Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 10-5-2011 Proton Nuclear Magnetic Resonance Investigation of the Native and Modified Active Site Structure of Heme Proteins Zhonghua Wang Florida International University, [email protected] DOI: 10.25148/etd.FI11120706 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Recommended Citation Wang, Zhonghua, "Proton Nuclear Magnetic Resonance Investigation of the Native and Modified Active Site Structure of Heme Proteins" (2011). FIU Electronic Theses and Dissertations. 513. https://digitalcommons.fiu.edu/etd/513 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida PROTON NUCLEAR MAGNETIC RESONANCE INVESTIGATION OF THE NATIVE AND MODIFIED ACTIVE SITE STRUCTURE OF HEME PROTEINS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in CHEMISTRY by Zhonghua Wang 2011 To: Dean Kenneth Furton choose the name of dean of your college/school College of Arts and Sciences choose the name of your college/school This dissertation, written by Zhonghua Wang, and entitled Proton Nuclear Magnetic Resonance Investigation of the Native and Modified Active Site Structure of Heme Proteins, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. _______________________________________ Watson Lees _______________________________________ Fenfei Leng _______________________________________ Kathleen Rein _______________________________________ Lidia Kos _______________________________________ Xiaotang Wang, Major Professor Date of Defense: October 5, 2011 The dissertation of Zhonghua Wang is approved. _______________________________________ choose the name of dean of your college/school Dean Kenneth Furton choose the name of your college/school College of Arts and Sciences _______________________________________ Dean Lakshmi Reddi University Graduate School Florida International University, 2011 ii © Copyright 2011 by Zhonghua Wang All rights reserved. iii DEDICATION I dedicate this dissertation to my wife, Taiyi Chen, my mother, Fenglan Jiang and my father, You Wang. Without their understanding, encouragement, support, and love, the completion of this work would not have been possible. iv ACKNOWLEDGMENTS I am deeply grateful to many people that have helped me during my delightful and rewarding graduate study at Florida International University in the past few years. First, I would like to thank my research advisor, Dr. Xiaotang Wang, who has been not only an intelligent and respectable mentor, but also a close and thoughtful friend to me. His patience, guidance, and encouragement strongly supported me through my graduate studies and have offered me a great foundation to build a career in science. I would also like to thank all my committee members, Dr. Watson Lees, Dr. Fenfei Leng, Dr. Kathleen Rein and Dr. Lidia Kos, for all of their constructive advice and professional assistance. Thanks to all the members of Dr. Wang’s group, especially Wei Lin, Zheng Wang, Lin Jiang, Hui Tian, Rui Zhang, Hua Ling, Dr. Hedong Bian, and Dr. Yuchang Jiang, for all of the inspiring discussions, selfless help, and for creation of a pleasant lab environment. I would like to extend my appreciation to Yali Hsu and Dr. Yaru Song for their enthusiastic help and careful maintenance of the NMR and MS instruments. Special thanks go to Dr. Palmer Graves and Dr. Uma Swamy for all their kindness help and guidance to teach me how to be a good teaching assistant. I would like to especially acknowledge Dr. Chengxiao Zhang and Dr. Peng Lu for all their care, support and encouragement to me during the years. I also want to thank all of my family and friends for their continuous support, understanding, and encouragement. Finally, I would like to thank the Department of Chemistry and Biochemistry, Florida International University, the National Institutes of Health, and the National Science Foundation for the assistantship support and the funding support during my graduate studies. v ABSTRACT OF THE DISSERTATION PROTON NUCLEAR MAGNETIC RESONANCE INVESTIGATION OF THE NATIVE AND MODIFIED ACTIVE SITE STRUCTURE OF HEME PROTEINS by Zhonghua Wang Florida International University, 2011 Miami, Florida Professor Xiaotang Wang, Major Professor Hemoproteins are a very important class of enzymes in nature sharing the essentially same prosthetic group, heme, and are good models for exploring the relationship between protein structure and function. Three important hemoproteins, chloroperoxidase (CPO), horseradish peroxidase (HRP), and cytochrome P450cam (P450cam), have been extensively studied as archetypes for the relationship between structure and function. In this study, a series of 1D and 2D NMR experiments were successfully conducted to contribute to the structural studies of these hemoproteins. During the epoxidation of allylbenzene, CPO is converted to an inactive green species with the prosthetic heme modified by addition of the alkene plus an oxygen atom forming a five-membered chelate ring. Complete assignment of the NMR resonances of the modified porphyrin extracted and demetallated from green CPO unambiguously established the structure of this porphyrin as an NIII-alkylated product. A novel substrate binding motif of CPO was proposed from this concluded regiospecific N-alkylation structure. Soybean peroxidase (SBP) is considered as a more stable, more abundant and less expensive substitute of HRP for industrial applications. A NMR study of SBP using 1D vi and 2D NOE methods successfully established the active site structure of SBP and consequently fills in the blank of the SBP NMR study. All of the hyperfine shifts of the SBP-CN- complex are unambiguously assigned together with most of the prosthetic heme and all proximal His170 resonances identified. The active site structure of SBP revealed by this NMR study is in complete agreement with the recombinant SBP crystal structure and is highly similar to that of the HRP with minor differences. The NMR study of paramagnetic P450cam had been greatly restricted for a long time. A combination of 2D NMR methods was used in this study for P450cam-CN- complexes with and without camphor bound. The results lead to the first unequivocal assignments of all heme hyperfine-shifted signals, together with certain correlated diamagnetic resonances. The observed alternation of the assigned novel proximal cysteine β-CH2 resonances induced by camphor binding indicated a conformational change near the proximal side. vii TABLE OF CONTENTS CHAPTER PAGE 1 LITERATURE REVIEW ............................................................................................... 1 1.1 Introduction to Hemoproteins ................................................................................... 1 1.2 Heme-Thiolate Proteins ............................................................................................ 5 1.2.1 Cytochromes P450 ........................................................................................... 5 1.2.2 Chloroperoxidase ........................................................................................... 11 1.3 Heme Peroxidases ................................................................................................... 16 1.3.1 Horseradish Peroxidase ................................................................................. 17 1.3.2 Cytochrome c Peroxidase .............................................................................. 21 1.3.3 Soybean Peroxidase ....................................................................................... 22 1.4 Nuclear Magnetic Resonance of Hemoproteins ...................................................... 24 1.4.1 NMR Information Content ............................................................................ 26 1.4.2 Temperature Dependence of Hyperfine Shifts .............................................. 27 1.4.3 Nuclear Overhauser Effect ............................................................................ 29 1.5.2 Low-Spin Cynide Complex of Hemoprotein ................................................ 30 1.5 References ............................................................................................................... 31 2 ISOLATION AND STRUCTURE DETERMINATION OF A NOVEL HEME IN ALLYLBENZENE-MODIFIED CHLOROPEROXIDASE ........................................ 44 2.1 Introduction ............................................................................................................. 44 2.2 Materials and Methods ............................................................................................ 46 2.2.1 Materials ........................................................................................................ 46 2.2.2 Growth of Mold and Preparation of CPO ...................................................... 46 2.2.3 Preparation, Extraction and Purification of Allylbenzene-Modified Heme .. 47 2.2.4 Spectroscopic Characterization of Green Heme ............................................ 47 2.3 Results ....................................................................................................................