Date

2013

Document Type

Thesis

Degree

Master of Science

Department

Mechanical Engineering

First Adviser

Zhang, Xiaohui Frank

Abstract

Internal friction plays an important role in protein dynamics by modulating the protein's folding/unfolding process and other conformational changes. However, how to quantify internal friction and its contribution to protein folding/unfolding dynamics remains challenging. Single-molecule force spectroscopy has developed as a powerful tool to probe protein structure and dynamics. In this thesis, with the technique of atomic force microscopy (AFM), we measured the single-molecule force spectroscopy of the GB1 protein's unfolding process. By changing the solvent viscosity and the concentrations of denaturant GdmCl, we were able to extract the key mechanical properties, such as the spontaneous unfolding rate k0, the intrinsic lifetime τ0, the location of the activation state Δx, and the height of activation energy ΔG, according to both Bell-Evans model and Dudko's model. Moreover, we developed an extended Ansari-expression to describe the relation between the overall friction and internal friction. By fitting the extracted mechanical properties to the expression, we successfully quantified the internal friction, which decreases from ∼ 2.1 mPa s without any denaturant to ∼ 1.0 mPa s with 2M denaturant GdmCl. The single-molecule procedure provided a unique way to quantify internal friction in protein's folding/unfolding process.

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