Proteins are in constant motion and these motions impact their function. This thesis attempts to use simple perturbative techniques to track the changes in dynamics upon disrupting the native state of a protein. The protein studied within this thesis is the Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1). Pin1's function has been extensively studied (Lu 1996) (Ranganathan 1997) (Zhou 1999) (Verdecia 2000) (Wintjens 2001) (Bayer 2003) (Jacobs 2003) (Mueller 2011), yet a single, all-encompassing mechanistic explanation has not been provided. The dynamics of Pin1 has been shown to be closely related to catalysis and function (Namanja 2007) (T. Peng 2007) (Namanja 2011). Thus, Pin1 is an ideal candidate for both a toy system for studying different aspects of the relation between protein dynamics and function as well as a worthwhile protein for studying its specific, practically important functional mechanism. This thesis utilizes a wide variety of experimental and computer based techniques to study the dynamics of Pin1 over timescales ranging from ps to ms. First a novel study of ligand dynamics during catalysis is presented. These NMR experiments are completed at natural isotopic abundance and monitor the μs-ms dynamics of an enzyme-substrate pair. This work represents the first ever study of ligand relaxation dispersion measurements at natural isotopic abundance (Zintsmaster 2008).Next, a brief look at the application of a Gaussian Network Model (GNM) (Bahar 1997) to monitor changes in dynamics upon mutation/deletion is presented. GNM flexibility profiles provide a quick, qualitative means for looking at changes in flexibility upon changes in 3-dimensional structure. Experimental data is compared to the GNM profiles and a good agreement between experiment and GNM is seen. This section will focus on the study of the WW domain of Pin1. Chapter 6 addresses the issue of domain-domain coupling. Pin1 is a two domain protein connected by a flexible 10 residue linker. First NMR order parameters from experiment and MD simulations are compared in an effort to scrutinize the results of both simulation and experiment. Next, the conditions with the greatest degree of agreement are used to simulate the dynamics of full length Pin1 vs. the two isolated domains, the WW domain and the PPIase domain. It is hypothesized that the difference in dynamics of these two simulations can shed light on the weak interactions contributing to domain-domain coupling in full length Pin1. Analysis of these differences dynamic changes at sites that coincide with those undergoing changes upon substrate binding. The last chapter, Chapter 7, deals with MD simulations of three Pin1 single residue mutants. The first two mutants, C113A (Winkler 2000) and T152A (Mueller 2011), have been previously shown to inactivate enzymatic activity in Pin1. Furthermore, Winkler et al. have shown that in crystal structures of Par14, a close relative of human Pin1, an extended hydrogen bonding network can be seen stretching from T152 to C113. Mutations of these two, distant residues cause similar changes in flexibility throughout Pin1. The third mutant, I28A, has been recognized as playing a role in the domain-domain interaction in Ch.6 and has been chosen to further identify key dynamics related to domain coupling. The results from the I28A mutant provide new views of the domain-domain interaction surface and furthers the understanding of which residues are involved in domain-domain communication.