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Computational and Experimental Analysis of Retroviral Rev-Like Proteins Chijioke Umunnakwe Iowa State University

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Computational and Experimental Analysis of Retroviral Rev-Like Proteins Chijioke Umunnakwe Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Computational and experimental analysis of retroviral Rev-like proteins Chijioke Umunnakwe Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Bioinformatics Commons, Genetics Commons, and the Virology Commons Recommended Citation Umunnakwe, Chijioke, "Computational and experimental analysis of retroviral Rev-like proteins" (2014). Graduate Theses and Dissertations. 14239. https://lib.dr.iastate.edu/etd/14239 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Computational and experimental analysis of retroviral Rev-like proteins by Chijioke Umunnakwe A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Genetics Program of Study Committee: Susan Carpenter, Major Professor Drena Dobbs Karin Dorman W. Allen Miller Michael Shogren-Knaak Iowa State University Ames, Iowa 2014 Copyright © Chijioke Umunnakwe, 2014. All rights reserved. ii DEDICATION This work is dedicated to my family: my brother, Scout, who is part of my soul; my sisters, Agbani, Nene, and Amy, whose waves of love wash over me daily; my parents, Uche and Ngozi, whose sacrifices cannot be described by mere words. This is also for Marie. iii TABLE OF CONTENTS DEDICATION .............................................................................................................................. ii LIST OF TABLES ....................................................................................................................... iv LIST OF FIGURES ...................................................................................................................... v ACKNOWLEDGMENTS .......................................................................................................... vii ABSTRACT .............................................................................................................................. viii CHAPTER 1. GENERAL INTRODUCTION ............................................................................ 1 Dissertation Organization ................................................................................................................................. 1 Overall Goals ......................................................................................................................................................... 33 References ............................................................................................................................................................. 34 COMPUTATIONAL MODELING SUGGESTS DIMERIZATION OF EQUINE INFECTIOUS ANEMIA VIRUS REV IS REQUIRED FOR RNA BINDING ..................... 52 Abstract .................................................................................................................................................................. 53 Background ........................................................................................................................................................... 55 Results ..................................................................................................................................................................... 58 Discussion .............................................................................................................................................................. 72 Conclusion ............................................................................................................................................................. 75 Methods .................................................................................................................................................................. 76 Authors’ Contributions .................................................................................................................................... 92 Acknowledgments ............................................................................................................................................. 92 References ............................................................................................................................................................. 93 CHAPTER 3. COILED-COILS COULD BE AN IMPORTANT STRUCTURAL MOTIF IN RETROVIRAL REV-LIKE PROTEINS .................................. 99 Abstract ................................................................................................................................................................ 100 Background ......................................................................................................................................................... 101 Results ................................................................................................................................................................... 104 Discussion ............................................................................................................................................................ 120 Conclusion ........................................................................................................................................................... 124 Methods ................................................................................................................................................................ 124 References ........................................................................................................................................................... 131 CHAPTER 4. GENERAL CONCLUSIONS AND FUTURE DIRECTIONS ...................... 137 Identification and analysis of Rev coiled-coil motifs ........................................................................ 138 Structural homology in retroviral Rev-like proteins ........................................................................ 138 Future Studies .................................................................................................................................................... 141 Analysis of Rev sequences differentially predicted to contain coiled-coils ........................ 141 The origin of retroviral Rev-like proteins ......................................................................................... 145 References ........................................................................................................................................................... 149 iv LIST OF TABLES Table 1: Summary of NES and ARMs of retroviral Rev-like proteins ............................... 22 Table 2: Computational prediction of Rev structural models .............................................. 60 Table 3: Additional File 2.1. Quality assessment of Rev models ......................................... 82 Table 4: Additional File 2.2. Accession codes and sequences of the EIAV Rev central region ........................................................................................ 87 Table 5: Additional file 3.1: Accession codes of retroviral Pol aa sequences ............. 127 Table 6: Additional file 3.2: Accession codes of Rev-like encoding retroviruses ..... 128 v LIST OF FIGURES Figure 1. 1: Retrovirus morphology ................................................................................................... 4 Figure 1. 2: Orthoretrovirus replication ........................................................................................... 6 Figure 1. 3: Schematic of proviral structures of select retroviruses and RNA export elements .......................................................................................... 11 Figure 1. 4: HIV-1 Rev nuclear export ............................................................................................ 12 Figure 1. 5: Comparison of HIV-1 and EIAV Rev ........................................................................ 16 Figure 1. 6: HIV-1 Rev crystal structure and SAXS structure of the RRE ........................ 24 Figure 1. 7: Jellyfish model of HIV-1 Rev mediated RNA export ......................................... 26 Figure 2. 1: Rev sequences used for computational prediction of tertiary structure ..................................................................................................... 59 Figure 2. 2: Comparison of model quality scores for EIAV Rev elongated and globular models ............................................................................... 61 Figure 2. 3: Structural features of Rev models ........................................................................... 64 Figure 2. 4: An identified coiled-coil motif in Rev is predicted to mediate dimerization ............................................................................................. 67 Figure 2. 5: Specific residues within the predicted coiled-coil motif are required for dimerization and RNA binding ............................................. 70 Figure 3. 1: Retrovirus phylogeny ................................................................................................. 106 Figure 3. 2: Rev-like protein domain architecture and location of
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