Date of Award

Summer 2011

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group


First Advisor

Feng Gai


Proteins are polymers, whose complex chemistry and physics, in the course of evo-
lution, permitted their recruitment for immensely diverse functions in the biological
machinery. Therefore, the study of protein conformational behavior and interactions
of proteins with other entities of the intra- and extra-cellular milieu is of great inter-
est. In this Thesis, we do not only quantitatively study the folding of peptide and
protein systems using well-established spectroscopic techniques, but also, in recognizing the limits of existing experimental techniques, develop novel methods for studying protein folding, protein-protein and protein-membrane interactions.
In the first part of this Thesis, we are concerned with studying the folding process
under various conditions using small peptides or proteins as model systems that al-
low a tractable, quantitative description of the order-disorder transition. Employing
a combined site-directed mutagenesis/temperature-jump kinetics approach, we eluci-
dated the folding mechanism of a helical hairpin, which is an important intermediate
in protein folding reactions. We further considered how the folding kinetics of such
model peptides and proteins are altered in the presence of high concentrations of
macromolecular cosolutes, which are thought to provide a simplified model system
for the interior of the cellular environment. In another study, we addressed current
questions concerning the structural properties of the unfolded state ensemble using a
polypeptide that is unstructured by design as a model system.
The second part of this Thesis is focused on the development of novel methods to
study both protein folding and interactions of proteins with other molecular species.
In recent years, the nitrile stretching bands of nitrile-derivatized amino acid side-
chains have emerged as attractive probes for monitoring biomolecular processes. In
this Thesis, we theoretically and experimentally studied the molecular determinants
of the bandwidth of the nitrile stretching band of 5-cyanotryptophan. We further
evaluated the feasibility of using light-induced reductive cleavage of disulfide bonds
as a means to phototrigger protein folding reactions.

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