UNIVERSITY OF CALIFORNIA, SAN DIEGO Stretching and twisting chromatin A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Engineering Science (Engineering Physics) by Irina V. Dobrovolskaia Committee in charge: Professor Gaurav Arya, Chair Professor Prabhakar Bandaru Professor Sergei Krasheninikov Professor Bo Li Professor Vlado Lubarda 2012 © Irina V. Dobrovolskaia, 2012 All rights reserved. The Dissertation of Irina V. Dobrovolskaia is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2012 iii TABLE OF CONTENTS Signature Page...............................................................................................................iii List of Figures...............................................................................................................vii List of Tables................................................................................................................viii Acknowledgments..........................................................................................................ix Vita..................................................................................................................................x Publications.....................................................................................................................x Abstract of the Dissertation...........................................................................................xi 1. Introduction.................................................................................................................1 1.1. DNA structure and function................................................................................1 1.2. Chromatin as a DNA packager............................................................................3 1.3. Chromatin as a gene regulator.............................................................................8 1.4. Forces on chromatin .........................................................................................12 1.5. Torsional forces on chromatin...........................................................................17 1.6. Thesis objective.................................................................................................21 1.7. References.........................................................................................................23 2. Force-induced unraveling of nucleosomes................................................................36 2.1. Introduction.......................................................................................................36 2.2. Model Development..........................................................................................38 2.2.1 Modeling of DNA and histone octamer......................................................39 2.2.2 Brownian dynamics simulations.................................................................43 iv 2.2.3 Parametrization of octamer groove charges...............................................46 2.3. Results...............................................................................................................51 2.3.1 Force-extension behavior............................................................................52 2.3.2 DNA unwrapping dynamics.......................................................................54 2.3.3 Kinematics of nucleosome unraveling........................................................57 2.3.4 Energetics of nucleosome unraveling.........................................................62 2.3.5 Role of non-uniform DNA/histone interactions.........................................64 2.4. Discussion.........................................................................................................70 Acknowledgments.........................................................................................................74 2.5. References ........................................................................................................74 3. Torsional behavior of dinucleosome arrays..............................................................80 3.1. Introduction.......................................................................................................80 3.2. Model and Simulation Methods........................................................................83 3.2.1 Linker and nucleosome model ...................................................................83 3.2.2 Dinucleosome mechanics and energetics...................................................85 3.2.3 Monte Carlo twisting protocol....................................................................88 3.3. Results...............................................................................................................90 3.3.1 Twist inversion............................................................................................90 3.3.2 Nucleosome flipping...................................................................................96 3.4. Discussion.......................................................................................................101 Acknowledgments.......................................................................................................105 3.5. References.......................................................................................................106 v 4. Conclusions and future work..................................................................................109 4.1. Summary.........................................................................................................109 4.2. Future directions..............................................................................................111 4.3. References.......................................................................................................113 Appendix 1..................................................................................................................114 Appendix 2..................................................................................................................115 vi LIST OF FIGURES Figure 1.1: DNA double helix.........................................................................................2 Figure 1.2: Top and side view of the crystal structure of the nucleosome core. ............5 Figure 1.3: Major structures involved in DNA compaction............................................7 Figure 1.4: Single molecule experimental techniques and their natural force ranges.. 13 Figure 1.5: Forces and torques imposed by chromatin-acting enzyme.........................14 Figure 2.1: Coarse-grained model of the nucleosome..................................................39 Figure 2.2: Normalized charge values assigned to the octamer groove beads as a function of their location along the wound DNA relative to the dyad.......48 Figure 2.3: Mean unraveling force as a function of the normalized loading rate.........51 Figure 2.4: Computed force-extension curves..............................................................53 Figure 2.5: Time evolution of extent of nucleosome wrapping....................................55 Figure 2.6: The octamer center of mass as a function of time for BD simulations......59 Figure 2.7: Time evolution of the nucleosome during simulation................................61 Figure 2.8: Time evolution of the total energy..............................................................63 Figure 2.9: Representative force-extension plots..........................................................65 Figure 2.10: Comparison of the time evolution number of wrapped turns of DNA and octamer orientation for canonical and noncanonical nucleosomes............68 Figure 3.1: Dinucleosome array model and nucleosome and linker bead coordinate systems.......................................................................................................84 Figure 3.2: Schematic of the applied and induced twist from the MC simulations......85 Figure 3.3: Twist inversion............................................................................................91 Figure 3.4: Twist propagation simulation results..........................................................93 Figure 3.5: Effect of applied twist on the linker and nucleosome coordinate systems.95 Figure 3.6: Nucleosome flipping dynamics..................................................................97 Figure 3.7: Dinucleosome energy contributions.........................................................100 Figure 3.8: Total applied and induced twist................................................................101 vii LIST OF TABLES Table A.1: Physical parameters associated with the coarse-grained nucleosome and Brownian dynamics simulations...................................................................114 Table A.2: Physical parameters used in the Monte Carlo simulations........................115 viii ACKNOWLEDGMENTS I would like to thank Dr. G.Arya for being an inspiring scientific adviser and for his unresting enthusiasm. Its been a privilege to work under his guidance. All the members of Dr. G. Arya group, past and current, have been very supportive and helpful. The text of Chapter 2 is partly based on paper I. V. Dobrovolskaia and G. Arya “Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions”, in press, Biophysical Journal, 2012. The text