The Integration of Oxidative Surface Mapping and Molecular Dynamics Simulation Techniques as a Strategy for Studying Protein Conformational Change

The range and number of new and unknown proteins is increasing at a staggering rate due to the recent genome sequencing projects. The next step in understanding how biological systems, even including the human body, work is by understanding the function of all the various proteins. Solving the structure of a protein is an important first step in elucidating its function; however, the study of its dynamic movements can specifically implicate regions involved in its function and even demonstrate the mechanism by which function is performed.

Molecular dynamics simulations are a powerful computational approach for visualizing the dynamic movement of proteins. Computational tools are predominantly theory based predictions. Therefore, they require validation by experimental results. Oxidative surface mapping is an experimental labeling method which can be used to identify “buried” vs. “solvent-accessible” regions in a folded protein. Movement in specific regions of a protein can be mapped and monitored using this method.

β-lactoglobulin is a well studied protein that undergoes a pH induced conformational change. It was chosen as the target protein for this study because it has been the focus of numerous studies in the past and much information is known about it. Even so, many aspects of this protein’s structure still remain a mystery.

This thesis work is an attempt to integrate computational and experimental techniques as a strategy for studying the protein conformational change of a well studied protein system. The degree of overlap displayed by the integration of these two techniques is limited, however it provides a foundation from which improvements can be implemented for future attempts of studying protein systems using this approach.