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Molecular Simulation Studies of Dynamics and Interactions in Nucleic Acids

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Molecular Simulation Studies of Dynamics and Interactions in Nucleic Acids University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Spring 2021 Molecular Simulation Studies of Dynamics and Interactions in Nucleic Acids Lev Levintov University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Levintov, Lev, "Molecular Simulation Studies of Dynamics and Interactions in Nucleic Acids" (2021). Doctoral Dissertations. 2580. https://scholars.unh.edu/dissertation/2580 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. MOLECULAR SIMULATION STUDIES OF DYNAMICS AND INTERACTIONS IN NUCLEIC ACIDS BY Lev Levintov BS, Chemical Engineering, University of New Hampshire, 2016 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Chemical Engineering May, 2021 ALL RIGHTS RESERVED ©2021 Lev Levintov ii This dissertation has been examined and approved in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Engineering by: Dissertation Director, Dr. Harish Vashisth Associate Professor, Department of Chemical Engineering Dr. Nivedita Gupta Professor, Department of Chemical Engineering Dr. Kang Wu Associate Professor, Department of Chemical Engineering Dr. Krisztina Varga Associate Professor, Department of Molecular, Cellular, and Biomedical Sciences Dr. Paul Robustelli Assistant Professor, Department of Chemistry (Dartmouth College) On [Date of Defense] Original approval signatures are on file with the University of New Hampshire Graduate School. iii DEDICATION I dedicate this to my family. iv ACKNOWLEDGEMENTS First, I want to acknowledge my advisor, Prof. Harish Vashisth, who continuously guided and supported me throughout my PhD study. His dedication and professional attitude to work always inspired me to work harder. Moreover, I want to thank him for all the professional skills that I have learned from him during my PhD. I also want to thank Professors Nivedita Gupta, Kang Wu, Krisztina Varga, and Paul Robustelli, for serving on my thesis committee. I am very grateful to all my collaborators, Dr. Shambhavi Tannir (University of Wyoming), Dr. Krisztina Varga (University of New Hampshire), Dr. Mark Townley (University of New Hampshire), Dr. Milan Balaz (Yonsei University), Dr. Brian Leonard (University of Wyoming), and Dr. Jan Kubelka (University of Wyoming) for a collaborative work on the porphyrin/DNA system. Specifically, I want to thank Dr. Krisztina Varga and Dr. Milan Balaz for insightful conversations on the self-assembly of the porphyrin/DNA systems and for the opportunity to study these systems. I also thank Dr. Sanjib Paul (New York University) for a collaborative work on the base flipping mechanism in dsRNA. Moreover, I want to thank him for his patience in teaching me the foundations of the transition path sampling methods and for sharing his codes and scripts with me. I thank the past and present lab members for all the questions and the constructive criticism that I have received from them during our group meetings. These conversations were always helpful and improved my critical thinking. I am forever grateful to all my family who have always supported me and believed in v my dreams. No matter how far they are, I can always feel their love and support for me. I greatly thank my grandfather, Boris Levintov, who nurtured love for science in me when I was a small kid. He taught me to always ask questions about nature around us and gifted me a lot of books about biology. Lastly, but importantly, I thank my girlfriend Eivet for all her love, support, care, and patience. vi TABLE OF CONTENTS DEDICATION iv ACKNOWLEDGEMENTS v LIST OF TABLES xv LIST OF FIGURES xvii LIST OF ABBREVIATIONS xxxvii ABSTRACT xxxix 1 INTRODUCTION 1 1.1 BriefHistoryofNucleicAcidsResearch . .... 1 1.2 StructuresofNucleicAcids. .. 3 1.3 RNADynamics.................................. 5 1.4 RNA-LigandsInteractions . 5 1.5 BackgroundofSystemsStudied . ... 6 1.5.1 ViralRNAMolecules........................... 7 1.5.2 Double-strandedRNA(dsRNA) . 10 1.5.3 Porphyrin/DNASystem . 11 1.6 SpecificAims ................................... 13 1.6.1 Specific Aim 1: Probe the conformational dynamics in HIV-1 TAR RNAwith/withoutligands. 13 vii 1.6.2 Specific Aim 2: Characterize conformational transitions associated with recognition of a small molecule inhibitor by the HIV-1 TAR RNA 13 1.6.3 Specific Aim 3: Probe the recognition mechanism of a helical peptide bytheHIV-1RRERNA......................... 14 1.6.4 Specific Aim 4: Perform a systematic examination of collective vari- ablestodescribethebaseflippingmechanismin RNA . 