Structure, Dynamics and Complex Formation of Eukaryotic Transcriptional Regulators Jordi Medina Vives Aquesta tesi doctoral està subjecta a la llicència Reconeixement- NoComercial – SenseObraDerivada 3.0. Espanya de Creative Commons. Esta tesis doctoral está sujeta a la licencia Reconocimiento - NoComercial – SinObraDerivada 3.0. España de Creative Commons. This doctoral thesis is licensed under the Creative Commons Attribution-NonCommercial- NoDerivs 3.0. Spain License. EDINA M BARCELONA, 2017 ORDI J STRUCTURE, DYNAMICS EGULATORS R AND COMPLEX FORMATION OF UKARYOTIC E RANSCRIPTIONAL T TRANSCRIPTIONAL REGULATORS UKARYOTIC E JORDI MEDINA OF ORMATION F OMPLEX C AND YNAMICS , D PHD THESIS TRUCTURE S Declaration 1. This work has been carried out in the Structural Characterisation of Macromolecular Assemblies laboratory, part of the Structural and Computational Biology program at the Institute for Research in Biomedicine – IRB Barcelona, under the supervision of its Principal Investigator Maria J. Macias (ICREA research professor). 2. No portion of the work referred to in this thesis as original has been submitted in support of an application for a degree qualification to any University. 3. Part of the work exposed in this thesis has been published in one peer- reviewed journal. 4. Financial support for the research included in this thesis has been provided by the IRB Barcelona International PhD Programme Fellowship and the Spanish National Research Program, Ministry of Economy and Competitiveness Grants SAF2011-25119 and BFU2014- 53787-P. Acknowledgements First, I would like to thank my thesis director and principal supervisor, Prof. Maria J. Macias, for giving me the opportunity to carry out this research in her laboratory, for her support through these years and encouragement to persist on my goals. I am very grateful to the members of my thesis advisory committee: Prof. Antonio Zorzano, who is also the tutor of this thesis, Dr. Jesus Garcia, Dr. Joan Pous and Dr. Montserrat Soler-Lopez. To all of them, I thank their advice during these years and their useful suggestions to improve the quality of the research presented in this thesis. I also want to thank Prof. Harold A. Scheraga and Dr. Gia G. Maisuradze for our fruitful collaboration. I also want to show my gratitude to all the researchers at the IRB Barcelona and the University of Barcelona that at some point have assisted me technically and provided their advice, with a special mention to Dr. Irene Fernandez and Dr. Gerardo Acosta. The main support during this stage of my life have been my colleagues, many of which I consider my friends now. To begin with, I want to show my gratitude to Pau and Lidia, to you I owe you more than I can write here, both as a scientist and as a person. To Àngela, David, Jorge, Marta, Oriol and Tiago, I thank you the good moments and coffee times between EMSA and EMSA and the silly tunes in the lab. To Toni and Alessia, respectively my mentor and mentee in the world of peptide synthesis: thanks for your patience and the language lessons. To my Riera colleagues, Álvaro and Anna, for the funny times assigning and purifying. To Albert, Constanze, Eric and James: I am very grateful for your guidance through ACKNOWLEDGEMENTS the laboratory when I arrived. To Ewelina, Marco and Regina, thanks all the knowledge you shared with me. I also want to thank my dear friends, Guille and Valèria, whom even if the distance separates us, I know I can rely on you. To Neus, Alba and Anna, whom I hope to see more often from now on. To my reunited friends from high school, Alícia, Ernest and Laura, let’s do another room escape soon. To my favourite Spanish learners, Elisabetta, Lorenzo, Michal and Tomer, thanks for the great times (and meals!) together. Finally, I am infinitely thankful to my family for all their endless support and warmth. To my sister, Laura: you know you are my favourite. To my special one, Antonio, I cannot imagine how these years would have been without you by my side. To my nephews, Marc and Clàudia, which bring me back the innocence and happiness of childhood. But most of all, to my parents, Joan and Rosa, thanks to be always by my side, to keep watching over me even if I am continuously complaining and for loving me. To all of them I dedicate this thesis. Table of Contents Chapter 1. Introduction 1 1.1. Transcriptional Regulation via Smad 1 Proteins in TGF-β Signalling 1.1.1. The Canonical Signalling Pathway of the TGF-β 2 Superfamily of Cytokines 1.1.2. General Features of the Smad Transcription Factors 5 1.1.3. The MH1 Domain Binds to DNA Regulatory Sequences 7 1.1.4. The Smad Linker Region Is a