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List of Figures

 1.1 Folding@home distributes work units worldwide to run simulations
 1.2 Scheme highlighting the conversion of a simulation dataset into a Markov State Model (MSM)
 2.1 Structures of CAP in apo and holo forms.
 2.2 Workflow for identifying ordered and disordered regimes.
 2.3 Residues whose dihedrals are capable of disorder-mediated communication.
 2.4 Communication to a single CBD.
 2.5 Change in coupling to a single CBD pocket upon the S62F mutation.
 2.6 Hubs of backbone-side-chain communication in wild-type CAP.
 2.7 Global communication strength of each residue in apo CAP.
 3.1 Structure of Gαq with key secondary structure elements labeled according to the Common Gα Numbering (CGN) system.
 3.2 Structural and dynamical changes during the rate limiting step for GDP release.
 3.3 Tilting of H5 is correlated with GDP release but translation of H5 is not.
 3.4 Allosteric network connecting H5 motion to the nucleotide binding-site via s6h5.
 3.5 Change in the s6h5 loop conformation across the rate-limiting step.
 3.6 Probability distributions of the distance between the side-chains of Lys275G.s5hg.1 and Glu49G.s1h1.4.
 3.7 Allosteric network connecting hNs1 motion to the nucleotide-binding site via the -sheets.
 3.8 Allosteric network connecting the GPCR- and nucleotide-binding interfaces.
 3.9 π–stacking between S2 and H1 is disrupted during the rate-limiting step.
 3.10 Switch 2 moves towards GDP across the rate-limiting step.
 4.1 Crystal structure of two copies of VP35’s IID bound to dsRNA.
 4.2 Exposons identify a large cryptic pocket and suggest potential allosteric coupling
 4.3 eVP35 allosteric network revealed by the CARDS algorithm
 4.4 Thiol labeling supports the existence of the predicted cryptic pocket.
 4.5 Stabilizing the open cryptic pocket in VP35’s IID disrupts dsRNA binding.
 5.1 Sequence and structural summary of N protein.
 5.2 The N-terminal domain (NTD) is disordered with residual helical motifs.
 5.3 The RNA binding domain (RBD) and dimerization domains do not significantly interact and are connected by a disordered linker (LINK).
 5.4 The C-terminal domain (CTD) is disordered, engages in transient interaction with the dimerization domain, and contains a putative helical binding motif.
 5.5 Nucleocapsid protein undergoes phase separation with RNA
 5.6 A simple polymer suggests symmetry breaking can promote single-polymer condensates over multi-polymer assemblies.
 5.7 Summary and proposed model for N protein behavior.
 6.1 Summary of Folding@home’s computational power.
 6.2 Structural characterization of conformational masking in different spike complexes.
 6.3 Effects of glycan shielding and conformational masking on the accessibility of different parts of the spike to potential therapeutics.
 6.4 Examples of cryptic pockets and functionally-relevant dynamics.
 7.1 β-Lactamase mechanism.
 7.2 Structures of antibiotics and CTX-M-14 β-lactamase.
 7.3 Thermal stability of WT and mutant β-lactamases, as measured by CD.
 7.4 Steady-state protein levels of WT CTX-M-14 and mutant β-lactamases.
 7.5 Structures of the active-site region of WT CTX-M14 β-lactamase, as well as P167S, D240G, and P167S/D240G mutant enzymes in the apo form.
 7.6 Normalized B-factors for the 103–106 loop and the 164–179 Ω-loop in the CTX-M enzyme structures.
 7.7 Structures of the active-site region of CTX-M-14 mutant β-lactamase acyl-enzyme complexes with ceftazidime.
 7.8 Structures of the active-site region of CTX-M-14 mutant β-lactamase acyl-enzyme complexes with ceftazidime.
 7.9 The conformational heterogeneity of the Ω-loop is greater in the single mutants than in the WT or double mutant.
 7.10 Conformational changes between inactive and active forms of the acyl-enzyme.
 A.1 CARDS sensitivity analysis
 A.2 Distribution of ordered and disordered times for a single dihedral across a single simulation trajectory.
 A.3 The average ordered and disordered times for CAP
 A.4 Residues with separable dihedrals into disordered regimes

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