Date of Award

2012

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Biochemistry & Molecular Biophysics

First Advisor

S Walter Englander

Second Advisor

Ben E. Black

Abstract

Models derived from X-ray crystallography can give the impression that proteins

are rigid structures with little mobility. NMR ensembles may suggest a more dynamic

picture, but even these represent a rather narrow range of possibilities close to the lowest

energy state. In reality proteins participate in a wide range of dynamics from the subtle

and rapid sidechain dynamics that occur in nanoseconds in the PDZ signaling domain to

the large and slow rearrangement of secondary structure that takes days in the mitotic

checkpoint protein Mad2. Between these extremes are motions on time scales typically

associated with protein function, such as those in SNase monitored by hydrogen

exchange. The dynamic character of several protein systems, including PDZ domain,

Calmodulin, SNase, and Mad2, were explored using a variety of biophysical techniques.

This broad investigation demonstrates the dynamic variability between and within

proteins. The study of PDZ and Calmodulin illustrates how a computational technique

can recapitulate experimental results and provide additional insight into signal

transduction. The case of SNase shows that HX NMR data can be exploited to reveal

protein dynamics with unprecedented detail. The Mad2 system highlighted some of the

pitfalls associated with this technique and some alternative strategies for investigating

protein dynamics.

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