Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2016 Knowledge-based approaches for understanding structure-dynamics-function relationship in proteins Kannan Sankar Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biochemistry Commons, Bioinformatics Commons, and the Biophysics Commons Recommended Citation Sankar, Kannan, "Knowledge-based approaches for understanding structure-dynamics-function relationship in proteins" (2016). Graduate Theses and Dissertations. 16007. https://lib.dr.iastate.edu/etd/16007 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]. Knowledge-based approaches for understanding structure-dynamics-function relationship in proteins by Kannan Sankar A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Bioinformatics and Computational Biology Program of Study Committee: Robert L. Jernigan, Co-Major Professor Drena Dobbs, Co-Major Professor Amy Andreotti Guang Song Sanjeevi Sivasankar Iowa State University Ames, Iowa 2016 Copyright © Kannan Sankar, 2016. All rights reserved. ii DEDICATION To my parents and my sister for their unconditional support throughout this journey iii TABLE OF CONTENTS Page NOMENCLATURE ................................................................................................. vii ACKNOWLEDGMENTS ....................................................................................... xii ABSTRACT………………………………. ............................................................. xiv CHAPTER 1 OVERVIEW .................................................................................. 1 1.1. Background ................................................................................................... 1 1.1.1. Protein Dynamics: the Link between Structure and Function ............. 1 1.1.2. Experimental Determination of Protein Structure and Dynamics ....... 3 1.1.3. Computational Approaches to Protein Structure and Dynamics ......... 4 1.2. Motivation and Specific Aims ...................................................................... 13 1.3. Dissertation Organization ............................................................................. 15 CHAPTER 2 DISTRIBUTIONS OF EXPERIMENTAL PROTEIN STRUCTURES ON COARSE-GRAINED FREE ENERGY LANDSCAPES .. 20 2.1. Introduction ................................................................................................... 21 2.2. Theory and Methods ..................................................................................... 27 2.2.1. Datasets ................................................................................................ 27 2.2.2. PCA ...................................................................................................... 28 2.2.1. Knowledge based potential functions .................................................. 29 2.2.2. Structural entropy evaluation ............................................................... 30 2.2.1. Construction of free energy landscapes ............................................... 31 2.2.2. Generation of a transition path between two structures on the free energy landscape ............................................................................................ 32 2.3. Results ......................................................................................................... 34 2.2.1. Distribution of structures in low energy regions of the landscape....... 34 2.2.2. Case study I: T4 Lysozyme .................................................................. 37 2.2.3. Case study II: Human Serum Albumin (HSA) .................................... 40 2.2.2. Case Study III: SERCA ....................................................................... 42 2.2.2. Predicting the transition pathway between the open and closed forms of HIV-1 protease .......................................................................................... 45 2.4. Conclusions ................................................................................................... 48 2.5. Acknowledgements ....................................................................................... 50 2.6. Supplementary Material ................................................................................ 50 iv CHAPTER 3 KNOWLEDGE-BASED ENTROPIES IMPROVE THE IDENTIFICATION OF NATIVE PROTEIN STRUCTURES ........................... 51 3.1. Introduction ................................................................................................... 52 3.2. Results ......................................................................................................... 56 3.2.1. Patterns of amino acid contact changes during protein conformational changes ......................................................................................................... 56 3.2.2. Correlation between contact-change patterns and nature of amino acids 60 3.2.1. Knowledge based entropy functions .................................................... 62 3.2.2. Knowledge-based free energy function (KBF) for protein native structure recognition ...................................................................................... 63 3.3. Discussion ..................................................................................................... 67 3.4. Materials and Methods .................................................................................. 69 3.4.1. Datasets ................................................................................................ 69 3.4.2. Evaluation of normalized amino acid contact changes ........................ 70 3.4.3. Evaluation of local entropies based on contact changes ...................... 71 3.4.4. Optimization of weights for potential and entropy terms .................... 72 3.4.5. Comparison of performance measures................................................. 73 3.5. Author Contributions .................................................................................... 73 3.6. Acknowledgements ....................................................................................... 74 3.7. Supplementary Material ................................................................................ 74 CHAPTER 4 MOLECULAR DETERMINANTS OF CADHERIN IDEAL BOND FORMATION: CONFORMATION DEPENDING UNBINDING ON A MULTIDIMENSIONAL LANDSCAPE............................................................ 75 4.1. Introduction ................................................................................................... 76 4.2. Results ......................................................................................................... 79 4.2.1. Cadherin energy landscape and transition pathway for the interconversion between X-dimers and S-dimers .......................................... 79 4.2.2. Wild type and conformational shuttling mutants form a metastable intermediate, dimer state ................................................................................ 83 4.2.3. Conformational interconversion depends on the K14-D138 salt- bridge interactions .......................................................................................... 88 4.2.4. Intermediate dimer states exhibit force-induced conformational motion perpendicular to the pulling direction ................................................ 90 4.2.5. Cadherins trapped in an intermediate dimer state form ideal bonds .... 94 4.3. Discussion ..................................................................................................... 98 4.4. Methods......................................................................................................... 101 4.4.1. Principal component analysis .............................................................. 101 4.4.2. Projecting energy landscapes onto PC coordinates ............................. 102 4.4.3. Determination of transition path between X-dimers and S-dimers ..... 103 4.4.4. MD and SMD simulations and structural analysis .............................. 103 4.4.5. E-cadherin constructs and single molecule force-clamp measurements 105 4.5. Author Contributions .................................................................................... 107 4.6. Acknowledgements ....................................................................................... 108 4.7. Supplementary Material ................................................................................ 108 v CHAPTER 5 AN ANALYSIS OF CONFORMATIONAL CHANGES UPON RNA-PROTEIN BINDING ........................................................................ 109 5.1. Introduction ................................................................................................... 110 5.2. Materials and Methods .................................................................................. 114 5.2.1. Dataset.................................................................................................. 114 5.2.2. Identification of ‘flexible’ regions ....................................................... 114 5.2.3. Identification of interface residues......................................................