Protein dynamics: From unfolded to crystalline

Yi Xue, Purdue University

Abstract

Knowing the three-dimensional structure of a protein is important for understanding protein function. It is less appreciated that protein function is also dependent on internal dynamics. As a uniquely powerful tool to study protein dynamics, NMR can probe protein motions on the time scale from picoseconds to seconds and above. This thesis addresses three different protein states: unfolded and folded states in solution, as well as (folded) crystalline states. In the first part of this work, unfolded proteins have been studied by paramagnetic relaxation enhancement (PRE) technique. Motivated by a lack of proper theoretical treatment for the PRE effect in unfolded proteins, we developed several analytical and computational models and compared the theoretical predictions with the experimental data from two unfolded proteins: chemically denatured drkN SH3 domain and ubiquitin. In the second part of this thesis work, we compared side-chain dynamics in the α-spectrin SH3 domain using methyl relaxation data from solution- and solid-state samples of this small globular protein. The results clearly indicate that dynamic behavior of the protein hydrophobic core in a well-hydrated crystalline sample strongly resembles that observed in solution. In addition, we demonstrated that combined analysis of the solid- and solution-state backbone dynamics data provides a simple and efficient method for characterization of slow time-scale (ns-μs) dynamics. In the third part of this work, we measured methyl rotation barriers in the α-spectrin SH3 domain. Based on the experimental data and MD simulations, we conclude that 2.5.3 kcal/mol is a typical barrier height characteristic of a fluid hydrophobic core which lacks any tight packing effects. We have found that rigid methyl barriers, derived from static protein structures, can provide a useful measure of structure quality.

Degree

Ph.D.

Advisors

Skrynnikov, Purdue University.

Subject Area

Analytical chemistry|Biochemistry|Biophysics

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