University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2016 Molecular Dynamics Simulations of Enzymes with Quantum Mechanical/Molecular Mechanical Potentials Yufei Yue University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Yue, Yufei, "Molecular Dynamics Simulations of Enzymes with Quantum Mechanical/Molecular Mechanical Potentials. " PhD diss., University of Tennessee, 2016. https://trace.tennessee.edu/utk_graddiss/3984 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 Yufei Yue entitled "Molecular Dynamics Simulations of Enzymes with Quantum Mechanical/Molecular Mechanical Potentials." 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 Biochemistry and Cellular and Molecular Biology. Hong Guo, Major Professor We have read this dissertation and recommend its acceptance: Albrecht von Arnim, Jerome Baudry, Chunlei Su Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Molecular Dynamics Simulations of Enzymes with Quantum Mechanical/Molecular Mechanical Potentials A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Yufei Yue August 2016 Copyright © 2016 by Yufei Yue All rights reserved. ii DEDICATION To my parents Xiangyu Zhang and Rulin Yue To my grandparents Tianju Lei, Fenghe Yue and Qifeng Long iii ACKNOWLEDGEMENTS I would like to express the deepest appreciation to my advisor, Dr. Hong Guo, who has the attitude and the substance of a genius, for his professional advice, continuous encouragement and support for my academic study and career planning in the past 5 years. Beyond that, I am feeling very fortunate to have worked with someone who could be your lifelong mentor. I would like to sincerely thank my committee members, Dr. Albrecht von Arnim, Dr. Jerome Baudry and Dr. Chunlei Su for their valuable suggestions during my course of study and completion of the dissertation. I also want to thank Dr. Cynthia Peterson and Dr. Feng Cheng who once served in my committee. I want to thank all the members of Dr. Hong Guo’s lab, including Dr. Qin Xu, Dr. Jianzhuang Yao, Dr. Yuzhuo Chu, Dr. Haobo Guo, Dr. Peng Lian and Dr. Ping Qian for their technical help and meaningful discussions, and our collaborator Dr. Xiaohan Yang from Oak Ridge National Lab. Completion of this dissertation is impossible without their support. Finally, I would like to send my gratitude to my parents Xiangyu Zhang and Rulin Yue. They are always encouraging and supporting me with their best wishes. iv ABSTRACT S-adenosyl methionine (SAM) dependent methylation process is universally found in all branches of life. It has important implications in mammalian pathogenesis and plant metabolism. The methyl transfer is normally catalyzed by SAM- dependent methyltransferases(MTases). Two MTases are studied in this dissertation: the 1,7-dimethylxanthine methyltransferase (DXMT) which involve in plant caffeine biosynthesis, and the protein arginine methyltransferase 5(PRMT5) that participates in eukaryotic posttranslational modification. The late phase of caffeine biosynthesis starts from the substrate xanthosine and ends with the product caffeine, with theobromine as an intermediate product. DXMT is a key enzyme in this process and catalyzes two methylation steps: 1)methylation of 7- methylxanthine to form theobromine; 2)methylation of theobromine to form caffeine. The catalytic mechanism and product promiscuity of DXMT is intriguing. In Chapter 1, the quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations were performed to explain the dual catalytic roles of DXMT. Simulation results show that a histidine residue may act as a general base catalyst during methylations. PRMTs can work as modifiers for histones and methylate the substrate arginine, thus interfering with histone code orchestration. The product specificity of PRMTs refers to their ability to produce either symmetric di-methylarginine(SDMA), asymmetric di-methylarginine(ADMA) or mono-methylarginine(MMA). Understanding the product specificity of PRMTs is important since different methylations may cause distinctive, even inverse v biological consequences. PRMT5 produces SDMA, as compared to PRMT1 and PRMT3 that produce ADMA. In Chapter 2, simulations of PRMT5 have drawn a theoretical insight into the catalytic difference between SDMA and ADMA. Neddylation is a type of eukaryotic Ubiquitin-like (UBL) protein modification that is essential in cell division and development. Unlike ubiquitin and other small ubiquitin-like modifiers which target variety of protein substrates, the UBL NEDD8 is highly selective on modifying cullin proteins and contributes to 10% ~20% of all cellular ubiquitination and ubiquitination-like modification. In Chapter 3, the crystal structure of a trapped E3-E2 ̴ NEDD8-CUL1 intermediate was used for modeling, and simulations were applied to investigate the catalytic mechanism of NEDD8 transfer from E2 to the substrate. Some important insights were observed that may be used to understand the functional properties of the enzyme. vi TABLE OF CONTENTS INTRODUCTION .................................................................................................. 1 Caffeine Biosynthesis and Dimethylxanthine Methyltransferase ....................... 1 Histone Code and Protein Arginine Methyltransferase ...................................... 3 CULLIN-RING E3 Catalyzed Transfer of Ubiquitin-Like Protein NEDD8 ........... 5 Computational Study of Enzymology through QM/MM Methods ....................... 8 Molecular Dynamic Simulations ................................................................... 10 QM/MM Free Energy Simulations ................................................................ 12 References ...................................................................................................... 14 CHAPTER 1 Catalytic Mechanism and the Role of Key Residues in Caffeine Biosynthesis Catalyzed by Dimethylxanthine Methyltransferase ................ 29 Abstract ........................................................................................................... 30 Introduction ..................................................................................................... 31 Methods .......................................................................................................... 33 Results and Discussion ................................................................................... 37 Conclusions ..................................................................................................... 44 Acknowledgement ........................................................................................... 45 References ...................................................................................................... 46 Appendix ......................................................................................................... 52 CHAPTER 2 Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 ............. 63 Abstract ........................................................................................................... 64 vii Introduction ..................................................................................................... 65 Methods .......................................................................................................... 68 Results and Discussion ................................................................................... 70 Conclusions ..................................................................................................... 77 Acknowledgement ........................................................................................... 78 References ...................................................................................................... 79 Appendix ......................................................................................................... 86 CHAPTER 3 Computational Study of Ubiquitin-like NEDD8 Transfer in RING E3-E2~NEDD8-Target Complex ....................................................................... 96 Abstract ........................................................................................................... 97 Introduction ..................................................................................................... 98 Methods ........................................................................................................ 100 Results and Discussion ................................................................................. 103 Conclusions ..................................................................................................