UC Merced

The “protein structure-function” paradigm, which states that proteins adopt nearly rigid 3-dimensional structures that are responsible for their function, is one of the central tenets of molecular biology, yet some proteins and protein domains exist as intrinsically disordered forms. In this dissertation, new approaches to define a metric for the dynamics of disordered proteins are developed which are also readily applicable to the study of non-equilibrium globular protein dynamics. First, standard metrics for comparing protein dynamics are applied to molecular dynamics (MD) simulations of a class of entirely disordered proteins (outside of a small anchoring domain) involved in nucleocytoplasmic transport, the FG-nucleoporins (FG-Nups). After this, clustering and dimensionality reduction techniques are utilized to reveal previously unknown characteristics regarding the convergence properties of disordered protein simulations. Next, the novel application of polymer models is used to assess the efficacy of clustering and dimensionality estimation algorithms applied to MD trajectories. Finally, the results are used to analyze the differences between FG-Nup dynamics and the dynamics of two fast-folding globular proteins, GB1 and Trp-cage. The results indicate that polymer models are an effective tool for validating computational techniques for studying protein simulations, and that the various proteins can be classified by differences in their underlying dynamics.