Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) January 2010 An Examination of Oxysterol Effects on Membrane Bilayers Using Molecular Dynamics Simulations Brett Olsen Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Olsen, Brett, "An Examination of Oxysterol Effects on Membrane Bilayers Using Molecular Dynamics Simulations" (2010). All Theses and Dissertations (ETDs). 420. https://openscholarship.wustl.edu/etd/420 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. Washington University in Saint Louis Division of Biology and Biological Sciences Program in Molecular and Cellular Biology Dissertation Examination Committee: Nathan Baker, Chair Douglas Covey Katherine Henzler-Wildman Garland Marshall Daniel Ory Paul Schlesinger An Examination of Oxysterol Effects on Membrane Bilayers Using Molecular Dynamics Simulations by Brett Neil Olsen A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2010 Saint Louis, Missouri Acknowledgments I would like to thank my doctoral adviser Nathan Baker, whose guidance and advice has been essential to my development as an independent researcher, and whose confidence in my abilities has often surpassed my own. Thanks to my experimental collaborators at Washington University: Paul Schlesinger, Daniel Ory, and Doug Covey, without whom this work never would have been begun. Many thanks to the past and present members of my thesis committee: Nathan Baker, Paul Schlesinger, Daniel Ory, David Sept, Lev Gelb, Doug Covey, Garland Marshall, and Katherine Henzler-Wildman, for their direction and criticism. Thanks to the multitude of other scientific colleagues who have offered contributions to and criticisms of this work in private discussions: Michael Bradley, Rachel Rice, Sunjoo Lee, Albert Mao, Marc Sherman, Peter Jones, Diana Wong, and others too numerous to mention. Thanks to the Texas Advanced Computing Center, which generously provided supercomputer time on which most of these simulations were run and to Malcolm Tobias, who has been instrumental in keeping the computational resources needed for this work up and running. Thanks to Leslie Lamport and Donald Knuth for LATEX and TEX, without which I would have had much less fun formatting my thesis. Thanks to my friends and family who kept me sane through the course of my doctoral work: my parents Reed and Lorraine Olsen, my brother Cullam and my sister Janel, and my friends Robin and Salomon Trujillo, Jon and Andrea Hunt, Daniel and Lena Koslover, Joe and Tina Wasem, Mike and Erin Connor, Tom and Sarah Pierce, Rebecca Craig-Shapiro, Albert Mao, Adam Greenbaum, Peter and Sarah Freddolino, and Robert Kern. This work is dedicated to my wife Clare. You have been in my life for nine years, and you have brought nothing but joy, happiness, and love into it. You have borne with my eccentricities with a smile and a kiss, you have been with me to laugh in happy times and comfort in sad. I picked up and started a new life to be with you, and every day I am grateful that I made the right decision. Thank you. ii Contents 1 Background and Introduction 1 1.1 Biomembranes . 1 1.1.1 Phospholipid Bilayers . 1 1.1.2 Membrane Composition and Regulation . 3 1.2 Sterols . 4 1.2.1 Sterol Structure . 5 1.2.2 Cholesterol . 6 1.2.3 Oxysterols . 7 1.2.4 Cholesterol Regulation . 8 2 Examination of Oxysterol Membrane Effects 10 2.1 Introduction . 10 2.2 Methods . 13 2.2.1 Parameters and Structures . 13 2.2.2 Simulations . 15 2.2.3 Analytical Methods . 15 2.3 Results . 16 2.3.1 Equilibration . 16 2.3.2 Areas and Volumes . 17 2.3.3 Densities . 21 2.3.4 Membrane Mechanical Properties . 22 2.3.5 Lipid Structure . 25 2.3.6 Sterol Orientation and Organization . 27 2.4 Discussion . 32 iii 2.5 Conclusions . 35 3 Interactions Between 25-Hydroxycholesterol and Cholesterol in POPC Bilayers 37 3.1 Introduction . 38 3.2 Methods . 39 3.2.1 Parameters and Structures . 39 3.2.2 Simulations . 40 3.2.3 Analysis Methods . 41 3.3 Results . 44 3.3.1 Equilibration . 44 3.3.2 Membrane Effects . 44 3.3.3 Molecular Effects . 49 3.4 Discussion . 56 4 Influence of Phospholipid Acyl Chains on 25-Hydroxycholesterol Membrane Interactions 59 4.1 Introduction . 60 4.2 Methods . 61 4.2.1 Parameters and Structures . 61 4.2.2 Simulations . 63 4.3 Results . 64 4.3.1 Membrane Effects . 64 4.3.2 Lipid Effects . 70 4.4 Discussion . 74 5 Conclusions 78 5.1 Summary of Simulations . 78 5.2 Mechanisms of Oxysterol Signaling . 81 5.3 Future Work . 82 6 Appendix 84 6.1 Supporting Information, Chapter 2 . 84 6.1.1 Statistical Inefficiency . 84 6.1.2 Kolmogorov-Smirnov Test . 85 6.1.3 Equilibration . 85 iv 6.1.4 Membrane System Construction . 86 6.1.5 Radial Distribution Functions . 87 6.1.6 Bilayer Structural Properties . 87 6.1.7 Sterol Parameters . 90 v List of Figures 1.1 Lipid assemblies. 2 1.2 Glycerophospholipid structure. 2 1.3 Sterol structures. 5 2.1 Cholesterol and 25-hydroxycholesterol structures. 12 2.2 Membrane areas over time. 16 2.3 Membrane SASA components. 19 2.4 Membrane volume distributions. 20 2.5 Bilayer density profiles. 21 2.6 Bulk POPC membrane properties. 24 2.7 POPC tail order parameters. 26 2.8 Sterol hydroxyl hydrogen bonding. 26 2.9 Demonstration of Euler angles. 28 2.10 Distributions of cholesterol orientation. 30 2.11 Distributions of 25-hydroxycholesterol orientation. 31 2.12 Representative cholesterols. 32 2.13 Representative 25-hydroxycholesterols. 33 3.1 Mixed sterol membrane area distributions. 45 3.2 Mixed sterol SASA contributions. 47 3.3 Mixed sterol bilayer mass density profiles. 49 3.4 Cholesterol SASA distributions. ..