., Parks, J.M., Hanson, B.L., Fischer, S.Z., Ostermann, A., Schrader, T.E., Graham, D.E., Coates, L., Langan, P. and Kovalevsky, A. Direct Determination of Protonation States and Visualization of Hydrogen Bonding in a Glycoside Hydrolase with Neutron Crystallography, Proc. Nat. Acad. Sci. USA, 2015, 112, 12384–12389.

Riccardi, D., Parks, J.M., Johs, A. and Smith, J.C. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales, J. Chem. Inf. Model. 2015, 55, 721–726.

Smith, S.D., Bridou, R., Johs, A., Parks, J.M., Elias, D.A., Hurt Jr., R.A., Brown, S.D., Podar, M. and Wall, J.D. Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation. Appl. Environ. Microbiol. 2015, 81, 3205–3217.

Lian, P., Guo, H.-B., Riccardi, D., Dong, A., Parks, J.M., Xu, Q., Pai, E.F., Miller, S.M., Wei, D.-Q., Smith, J.C. and Guo, H. X-ray Structure of a Hg2+ Complex of Mercuric Reductase and QM/MM study of Hg2+ Transfer Between the C-terminal and Buried Catalytic Site Cysteine Pairs. Biochemistry, 2014, 53, 7211–7222.

Langan, P., Sangha, A.K., Wymore, T., Parks, J.M., Yang, Z.-K., Hanson, B.L., Fisher, Z., Mason, S., Blakeley, M.P., Forsyth, T., Glusker, J.P., Carroll, H.L., Smith, J.C., Keen, D.A., Graham, D.E. and Kovalevsky, A. L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study, Structure, 2014, 22, 1–14.

Hong, L., Sharp, M.A., Poblete, S., Biehl, R., Zamponi, M., Szekely, N., Appavou, M.-S., Winkler, R.G., Nauss, R., Johs, A., Parks, J.M., Yi, Z., Cheng, X., Liang, L., Ohl, M., Miller, S.M., Richter, D., Gompper G. and Smith, J.C. Structure and Dynamics of a Compact State of a Multi-Domain Protein, the Mercuric Ion Reductase, Biophys. J., 2014, 107, 393–400.

Wymore, T. W., Field, M. J., Langan, P., Smith, J.C. and Parks, J.M. Hydrolysis of DFP and the Nerve Agent (S)-Sarin by DFPase Proceeds Along Two Different Reaction Pathways: Implications for Engineering Bioscavengers, J. Phys. Chem. B, 2014, 118, 4479–4489.

Lin, H., Hurt Jr., R.A., Johs, A., Parks, J.M., Liang, L., Elias, D.A. and Gu, B. Unexpected Effects of Gene Deletion on Mercury Interactions with the Methylation-Deficient Mutant ΔhgcAB, Environ. Sci. Technol. Lett., 2014, 1, 271–276.

Zhou, J., Riccardi, D., Beste, A., Smith, J.C. and Parks, J.M., Mercury Methylation by HgcA: Theory Supports Carbanion Transfer to Hg(II), Inorg. Chem. 2014, 53, 772–777. 

Sangha, A.K., Davison, B.H., Standaert, R.F., Davis, M.F., Smith, J.C. and Parks, J.M., Chemical Factors that Control Lignin Polymerization, J. Phys. Chem. B. 2014, 118, 164–170. 

Riccardi, D., Guo, H.-B., Parks, J.M., Gu, B., Summers, A.O., Miller, S.M., Liang, L. and Smith, J.C., Why Mercury Prefers Soft Ligands, J. Phys. Chem. Lett., 2013, 4, 2317−2322.

McClintock, C., Parks, J.M., Bern, M., Ghattyvenkatakrishna, P. K. and Hettich, R.L., Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC-MS/MS Data, J. Proteome Res., 2013, 12, 3307–3316.

Parks, J.M., Johs, A., Podar, M., Bridou, R., Hurt Jr., R.A., Smith, S.D., Tomanicek, S.J., Qian, Y., Brown, S.D., Brandt, C.C., Palumbo, A.V., Smith, J.C., Wall, J.D., Elias, D.A. and Liang, L., The Genetic Basis for Bacterial Mercury Methylation, Science, 2013, 339, 1332–1335.

Chaudret, R., Parks, J.M. and Yang, W.T., Pseudobond Parameters for QM/MM Studies Involving Nucleosides, Nucleotides and Their Analogs, J. Chem. Phys., 2013, 138, 045102.

