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https://hdl.handle.net/2142/31297
Description
Title
Chain dynamical theories of protein folding
Author(s)
Portman, John Joseph
Issue Date
2000
Doctoral Committee Chair(s)
Wolynes, P.G.
Department of Study
Physics
Discipline
Physics
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
protein folding
chain dynamics
polypeptide chain
Language
en
Abstract
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 λ-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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