List of Figures
List of Tables
Acknowledgments
Abstract
Chapter 1 Introduction
 1.1 Protein conformational landscapes encode functional information.
 1.2 The Folding@home platform allows access to protein motions at biologically relevant timescales.
 1.3 Allosteric communication is critical for protein function, but difficult to infer.
 1.4 Scope of thesis.
Chapter 2 Quantifying allosteric communication via both concerted structural changes and conformational disorder
 2.1 Abstract
 2.2 Introduction
 2.3 Theory and methods
 2.4 Results and discussion
 2.5 Conclusion
 2.6 Acknowledgements
Chapter 3 Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
 3.1 Abstract
 3.2 Introduction
 3.3 Results and Discussion
 3.4 Conclusion
 3.5 Materials and Methods
 3.6 Acknowledgements
Chapter 4 Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments
 4.1 Abstract
 4.2 Introduction
 4.3 Results
 4.4 Discussion.
 4.5 Methods
 4.6 Acknowledgements
Chapter 5 The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA.
 5.1 Abstract
 5.2 Introduction
 5.3 Results
 5.4 Discussion
 5.5 Methods
 5.6 Acknowledgements
Chapter 6 Citizen Scientists Create an Exascale Computer to Combat COVID-19
 6.1 Abstract
 6.2 Introduction
 6.3 Results and discussion
 6.4 Discussion
 6.5 Methods
 6.6 Acknowledgements
 6.7 Disclosures
Chapter 7 Antagonism between substitutions in $\beta$-lactamase explains a path not taken in the evolution of bacterial drug resistance
 7.1 Abstract
 7.2 Introduction
 7.3 Results
 7.4 Discussion
 7.5 Methods
 7.6 Author contributions
 7.7 Acknowledgments
 7.8 Additional information.
Chapter 8 Conclusions
 8.1 Main findings
 8.2 Future directions
Appendix A Supplementary Material on the CARDS method
 A.1 Supplementary Methods
 A.2 Supplementary Figures
Appendix B Supplementary figures highlighting the mechanism of GDP release
 B.1 Supplementary Figures
Appendix C Supplementary Material to ”Discovery of a cryptic allosteric site in Ebola’s ’undruggable’ VP35 protein”
 C.1 Supplementary Material
Appendix D Supplementary Material on the SARS-CoV-2 nucleocapsid protein
 D.1 Supplementary Methods
 D.2 Supplementary Figures
Appendix E Supplementary Material on ”Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance”
 E.1 Supplementary Data
Bibliography