University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2020-07-30 Elucidating the Interplay Between Lipids and Membrane Proteins Using Multiscale Computer Simulations Sejdiu, Besian I. Sejdiu, B. I. (2020). Elucidating the Interplay Between Lipids and Membrane Proteins Using Multiscale Computer Simulations (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/112372 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Elucidating the Interplay Between Lipids and Membrane Proteins Using Multiscale Computer Simulations by Besian I. Sejdiu A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JULY, 2020 © Besian I. Sejdiu 2020 Abstract Biological membranes are complex cellular structures formed by a large number of different lipid types, that also contain a variety of bound proteins, carbohydrates, and other molecules. The detailed orchestration of all these elements has been a major focus of scientific research during the last 5 decades. Computer- based methods, such as molecular dynamics (MD) simulations, have proven to be a valuable approach in addressing many of the details of lipid organization and membrane protein activity. I used MD simulations at both atomistic and coarse-grained level of detail to study the number of way lipids and proteins interact and their possible functional ramifications. In part of my work, I studied the interaction of G Protein- Coupled Receptors (GPCRs) with lipids at a family-wide level. Plenty of other computational studies had shown specific lipid-protein interactions for a handful of GPCRs but with quite different outcomes on their number, location, and lipid identity. In my work, I simulated 28 different GPCR structures and showed that they are distinguished by a unique interaction profile with membrane lipids. I provided a comprehensive analysis of simulation results with available crystallographic data. I also studied the lipid-protein interaction profile of AMPA receptors and cyclooxygenases (mainly COX-1), showing that they both form specific interactions with lipids, but do so in a quite different fashion. AMPA receptors interact specifically with diacylglycerol lipids, whereas COX-1 enzymes do so indiscriminately with glycerophospholipids, cholesterol, and fatty acids, but at different levels of interaction strength. Using atomistic simulations, we show the binding pathway of arachidonic acid to COX-1 and identify a series of arginine residues that guide it toward the hydrophobic cavity of the enzyme. As part of my work, I also developed a webserver that automates the analysis and visualization of lipid-protein interactions from MD simulations allowing for the creation of automated pipelines to study lipid-protein interactions in the future. Lastly, I provide a short review of some of the main challenges facing the field along with possible solutions going forward. My work expands our understanding of lipid-protein interactions. ii Preface The work presented in this thesis contains four chapters of original research and two reviews, also original work, on the field of lipid-protein interactions. Below I outline the content of each chapter and its status in terms of availability to the general scientific community. Chapter 1 provides a brief introduction to the biology of the problem and the methods I use. It is meant to serve as a general overview of lipid-protein interactions and as an intuitive guideline to MD simulations. Its primary purpose is to allow for an easier reading of later chapters. Chapter 2 includes a detailed review of GPCR-lipid interactions as derived primarily from MD simulations. It contains my contribution on a large and comprehensive review article that was published in Chemical Reviews in 2019. I also reviewed the same literature on bacterial mechanosensitive channels but that is not included in here. Chapter 3 presents the study of lipid-protein interaction profile of AMPA receptors. The work presented in this chapter highlights part of my contribution to a wider collaborative effort that was published in ACS Central Science in 2018. Chapter 4 details my work on the lipid-protein interaction profile of GPCRs. In it, I provide a comparative study of the interaction of 28 different GPCR structures with their lipid environment. Appendix A presents the supplementary information for this chapter. This work has been published in the Biophysical Journal. Chapter 5 includes a detailed study of the lipid interaction profile of COX-1 enzymes. In it, I show how these enzymes bind different membrane lipids in their hydrophobic cavity. I also detail the binding pathway of arachidonic acid to the same binding site. Appendix B contains the supplementary information for this chapter. This work has been made available online on bioRxiv and will be submitted for peer-review soon. Chapter 6 presents a webserver/software that I developed which aims at automating the analysis and visualization of lipid-protein interactions. The chapter provides an overview of some of the analysis applications that have been implemented and discusses the advantages they provide. The manuscript for this work has been completed and will be submitted soon. Chapter 7 provides a short review of the field of lipid-protein interactions. It focuses mainly on the challenges and obstacles facing the field, as well as providing novel analysis and a discussion on how the field should move forward. This work will be submitted for consideration to The Journal of Chemical Physics soon. iii Chapter 8 contains a brief summary of conclusions reached for all chapters. The following is a list of papers and reviews published during my PhD(1-4): 1. Corradi V., E. Mendez-Villuendas, H. I. Ingolfsson, R. X. Gu, I. Siuda, M. N. Melo, A. Moussatova, L. J. DeGagne, B. I. Sejdiu, G. Singh, T. A. Wassenaar, K. D. Magnero, S. J. Marrink, D. P. Tieleman. Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins. Acs Central Sci. 2018;4(6):709-717. 2. Corradi V., B. I. Sejdiu, H. Mesa-Galloso, H. Abdizadeh, S. Y. Noskov, S. J. Marrink, D. P. Tieleman. Emerging Diversity in Lipid–Protein Interactions. Chem Rev. 2019. 3. Sejdiu B. I., D. P. Tieleman. Lipid-Protein Interactions Are a Unique Property and Defining Feature of G Protein-Coupled Receptors. Biophys J. 2020;118(8):1887-1900. 4. Sejdiu B. I., D. P. Tieleman. COX-1 - lipid interactions: arachidonic acid, cholesterol, and phospholipid binding to the membrane binding domain of COX-1. bioRxiv. 2020. My contributions to each of the chapters presented in this thesis will be highlighted at the beginning of each chapter. iv Acknowledgement First and foremost, I would like to thank my supervisor Dr. Peter Tieleman for his mentoring throughout my PhD. There are many things to be appreciative about working in the Tieleman lab, but perhaps what I am grateful for most was the freedom that I was given to develop as a scientist and the (frankly, quite often misplaced) trust put on me for knowing what I am doing. I was always free to pursue any project of my interest even if they were only tangentially research related. I am also thankful to Peter for not only allowing but actively encouraging me to express myself freely in my scientific work, design projects and structure articles the way I saw fit and for giving me detailed feedback on my work where sometimes I thought I had mistakenly written manuscripts using a red font. A special thanks goes to my former colleagues in Peter’s group: Dr. Gurpreet Singh and Dr. Valentina Corradi for their help and mentorship. Valentina has been an inspiration for me throughout my PhD, and her dedication, organized planning and friendliness are things I will try to emulate in my future career. Similarly, I thank Dr. Anastassiia Moussatova for her support, advice and encouragement, and all other members of the Tieleman lab for their help, collaboration, and friendship. Thanks to my supervisory committee members, Dr. Kenneth Ng and Dr. Justin MacCallum for their advice and mentorship and for always being accommodating to my requests for meetings. I also appreciate the help of the supporting staff and program coordinators at the University of Calgary for making all the dreadful administrative paperwork so easy to deal with. The most important and most heartfelt appreciation goes to my parents for all the sacrifices they made and continue to make for me, my family, and my education. Both are much smarter than me yet neither got to pursue their passion for academic advancement to their desired extent. Their support towards my goals and dreams has been immense, unwavering, consistent, and so far, almost entirely one-sided. Last but not least, I thank my brothers for their love and support and my wife for guiding and always being there for me. Liridona, you left everything behind to follow me and I can never thank you enough for that. You created a home for us and provided far more than your fair share of work