14 1.6.5 Specific Aim 5: Characterize the self-assembly and dynamics of por- phyrin/DNAsystems........................... 15 1.7 ThesisOutline................................... 15 2 MODELS AND METHODS 16 2.1 Introduction.................................... 16 2.2 MolecularDynamics(MD)Simulations . ..... 17 2.2.1 Ensembles................................. 17 2.2.2 LangevinDynamics............................ 18 2.2.3 InitialConditions . 19 2.2.4 NumericalIntegration .......................... 19 2.2.5 Integration Timestep (∆t)........................ 20 2.2.6 Potential Energy (U)........................... 21 2.2.7 History of the Amber Force-Field for Nucleic Acids . ... 22 2.2.8 BoundaryConditions........................... 25 2.2.9 Minimization ............................... 25 2.2.10 TemperatureandPressureControl . ... 25 2.3 SoftwarePackages................................ 26 2.3.1 MDSimulationSoftware . 26 2.3.2 ConductingMDSimulations . 26 2.3.3 ModelingandAnalysis .......................... 27 2.4 EnhancedSamplingMethods . 28 viii 2.4.1 SteeredMolecularDynamics(SMD). .. 29 2.4.2 TransitionPathSampling(TPS) . 32 2.5 Summary ..................................... 36 3 STUDY ON THE ROLE OF CONFORMATIONAL HETEROGENEITY IN LIGAND RECOGNITION BY VIRAL RNA MOLECULES 37 3.1 Abstract...................................... 37 3.2 Significance .................................... 37 3.3 Background .................................... 38 3.4 Methods...................................... 41 3.4.1 SystemPreparation............................ 41 3.4.2 SimulationDetails ............................ 42 3.4.3 ConformationalMetrics . 42 3.5 Results....................................... 47 3.5.1 Assessment of Torsional Flexibility and Ligand Stability ....... 47 3.5.2 LigandsRigidifyTARRNA . 48 3.5.3 Comparison of Average Structures and Formation of Conformational Clusters .................................. 50 3.5.4 LigandsAlterHelicalDynamicsinTARRNA . 54 3.5.5 Ligands Stabilize Nucleotide Flipping in TAR RNA . ... 56 3.5.6 Conformational Dynamics in TAR RNA Reveal Ligand Binding Pockets 60 3.6 Discussion..................................... 61 3.7 Conclusions .................................... 64 3.8 SupportingInformation. ... 64 3.9 Publication .................................... 65 4 STUDY ON THE BINDING/UNBINDING PROCESS OF A SMALL MOLECULEFROMAVIRALRNAMOLECULE 66 ix 4.1 Abstract...................................... 66 4.2 Significance .................................... 66 4.3 Background .................................... 67 4.4 Methods...................................... 69 4.4.1 System Preparation and Simulation Details. ...... 69 4.4.2 SMD Simulations and the Potential of Mean Force (PMF) Calculation 71 4.4.3 BuriedSurfaceArea(BSA) . 71 4.5 ResultsandDiscussion . .. 72 4.5.1 Thermodynamics of Ligand Dissociation . .... 72 4.5.2 LigandEscapePathway . 75 4.5.3 Mechanistic Details of Ligand Dissociation . ....... 78 4.6 Conclusions .................................... 81 4.7 SupportingInformation. ... 82 4.8 Publication .................................... 82 5 STUDY ON THE BINDING/UNBINDING PROCESS OF A HELICAL PEPTIDEFROMAVIRALRNAMOLECULE 83 5.1 Abstract...................................... 83 5.2 Significance .................................... 83 5.3 Background .................................... 84 5.4 Methods...................................... 87 5.4.1 System Setup and Equilibration Details. ..... 87 5.4.2 SMDSimulations ............................. 88 5.4.3 PMFCalculation ............................. 89 5.4.4 InteractionEnergiesandSaltBridges . ..... 89 5.5 Results....................................... 89 5.5.1 Thermodynamics of Peptide Dissociation . ..... 89 5.5.2 Mechanistic Details: Peptide Dissociation Pathways .......... 95 x 5.6 Discussion..................................... 103 5.7 Conclusion..................................... 106 5.8 SupportingInformation. 107 5.9 Publication .................................... 107 6 STUDY ON THE BASE FLIPPING MECHANISM IN RNA MOLECULES108 6.1 Abstract...................................... 108 6.2 Significance .................................... 108 6.3 Background .................................... 109 6.4 Methods...................................... 111 6.4.1 System Preparation and Simulation Details. ...... 111 6.4.2 TransitionPathSampling . 112 6.4.3 Seed Trajectory and Definitions of Stable States . ....... 112 6.4.4 ListofCollectiveVariables. 113 6.4.5 RefinedReactionCoordinate. 114 6.4.6 FreeEnergyProfilealongRC . 114 6.5
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