Glassy models of protein folding

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Year dc:date

2012

Author dc:creator

• Bryngelson, Joseph Donald

Contributors dc:contributor

• Wolynes, P.G.

• glassy models
• protein folding

Statement dc:rights

• ©1988 Bryngelson

Language dc:language

en

Identifier

1565952

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/30681