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Self-Assembly of Biomineralization Protein Mms6 and Its Function As a Ferric Iron Reductase That Associates with Lipid Membranes Shuren Feng Iowa State University

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Self-Assembly of Biomineralization Protein Mms6 and Its Function As a Ferric Iron Reductase That Associates with Lipid Membranes Shuren Feng Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2015 Self-assembly of biomineralization protein Mms6 and its function as a ferric iron reductase that associates with lipid membranes Shuren Feng Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biochemistry Commons Recommended Citation Feng, Shuren, "Self-assembly of biomineralization protein Mms6 and its function as a ferric iron reductase that associates with lipid membranes" (2015). Graduate Theses and Dissertations. 14845. https://lib.dr.iastate.edu/etd/14845 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Self-assembly of biomineralization protein Mms6 and its function as a ferric iron reductase that associates with lipid membranes by Shuren Feng A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Molecular, Cellular, and Developmental Biology Program of Study Committee: Marit Nilsen-Hamilton, Major Professor Edward Yu Eric R Henderson Mark S Hargrove Gregory J Phillips Iowa State University Ames, Iowa 2015 Copyright © Shuren Feng, 2015. All rights reserved. ii DEDICATION To my family who have been supporting me unconditionally through the years, to my beloved wife Fan, and my daughter Eileen who have been my sources of impetus and inspiration in life… iii TABLE OF CONTENTS Page DEDICATIONS ......................................................................................................... ii TABLE OF CONTENTS ........................................................................................... iii ACKNOWLEDGMENTS ......................................................................................... v ABSTRACT………………………………. .............................................................. vii CHAPTER 1 GENERAL INTRODUCTION ...................................................... 1 1.1 Thesis Organization ...................................................................................... 1 1.2 Literature Review .......................................................................................... 3 1.2.1 Biomineralization theories and examples .............................................. 3 1.2.2 Structural and functional basis of biomineralization proteins ................. 20 1.2.3 Magnetotactic bacteria and magnetosomes ............................................. 31 1.2.4 Membrane proteins in magnetosome biogenesis .................................... 37 1.2.5 Magnetic nanoparticles: properties, applications, and synthesis ............. 61 1.2.6 Tables and Figures .................................................................................. 74 1.3 References ..................................................................................................... 75 CHAPTER 2 INTEGRATED SELF-ASSEMBLY OF THE MMS6 MAG- NETOSOME PROTEIN TO FORM AN IRON-RESPONSIVE STRUCTURE ...... 109 2.1 Introduction .................................................................................................. 110 2.2 Results and Discussion .................................................................................. 112 2.3 Experimental Section ..................................................................................... 118 2.4 Conclusions .................................................................................................. 122 2.5 References .................................................................................................. 123 2.6 Tables and Figures ..................................................................................... 125 CHAPTER 3 DYNAMIC STRUCTURAL CHANGE OF MMS6 WITH IRON BINDING: STRUCTURAL PREPARATION FOR BIOMINERALIZATION ....... 130 3.1 Introduction .................................................................................................. 131 3.2 Materials and Methods ................................................................................... 132 3.3 Results ........................................................................................................ 134 3.4 Discussion ..................................................................................................... 139 3.5 References ..................................................................................................... 141 3.6 Figure Legends .............................................................................................. 143 3.7 Tables and Figures ......................................................................................... 145 iv CHAPTER 4 THE BIOMINERALIZATION PROTEIN MMS6 IS A LIPID- ACTIVATED FERRIC REDUCTASE ................................................................... 148 4.1 Introduction .................................................................................................. 149 4.2 Materials and Methods .................................................................................. 150 4.3 Results ........................................................................................................... 154 4.4 Discussions .................................................................................................. 159 4.5 References ................................................................................................... 163 4.6 Figure legends .............................................................................................. 166 4.7 Tables and Figures ..................................................................................... 169 CHAPTER 5 CONCLUSIONS............................................................................. 173 5.1 Conclusions .................................................................................................... 173 5.2 References ................................................................................................... 176 v ACKNOWLEDGMENTS I would like to thank my major professor Dr. Marit Nilsen-Hamilton for her constant support and guidance through the years. I am grateful for her constant support and patient help all through the process of completing this thesis. I am appreciative of her efforts to teach me to evaluate data objectively, to think critically, and to effectively manage my time and resources. These training that I got will be invaluable for the future of my career, no matter what career path I might be going for. Without her devoted help and guidance, I could not have made it to the completion of this thesis. I am especially grateful for the caring, encouragement, and kind help from Dr. Marit Nilsen-Hamilton and her husband, Dr. Richard Hamilton, when I had to go through some hard times of my life. “Hardship is good for you, young man…” I was told these words by Dr. Richard Hamilton. These words always popped up on my mind and helped me to move on when I was in times of trouble and at the brim of giving up. Also, I would like to thank my committee members, Dr. Edward Yu, Dr. Eric Henderson, Dr. Gregory Phillips, Dr. Mark Hargrove, and my previous committee member Dr. Alan Dispirito for their guidance, constructive critiques, and kind help through the years. Special thanks are given to our lab manager Lee Bendickson who has been always there to help, with him being our lab manager, my mentor, and friend all at the same time. I would like to thank our collaborators from Ames Laboratory, Department of Chemical Engineering, and Department of Material Science and Engineering. Dr. Surya Mallapragada as our project leader has been always supporting, and working hard to make sure that our research moves towards the right directions. I would like to thank all our collaborators vi including Dr. David Vaknin, Dr. Wenjie Wang, Dr. Mufit Akinc, Dr. Monica Lamm, Dr. Klaus Schmidt-Rohr, Dr. Tanya Prozorov, Dr. Xunpei Liu, Keith Fritzsching, and Honghu Zhang for their collaborations, hardwork, and thoughtful discussions during the years. I really enjoyed and learned a lot from this multidisciplinary group, and some of the friendships developed will be cherished for the rest of my life. Also, my current and past colleagues in MNH lab; Dr. Alison Pappas, Dr. Lijun Wang, Dr. Wei Zhao, Dr. Xiaoling Song, Dr. Muslum Ilgu, Dr. Ilchung Shin, Supipi Liyamali Auwardt, Dr. Judhajeet Ray, Samir Mehanovic, Dr. Pierre Palo, Dr.Tianjiao Wang, Dr. Lijie Zhai, Shambhavi Shubang , Michael Zeller, Mathew Luriano and any other rotational, SULI and visiting students. This inspiring group has been a constant source of friendship, good advice and acompany. I would like to thank my family for their unconditional love and support during good and difficult times throughout this work. I would like to thank my wife for her constant love and support during my PhD life. I am appreciative of my parents, my sister Shiren Feng, and my brother-in-law Hong Shi for their unconditional love and support. Lastly, I want to thank god to send an angle to me and my family-Eileen. She teaches so many things as a four-year-old, far more than what I could have imagined. And, Eileen, dad loves you forever. vii ABSTRACT Biomineralization by living organisms provides excellent examples of controlled mineral synthesis
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