MOLECULAR DYNAMICS SIMULATIONS OF LIPID MEMBRANES: THE EFFECTS OF PROBES, LIPID COMPOSITION AND PEPTIDES A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Geoffrey Ackerman August 2015 © 2015 David Geoffrey Ackerman MOLECULAR DYNAMICS SIMULATIONS OF LIPID MEMBRANES: THE EFFECTS OF PROBES, LIPID COMPOSITION AND PEPTIDES David Geoffrey Ackerman, Ph.D. Cornell University 2015 The cell plasma membrane is comprised of hundreds of different lipid species as well as a variety of integral and peripheral proteins. The diversity of molecular constituents leads to the formation of functional lateral heterogeneities within the plane of the membrane, known as lipid rafts, which are distinct from the surrounding membrane. Given the complexity of the plasma membrane, and the importance of rafts in the life of a cell, simplified model mixtures capturing the characteristics of the plasma membrane have been essential for unraveling its underlying behavior. In this work, we use molecular dynamics simulations to study model membranes at resolutions not possible with experimental techniques. We first investigated a fundamental assumption in model membrane experiments: that extrinsic probes added to the membrane do not disrupt membrane behavior. We addressed this issue by simulating single component model membranes that contained commonly used fluorescent lipid analogs. We found that the probes are able to disorder the bilayer and reorient lipid headgroups due to the probes’ large, positively charged headgroups and long, interdigitating acyl chains. Importantly though, these effects die off within a couple of nanometers of the probe. This means that the probes do not disrupt large-scale membrane behavior and can effectively be used for experimental membrane studies. However, the short-ranged perturbations also indicate that probes may provide incorrect information if they report directly on their local, disrupted, environment. Next, we studied the behavior of more complex model membranes containing multiple lipid species. Experimentally, model membranes comprised of four lipid components can yield coexisting phases, mimicking raft and non-raft environments, ranging in size from nanometers to microns. Through simulations, we found that domain size and alignment are highly coupled and that they both change abruptly at certain lipid compositions. We also found that the phase interface between domains was only a couple of nanometers wide regardless of the properties of the two coexisting phases. Addition of transmembrane α-helical peptides of various lengths to the lipid-only mixtures significantly increased both domain size and alignment. These effects were largest for the shortest peptides and increased with peptide concentration. Thus cells may be able to control raft size and alignment, and in turn a variety of cellular processes, simply by altering lipid and protein concentrations. BIOGRAPHICAL SKETCH David Ackerman grew up on the south side of the tracks in Westfield, New Jersey. He persevered in a childhood without cable, often finding solace in public broadcasting and a variety of science and nature shows. Thanks to parents who never grew frustrated of his non-stop questions, and instead fed his curiosity with science articles and toys, David continued to find joy in science. Though set on pursuing a scientific education, in typical lazy David fashion, he did not enjoy putting in effort to actively seek out undergraduate institutions. Due to a suggestion by his father, David applied to and joined Northwestern University’s interdisciplinary Integrated Science Program in 2006. At Northwestern, David majored in integrated sciences, physics and math. Outside of classes, David performed theoretical research on extrasolar planets for Professor Fred Rasio. When it came time for graduate school, David decided to apply to institutions where he could use his broad scientific background to study problems at the boundaries between fields. David joined the Ph.D. program in Biophysics at Cornell University in 2010. He was interested in performing simulations, so logically he joined a predominantly experimental lab in a field in which he had no experience: Professor Gerald Feigenson’s membrane physical chemistry lab. As a member of Jerry’s lab, David has enjoyed performing research which links simulations to experiments. He hopes to continue using similar research methodologies in his next career, whenever and wherever that might be. iii To My Parents iv ACKNOWLEDGMENTS I would first like to thank my advisor Dr. Gerald Feigenson. Jerry is a constant source of knowledge and advice, and is invested in every project going on in the lab. His scientific integrity, passion and dedication are both inspirational and infectious. These traits, along with his willingness to let me pursue molecular dynamics even though neither he nor I had any experience with them, convinced me to join his lab. Throughout my 5 years at Cornell, he has been encouraging throughout my various projects spanning from simulations to experiments. It has been a real joy to work in his lab. Lab members past and present have also provided unique points of view which have benefited my work. These close friends and labmates include Dr. Fred Heberle, Dr. Lynda Goh, Dr. Robin Smith Petruzielo, (Fighting Mongeese Teammate) Dr. Jon Amazon, Dr. Tatyana Konyakhina, Milka Doktorova, Michael Weiner, Rebecca Simpson, Yi Wen, Dr. Kai Yang and the undergraduates Sanjula Wickramsinghe, Nimit Sohoni and Mary Kim. Additionally, I would like to thank my committee members Dr. John Brady and Dr. Warren Zipfel who provided guidance during my dissertation work and who took the time to attend my presentations and read my thesis. Importantly, my time in Ithaca has been made exponentially better by the friendships I have made here. Huimin Chen, Avtar Singh, Joshua Tokuda, Stella Li, Vinh Le, Jeahoo Kwon, Digbijay Mahat and Rupa Shah Mahat have put up with my annoying questions and stupid get rich quick schemes and have shown me how creativity, fun, a sense of adventure, and stupidity can thrive well into adulthood. Huimin has been an especially supportive, helpful, encouraging, adventurous, informative and important person during my years at Cornell. v Finally I would like to thank my family. My parents, Susan (aka Suebert) and Louis (aka Loubert), have been extremely caring and supportive throughout my life and always make sure I am prepared for what comes next, including making sure I always have my phone charger. My sisters Rachel and Sara have been successful in their very different careers and hobbies showing me what it takes to be successful when venturing out on my own. And of course my niece Esme, who always provides advice, whether it is in English, French or our own private language. Though research is often a somewhat independent endeavor, all these people have been essential to the successful completion of my dissertation. And for that, I am extremely grateful. vi TABLE OF CONTENTS TABLE OF CONTENTS .............................................................................................................. vii LIST OF FIGURES ........................................................................................................................ x LIST OF TABLES ........................................................................................................................ xii LIST OF ABBREVIATONS ....................................................................................................... xiii Chapter 1 Introduction........................................................................................................... 1 1.1 Overview ............................................................................................................................. 1 1.2 Lipid bilayer phases ............................................................................................................ 2 1.2 The cell plasma membrane ................................................................................................. 5 1.2.1 Plasma membrane composition ................................................................................. 5 1.2.2 Lateral membrane heterogeneity ................................................................................ 6 1.2.3 Lipid rafts ................................................................................................................... 8 1.3 Model membranes ............................................................................................................. 11 1.3.1 Model membrane components ................................................................................. 11 1.3.2 Ternary lipid mixtures .............................................................................................. 12 1.3.3 Type I and Type II ternary lipid mixtures ................................................................ 15 1.3.4 Quaternary lipid mixtures ........................................................................................ 16 1.3.5 Relevance to lipid rafts ............................................................................................ 18 1.4 Molecular dynamics (MD) simulations ............................................................................ 19 1.4.1 Basic MD methodology ........................................................................................... 19 1.4.2