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Structure-Function Correlation of the M2 Proton Channel Characterized by Solid-State Nuclear Magnetic Resonance Spectroscopy Jun Hu

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Structure-Function Correlation of the M2 Proton Channel Characterized by Solid-State Nuclear Magnetic Resonance Spectroscopy Jun Hu Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2005 Structure-Function Correlation of the M2 Proton Channel Characterized by Solid-State Nuclear Magnetic Resonance Spectroscopy Jun Hu Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES STRUCTURE-FUNCTION CORRELATION OF THE M2 PROTON CHANNEL CHARACTERIZED BY SOLID-STATE NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY By JUN HU A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Spring Semester, 2005 The members of the Committee approve the dissertation of Jun Hu defended on January 24, 2005. Timothy A. Cross Professor Directing Dissertation Peter G. Fajer Outside Committee Member Michael S. Chapman Committee Member Naresh Dalal Committee Member Timothy M. Logan Committee Member The Office of Graduate Studies has verified and approved the above named committee members. ii To my wife, Yan Gu, who makes my life integrate and cheerful, to my parents, Zhaoxin Hu and Qifang Li, for their continuous love and support, and to our expecting son, Joseph G. Hu, whom we have already met twice on the ultrasound screen. iii ACKNOWLEDGMENTS Writing a dissertation is something like drafting a short memoir. The road of science is never even, as we all know. In the years as I was teetering along it, I met so many people giving me warm hands. I want their names to be printed in my dissertation and to be remembered in my science journey. First meeting with Professor Tim Cross was delightful. For an oriental student just stepping on this land and overwhelmed by a whole bunch of words and accents never taught in his English classes, Tim was the first person who I felt was not speaking a foreign language. He has an amazing skill to understand Sino-English. Although at that time I was not completely certain whether I liked his research or not, his knowledge, enthusiasm, shrewdness and humor told me that this was the lab I wanted to join in. His office is always open when he is there. If I want to see him, he always stops any work at hand and talks to me. I do not know how may times I sat in his office with frustration and walked out cheerfully with ideas and hope. I always enjoy those funny stories he told me. He is patient with my naïve ideas. He encourages me to attend many conferences and present my work, while many professors do not do. Now I gradually realize that how important it is to communicate my research with other scientists and conference experience has become a precious wealth to me. His judgment on possibilities, diligence in science, leadership in the lab and coordination of personnel with various expertise have a strong impact on me. I am fortunate in being his student. He is the best mentor of mine. Dr. Riqiang Fu is a brilliant NMR spectroscopist at the National High Magnetic Field Laboratory (NHMFL). I learned much of the fundamental and practical NMR knowledge from him. Whenever I have NMR-related questions and ideas (sometimes very nonsensical and stupid), I go to his office and we talk. He is very patient of explaining every step in the pulse program and encourages me to do NMR experiments independently on spectrometers. I am thankful for his help in these years. I also appreciate Dr. Zhehong Gan for his assistance on the Oxygen-17 project. iv I thank those colleagues for their help in the lab. Dr. Junfeng Wang introduced this lab to me. We had a very good time when he was here and talked a lot about PISEMA simulation on the phone when he was in Georgia. I learned Insight II from Dr. Sanguk Kim. That leaded my interest to the bio-computation. Dr. Kastuyuki Nishimura and I worked on the M2 project when he was here. We are still very good friends. Dr. Fei Gao taught me how to express the M2 protein, which will certainly help my future career on the biological NMR. Dr. Eduard Chekmenev joined the lab last year. We collaborated on many projects and enjoyed working together. Through the project on the structure determination by PISEMA, Tom Asbury (IMB), Srisairam Achuthan (Department of Mathematics) and I work closely together. Tom is very good at structural modeling and refinement and plays a key role in the M2- TMD structure modeling. Without Sai’s help, I would spend much longer time on Jeff Denny’s dissertation. Prof. Jack Quine (Department of Mathematics) taught me the Euclidean rotation and how to use Maple. Certainly, I will not forget the delicious summer soup in his house and the elegant music performed by Dr. Richard Bertram (Tom’s advisor, IMB & Department of Mathematics) and him. Also, I want to remember those folks here in the big family: Dr. Changlin Tian, Dr. Zhiru Ma, Dr. Farhod Nozirov, Yiming Mo, Conggang Li, Alicia Hopkins, Yuanzi Hua, Jacob Moore, Nguyen Hau, Rick Page, Lee Miller and Mukesh Sharma. I thank Yi Xiong from Prof. Alan Marshall group for her help on the Mass spectroscopy. I wish to thank those staff members: Hank Henricks and Umesh Goli in the BASS lab, Judy McEachern, Karol Bickett and Ashley Blue here at MagLab, for their support. I am also grateful to two secretaries in the chemistry graduate office, Sarah Armour and Ginger Martin, for their assistance on my graduate study. Finally, I would like to thank my committee professors: Prof. Peter G. Fajer, Prof. Michael S. Chapman, Prof. Naresh Dalal and Prof. Timothy M. Logan, for directing my Ph.D. study. v TABLE OF CONTENTS LIST OF TABLES......................................................................................................... ix LIST OF FIGURES ........................................................................................................ x ABSTRACT................................................................................................................. xiv INTRODUCTION .................................................................................................... 1 1.1 Membrane Protein Structural Biology................................................................ 1 1.2 Membrane Protein Structures ............................................................................. 5 1.2.1 Lipid Bilayers and Membrane Proteins ...................................................... 5 1.2.2 Membrane Proteins versus Soluble Proteins............................................... 9 1.3 Ion Channels ....................................................................................................... 9 1.3.1 Potassium Channels .................................................................................. 10 1.3.2 Proton Channels........................................................................................ 13 1.4 Solid-state NMR ............................................................................................... 15 1.4.1 Nuclear Spin Hamiltonian......................................................................... 15 1.4.2 Zeeman Hamiltonian and Radio Frequency Hamiltonian ........................ 16 1.4.3 Chemical Shift Hamiltonian ..................................................................... 16 1.4.4 Dipolar Coupling Hamiltonian ................................................................. 17 1.4.5 J-coupling Hamiltonian............................................................................. 17 1.4.6 Quadrupolar Hamiltonian ......................................................................... 18 1.4.7 Spin-Rotation Hamiltonian ....................................................................... 18 1.4.8 Chemical Shift Tensors and Chemical Shielding Tensors........................ 18 1.4.9 Dipolar Coupling Tensors......................................................................... 22 WAVES, WHEELS AND HELICES: ORDERLINESS IN PISEMA FUNCTIONS........................................................................................ 25 2.1 Introduction....................................................................................................... 25 2.2 Torsion Angle ................................................................................................... 25 2.3 Continuous Frenet Frame and Discrete Frenet Frame ...................................... 27 2.4 Frames and NMR.............................................................................................. 30 2.4.1 Standard Peptide Plane Geometry ............................................................ 30 2.4.2 Principal Axis Frame and Peptide Plane Frame ....................................... 31 2.4.3 Helical Axis Frame and Laboratory Frame .............................................. 32 2.5 PISEMA Powder Spectrum Simulation............................................................ 33 2.6 PISA Wheels..................................................................................................... 36 2.6.1 Transformation from PAF to HAF ........................................................... 36 2.6.2 PISA Wheels................................................................................................. 42 vi 2.7 PISEMA Waves................................................................................................ 43 2.7.1 PISEMA Waves........................................................................................ 44 HISTIDINES: HEART OF THE PROTON CHANNEL FROM THE INFLEUNZA A VIRUS .........................................................................
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