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https://hdl.handle.net/2142/30681
Description
Title
Glassy models of protein folding
Author(s)
Bryngelson, Joseph Donald
Issue Date
1988
Doctoral Committee Chair(s)
Wolynes, P.G.
Department of Study
Physics
Discipline
Physics
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
glassy models
protein folding
Language
en
Abstract
In this thesis we have used concepts from the physics of disordered
materials to study protein folding. The first chapter consists of a general
introduction to proteins and protein folding. In Chapter Two we develop a
simple protein folding model and use a random energy approximation to
calculate its equilibrium properties. The model has unfolded, folded and
glassy phases. In Chapter Three we investigate the dynamics of the model.
The model has many metastable states and the distribution of the lifetimes of
these states is log-normal at high temperatures and becomes much broader in
the glassy phase. Also, we calculate the folding time by deriving a
generalization of transition state theory that takes into account some of the
glassy behavior of our model. The results for the folding time are physically
reasonable. In Chapter Four we combine the ideas of the preceding chapters
with the theory of polymer collapse. First we study the collapse of random
hetropolymers and find that hetropolymers have a frozen collapsed phase that
does not occur in homopolymers. Then we study the equilibrium properties
and folding time of a model of protein folding that incorporates some features
of polymer collapse. The properties of this model are found to be qualitatively
similar to those of our earlier model. We also find that in this new model the
rate limiting step in folding occurs after much of the native structure has been
formed, which agrees with experiments.
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