Completely microscopic theories of protein folding must take into account chain dynamics. The energy landscape description of protein folding accommodates two rather distinct behaviors of the polypeptide chain: the glassy dynamics expected for heteropolymers with random interactions and the organized dynamics expected for minimally frustrated proteins that fold rapidly on a funneled landscape. The chain dynamical phenomena relevant to both these extremes are studied in this thesis. First, we derive a mode-coupling theory for the dynamics of a random heteropolymer and study the dynamical glass transition signaled by a violation of the fluctuation-dissipation theorem. Next, we develop a variational theory for the smooth free energy surface of minimally frustrated proteins. In this theory, ensembles of structures along an average folding route (identified by the stationary points in the free energy surface) are characterized by the local Debye-Waller factor for each residue about its native position. The description of the folding dynamics of minimally frustrated proteins is completed by considering the chain dynamics of crossing barriers on the resulting free energy profile. We choose the lambda-repressor protein as a specific example to illustrate the model, but address the interesting polymer physics that influence free energy profiles and barrier crossing dynamics. Direct observation of chain dynamics experimentally involves measuring the fluorescence quenching between individual pairs of monomers. As a first step to providing the theory for this, a variational formalism is developed to study diffusion influenced reactions (easily extended to model intrachain quenching in polymers) and applied to simple one-dimensional problems in order to evaluate the method. Lastly, we investigate how functioning proteins that bind from the unfolded state exploit protein folding to speed their function.
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