Riccardi, D., Guo, H.-B., Parks, J.M., Gu, B., Liang, L. and Smith, J.C., Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations, J. Chem. Theory Comput., 2013, 9, 555–569.

Tschaplinski, T.J., Standaert, R.F., Engle, N.L., Martin, M.Z., Sangha, A.K., Parks, J.M., Smith, J.C., Samuel, R., Jiang, N., Pu, Y., Ragauskas, A.J., Hamilton, C.Y., Fu, C., Wang, Z.-Y., Davison, B.H., Dixon, R.A. and Mielenz, J.R., Down-regulation of the Caffeic Acid O-Methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog, Biotechnol. Biofuels, 2012, 5:71.

Sangha, A.K., Parks, J.M., Standaert, R.F., Ziebell, A., Davis, M.F. and Smith, J.C., Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study, J. Phys. Chem. B, 2012, 116, 4760–4768.

Mintz, B. J. and Parks, J. M., Benchmark Interaction Energies for Biologically Relevant Noncovalent Complexes Containing Divalent Sulfur, J. Phys. Chem. A., 2012, 116, 1086–1092.

Sangha, A. K.; Petridis, L.; Smith, J.C., Ziebell, A. and Parks, J. M., Molecular Simulation as a Tool for Studying Lignin, Environ. Prog. Sustain. Energy, 2012, 31, 47–54.

Johs, A., Harwood, I.M., Parks, J.M., Nauss, R. Smith, J.C., Liang, L., Miller, S.M. Structural Characterization of Intramolecular Hg2+ Transfer Between Flexibly Linked Domains of Mercuric Ion Reductase, J. Mol. Biol. 2011, 413, 639–656.

Brown, S.D., Guss, A.D., Karpinets, T.V., Parks, J.M., Smolin, N., Yang, S., Land, M.L., Klingeman, D.M., Bhandiwad, A., Rodriguez Jr., M., Raman, B., Shao, X., Mielenz, J.R., Smith, J.C., Keller, M. and Lynd, L.R., Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium thermocellum, Proc. Nat. Acad. Sci. USA, 2011, 108, 13752–13757.

Guo, H.-B., Johs, A., Parks, J.M., Olliff, L., Miller, S.M., Summers, A.O., Liang, L., and Smith, J.C., Structure and Comformational Dynamics of the Metalloregulator MerR Upon Binding of Hg(II), J. Mol. Biol., 2010, 398, 555–568.

Parks, J.M., Guo, H., Momany, C., Liang, L., Miller, S.M., Summers, A.O. and Smith, J.C., Mechanism of Hg-C Protonolysis in the Organomercurial Lyase MerB, J. Am. Chem. Soc., 2009, 131, 13278–13285.

Parks, J.M., Hu, H., Rudolph, J. and Yang, W.T., Mechanism of Cdc25b Phosphatase with the Small Molecule Substrate p-Nitrophenyl Phosphate from QM/MM-MFEP Calculations, J. Phys. Chem. B, 2009, 113, 5217–5224.

Parks, J.M., Hu, H., Cohen, A.J. and Yang, W.T., A Pseudobond Parameterization for Improved Electrostatics in Quantum Mechanical/Molecular Mechanical Simulations of Enzymes, J. Chem. Phys., 2008, 129, 154106.

Parks, J.M., Kondru, R.K., Hu, H., Beratan, D.N. and Yang, W.T., Hepatitis C Virus NS5b Polymerase: QM/MM Calculations Show the Important Roles of the Internal Energy in Ligand Binding, J. Phys. Chem. B, 2008, 112, 3168–3176.

Hu, H., Lu, Z., Parks, J.M., Burger, S.K., and Yang, W.T., QM/MM Minimum Free Energy Path for Accurate Reaction Energetics in Solution and Enzymes: Iterative Optimization on the Potential of Mean Force Surface, J. Chem. Phys., 2008, 128, 034105. 

Sohn, J., Parks, J.M., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., Edelsbrunner, H., Yang, W.T. and Rudolph, J., Experimental Validation of the Docking Orientation of Cdc25 with its Cdk2-CycA Protein Substrate, Biochemistry, 2005, 44, 16563–16573.

Parks, J.M., Ford, G.P. and Cramer, C.J., Quantum Chemical Characterization of the Reactions of the Phenylnitrenium Ion with Guanine, J. Org. Chem., 2001, 66, 8997–9004.

Patents

Mercury Methylation Genes in Bacteria and Archaea, J.M. Parks and A. Johs (U.S. Patent Application 14/132,906, filed December 2013).