Ubiquitination Target that 9 Regulates Smad Turnover 1.1.5. The MH2 Domain Is the Smad Hub for Protein-Protein 10 Interactions 1.1.6. FoxH1 Regulates the Expression of Cell-Lineage- 13 Defining Genes in Cooperation with Smad Proteins 1.1.7. General Transcriptional Coactivator NCOA6 Mediates 15 TGF-β Regulation of Cholesterol Metabolism 1.1.8. TRIM33 Recognises Histone Modifications and Regulates 17 Smad-Driven Gene Transcription 1.2. WW Domains: Folding and Aggregation 18 1.2.1. Introduction to Protein Folding 18 1.2.2. Structure and Function of WW Domains 21 1.2.3. WW Domains and Amyloid-Like Aggregation: The 22 Second WW Domain of Formin Binding Protein 28 1.2.4. Amyloid Fibrils and Disease 25 VII TABLE OF CONTENTS 1.3. Principles of Solution Nuclear Magnetic 27 Resonance Spectroscopy 1.3.1. Quantum Properties of Nuclei Are Exploited in NMR 28 1.3.2. Atoms Are Separated in Energy Populations Under a 29 Static Magnetic Field 1.3.3. The Total Magnetic Field Experienced by a Nucleus Is 30 Particular 1.3.4. The Vector Model Provides an Intelligible 31 Representation of NMR Spectroscopy o 33 1.3.5. Applying a -90y Pulse Using the Vector Model Chapter 2. Aims of the Thesis 35 Chapter 3. Materials and Methods 39 3.1. Molecular Biology Methods to Obtain 39 Recombinant Proteins 3.1.1. Cloning of DNA Sequences into Plasmids 40 3.1.2. Site-Directed Mutagenesis 40 3.1.3. Transformation of E. coli Competent Cells 41 3.1.4. Plasmid Preparation 41 3.1.5. Protein Expression and Solubilisation Trials 42 3.1.6. Ultra-Frozen Bacterial Cell Stocks 44 3.1.7. Scaled-Up Expression of Unlabelled Proteins 44 3.1.8. Scaled-Up Expression of Isotopically-Labelled 44 Proteins 3.1.9. Cell Lysis 45 3.1.10. Recombinant Protein Purification 45 3.1.11. Protein N-Terminal Fluorescence Labelling in Solution 47 3.2. Solid-Phase Peptide Synthesis 47 3.2.1. Amino Acid Couplings in Manual Solid-Phase Peptide 50 Synthesis 3.2.2. Tests for the Detection of Free Amines 50 3.2.3. Fmoc α-Amine Deprotection 51 VIII 3.2.4. Determination of the Resin Load 51 3.2.5. Automated Microwave-Assisted Solid-Phase Peptide 52 Synthesis 3.2.6. N-Terminal Modification of Peptides 52 3.2.7. Peptide Release and Side-Chain Deprotection 54 3.2.8. Peptide Purification and Characterisation 54 3.3. Biomolecular Solution NMR Spectroscopy 55 3.3.1. Sample Preparation and Equipment 56 3.3.2. Total Correlation Spectroscopy and Nuclear 56 Overhauser Effect Spectroscopy 3.3.3. Heteronuclear Single Quantum Spectroscopy 57 3.3.4. Tri-Dimensional NMR Experiments of proteins labelled 59 with either 15N or 13C 3.3.5. Tri-Dimensional NMR Experiments of proteins labelled 60 with both 15N and 13C 3.3.6. Protein Structure Calculation 61 3.4. Macromolecular Crystallography 61 3.4.1. Protein Crystallisation Experiments 62 3.5. Calorimetric Methods in Structural 62 Biology 3.5.1. Differential Scanning Calorimetry 64 3.5.2. Isothermal Titration Calorimetry 64 3.6. Intrinsic Fluorescence Spectroscopy 64 3.6.1. Experimental procedure 65 3.7. Thermofluor Shift Assay 66 3.8. Electrophoretic Mobility Shift Assay 66 3.8.1. Experimental procedure 67 3.9. Dynamic Light Scattering 67 IX TABLE OF CONTENTS Chapter 4. Results 69 4.1. Characterisation of Protein-Protein 69 Interfaces on the Smad2 MH2 Domain 4.1.1. Cloning and Expression of Smad2 MH2 Domain 73 Constructs Described in Literature 4.1.2. General Approach to the Chemical Synthesis of Smad- 78 Interacting Protein Fragments 4.1.3. Syntheses of Peptides Containing the FoxH1 SIM, FoxH1 79 FM and NCOA6 LXXLL-2 Motifs 4.1.4. General Considerations on the Observation of Smad2 81 MH2 Domain – Peptide Interactions by Electrophoretic Mobility Shift Assay 4.1.5. EMSA Can Specifically Reproduce the Interactions of 82 FoxH1 SIM and NCOA6 LXXLL-2 with the Smad2 MH2 Domain 4.1.6. Sequence Comparison of the MH2-Interacting Peptides 83 and TRIM33 Middle Shows a Potential Leucine-Proline Pattern 4.1.7. Syntheses of FoxH1 LP, TRIM33 Nter-LP and TRIM33 85 Cter-LP Peptides 4.1.8. The Tandem LP Sequence in TRIM33 Does Not Interact 86 with the Smad2/4 MH2 Domains in EMSA Experiments 4.1.9. Failure of First Crystallisation Screenings Suggests 87 Problems Caused by Protein Stability and Peptide Solubility 4.1.10. Improvement of FoxH1 SIM peptides solubility: FoxH1 90 D-SIM and FoxH1 E-LP 4.1.11. Designing New Smad2 MH2 Constructs Balancing 91 Protein Solubility and Linker Length 4.1.12. Affinity Constant Determination Indicates a Common 92 Low-Molar Range Affinity for All Interacting Peptides 4.1.13. Crystallisation Results Using Optimised Protein 94 Constructs and Peptides 4.1.14. Structure Analysis of the Smad2 MH2-Interacting 95 Peptides 4.1.15.