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IN SILICO MODELING the EFFECT of SINGLE POINT MUTATIONS and RESCUING the EFFECT by SMALL MOLECULES BINDING Zhe Zhang Clemson University, [email protected]

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IN SILICO MODELING the EFFECT of SINGLE POINT MUTATIONS and RESCUING the EFFECT by SMALL MOLECULES BINDING Zhe Zhang Clemson University, Jasonzhangz888@Gmail.Com Clemson University TigerPrints All Dissertations Dissertations 5-2013 IN SILICO MODELING THE EFFECT OF SINGLE POINT MUTATIONS AND RESCUING THE EFFECT BY SMALL MOLECULES BINDING Zhe Zhang Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Biological and Chemical Physics Commons Recommended Citation Zhang, Zhe, "IN SILICO MODELING THE EFFECT OF SINGLE POINT MUTATIONS AND RESCUING THE EFFECT BY SMALL MOLECULES BINDING" (2013). All Dissertations. 1126. https://tigerprints.clemson.edu/all_dissertations/1126 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. IN SILICO MODELING THE EFFECT OF SINGLE POINT MUTATIONS AND RESCUING THE EFFECT BY SMALL MOLECULES BINDING A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Physics and Astronomy by Zhe Zhang May 2013 Accepted by: Dr. Emil Alexov, Committee Chair Dr. Feng Ding Dr. Sumanta Tewari Dr. Charles Schwartz Dr. Maria Miteva Dr. Philippe Roche ABSTRACT Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will result in an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This investigation focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein. This choice is motivated by the fact that missense mutations are frequently found to affect the native function of proteins by altering their structure, interaction and other properties and cause diseases. A particular disease is the Snyder-Robinson syndrome (SRS), which is an X-linked mental retardation found to be caused by missense mutations in human spermine synthase (SMS). In this thesis, a rational approach to predict the effects of missense mutations on SMS wild-type characteristics was carried. Following this work, a structure-based virtual screening of small molecules was applied to rescue the disease-causing effect by searching the small molecules to stabilize the malfunctioning SMS mutant dimer. ii DEDICATION I dedicate my thesis to my parents. Without their love, the completion of this work would not have been possible. iii ACKNOWLEDGMENTS I would like to thank my advisor, Dr. Emil Alexov in Clemson University; and my advisor, Dr. Maria Miteva in University of Paris VII, for their guidance, patience, and financial support. I am very grateful to them for sharing with me their expertise in biophysics, bioinformatics, and structural biology and their help in scientific writing. I had a wonderful time of working with my advisors. Additionally, I appreciate the help from other committee members: Dr. Feng Ding for his kind help on my research and his recommendations for my job search; Dr. Charles Schwartz for providing the in vitro experimental datum; Dr. Sumanta Tewari for his help for my Ph.D. course work especially the Thermodynamics and Quantum Mechanics; Dr. Philippe Roche for his time in reviewing my thesis. At the same time I also want to thank my group members from both Clemson University and University of Paris VII for their help. Finally, thank you to the Chateaubriand fellowship supported by the Embassy of France in the U.S., which resulted in a Dual Ph.D. The research reported in the current thesis is supported by NIH, NLM, and the grant number is: 1R03LM009748. iv TABLE OF CONTENTS Page TITLE PAGE .................................................................................................................... i ABSTRACT ..................................................................................................................... ii DEDICATION ................................................................................................................ iii ACKNOWLEDGMENTS .............................................................................................. iv LIST OF TABLES ......................................................................................................... vii LIST OF FIGURES ........................................................................................................ ix CHAPTER I. INTRODUCTION ......................................................................................... 1 II. IMPORTANT METHODS FOR MODELING EFFECTS OF MISSENSE MUTATIONS. ....................................................................................... 11 III. COMPUTATIONAL ANALYSIS OF MISSENSE MUTATIONS CAUSING SNYDER-ROBINSON SYNDROME .................................................. 49 Abstract .................................................................................................. 49 Background ............................................................................................ 50 Materials and Methods ........................................................................... 53 Results .................................................................................................... 55 Discussion .............................................................................................. 67 References .............................................................................................. 69 IV. A Y328C MISSENSE MUTATION IN SPERMINE SYNTHASE CAUSES A MILD FORM OF SNYDER-ROBINSON SYNDROME ................. 74 Abstract .................................................................................................. 74 Background ............................................................................................ 74 Materials and Methods ........................................................................... 75 Results .................................................................................................... 82 Discussion .............................................................................................. 94 References .............................................................................................. 96 v Table of Contents (Continued) Page V. IN SILICO AND IN VITRO INVESTIGATIONS OF THE MUTABILITY OF DISEASE-CAUSING MISSENSE MUTATION SITES IN SPERMINE SYNTHASE… .................................................................. 98 Abstract .................................................................................................. 98 Background ............................................................................................ 99 Materials and Methods ......................................................................... 101 Results .................................................................................................. 107 Discussion ............................................................................................ 126 References ............................................................................................ 128 VI. ENHANCING HUMAN SPERMINE SYNTHASE ACTIVITY BY ENGINEERED MUTATIONS … ....................................................... 130 Abstract ................................................................................................ 130 Background .......................................................................................... 131 Materials and Methods ......................................................................... 132 Results .................................................................................................. 141 Discussion ............................................................................................ 154 References ............................................................................................ 161 VII. SNYDER-ROBINSON SYNDROME: RESCUING THE DISEASE- CAUSING EFFECT BY SMALL MOLECULE BINDING............... 165 Abstract ................................................................................................ 165 Background .......................................................................................... 166 Materials and Methods ......................................................................... 169 Results .................................................................................................. 176 Discussion ............................................................................................ 188 References ............................................................................................ 190 APPENDICES ............................................................................................................. 198 A: Publications resulting from the present research ....................................... 199 B: Supplementary Materials: Figures ............................................................. 201 C: Supplementary Materials: Tables .............................................................. 205 vi LIST OF TABLES Table Page 2.1 Comparison of linear regression of ΔΔGexp vs. sΔΔGcal with the sΔΔGcal performed with different length of residue segments for Training Database/Blind Test/Entire Dataset…………………………………...27 2.2 Comparison of linear regression of ΔΔGexp vs. ΔΔGcal with the ΔΔGcal performed with different methods……………………………………..29 2.3 The results of linear regression for training database, blind
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