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Understanding Mercury Transport and Transformation by Computational Simulations University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2017 Understanding Mercury Transport and Transformation by Computational Simulations Jing Zhou University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Zhou, Jing, "Understanding Mercury Transport and Transformation by Computational Simulations. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4675 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jing Zhou entitled "Understanding Mercury Transport and Transformation by Computational Simulations." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Jeremy Smith, Major Professor We have read this dissertation and recommend its acceptance: Jerry Parks, Xiaolin Cheng, Hong Guo, Francisco Barrera Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Understanding Mercury Transport and Transformation by Computational Simulations A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jing Zhou August 2017 Copyright © 2017 by Jing Zhou All rights reserved. ii DEDICATION To my mom, dad, and Yiwen iii ACKNOWLEDGEMENTS I would like to thank my Ph.D. advisor Prof. Jeremy Smith for giving me the opportunity to come to the U.S. and carried out my research in the Center for Molecular Biophysics at the University of Tennessee and Oak Ridge National Laboratory. He provided me guidance, resources and continuous support for my work throughout the years. Next, I would like to thank Dr. Jerry Parks for teaching me every aspect to become an excellent scientist, from conducting scientific research to presenting research findings. He is always patient and willing to teach. My written and spoken English have been improved significantly because of him. Then, I would like to thank everyone in CMB who has helped me with my research, especially Dr. Xiaolin Cheng, Dr. Demian Riccardi, Dr. Barmak Mostofian, and Dr. Micholas Smith for their generosity with their time and helpful discussion during the years of my Ph.D. Finally, I would like to thank my parents Jie Zhou and Qingying Liu for their unconditional love. They always have faith in me, which give me the courage and strength to go through all the difficulties I encountered during my Ph.D. and in my life. iv ABSTRACT Mercury is a global pollutant that can be transported over long distance and bio-amplified within food chains. It has been shown that anaerobic microorganisms can produce neurotoxin methylmercury from inorganic mercury. However, the mechanisms for Hg substrates uptake and bio-transformed mercury product export are still not clear. Also, once Hg substrates are inside the cells, the enzymatic mechanisms of mercury methylation are still unknown. In this dissertation, we focused on using computational approaches to understand how microorganisms uptake and export mercury complexes and the biotransformation mechanisms of inorganic mercury to methylmercury at the molecular level. Here, we first explored the catalytic mechanism of mercury methylation enzyme HgcA using a simplified model of methylcobalamin (the cofactor of HgcA). We found that the ligand substitution of the lower-axial side of methylcobalamin by the Cys residue from HgcA indeed facilitates methyl transfer. We then developed a consistent computational approach to investigate redox potential, pKas [pKitalic_as] and Co–ligand binding equilibrium constants for cobalamins. We used this approach to study the pH-dependent redox chemistry of aquacobalamin and yielded agreement with experimental values within 90 mV [millivolts] for reduction potentials and 1.0 log units both for pKas [pKitalic_as] and log Kon/off [Kitalic_on/off]. This study built the foundation to explore the redox requirements for another mercury methylation enzyme HgcB. Finally, we tested the possibility of passive permeation of Hg complexes through a model cytoplasmic membrane using molecular dynamics simulations. We concluded that small neutral Hg complexes in this study, i.e. CH3Hg– SCH3 and CH3S–Hg–SCH3, could permeate the model membrane without the facilitation of membrane proteins. We also investigated the kinetic aspect of the permeation processes and we v predicted the permeability coefficients for the Hg-containing compounds are ~10-5 cm s-1 [centimeter per second]. Our studies here shed light on understanding the fundamental enzymatic mechanisms of mercury methylation, build the foundation for future study on the pH-dependent redox chemistry of metal-containing species, and established the future direction for studying the transport mechanisms of mercury complexes in microorganisms. vi TABLE OF CONTENTS CHAPTER 1 Introduction .............................................................................................................. 1 1.1 Physical Properties of Mercury ............................................................................................. 1 1.2 Global Mercury Cycling ....................................................................................................... 1 1.3 Abiotic and Biotic Transformation of Mercury .................................................................... 3 1.3.1 Elemental mercury oxidation ......................................................................................... 3 1.3.2 Hg(II) reduction ............................................................................................................. 3 1.3.3 Hg(II) methylation ......................................................................................................... 4 1.3.4 MeHg demethylation ..................................................................................................... 4 1.4 Mercury Resistance Operon .................................................................................................. 5 1.5 Enzymes for Mercury Methylation ....................................................................................... 6 1.6 Uptake and Export of Mercury Complexes .......................................................................... 7 CHAPTER 2 Simulation Theory and Computation ....................................................................... 9 2.1 Theory of Quantum Mechanics ............................................................................................ 9 2.1.1 Newton’s equation of motion ......................................................................................... 9 2.1.2 Schrodinger equation ................................................................................................... 10 2.1.3 Density functional theory ............................................................................................. 11 2.1.4 Basis sets ...................................................................................................................... 13 2.2 Theory of Molecular Dynamics .......................................................................................... 15 2.2.1 Molecular mechanics force field .................................................................................. 16 2.2.2 Equation of motion ...................................................................................................... 18 2.2.3 Potential of mean force and umbrella sampling .......................................................... 19 CHAPTER 3 Mercury Methylation by HgcA: Theory Supports Carbanion Transfer to Hg(II) .. 20 vii Abstract ..................................................................................................................................... 22 3.1 Introduction ......................................................................................................................... 23 3.2 Computational Methods ...................................................................................................... 25 3.3 Results and Discussion ....................................................................................................... 28 3.3.1 Co-C bond homolysis .................................................................................................. 28 3.3.2 Co-C bond heterolysis .................................................................................................. 29 3.3.3 Reaction free energies .................................................................................................. 30 3.3.4 Nonenzymatic Hg methylation .................................................................................... 31 3.3.5 Ligand exchange reactions ........................................................................................... 32 3.4 Conclusions ......................................................................................................................... 33 3.5 Appendix 1 .........................................................................................................................
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