UC San Diego

Three dimensional structure determination and analysis of proteins is necessary for the understanding of how proteins participate in human disease, and are critical for the effective design of therapeutics for clinically important targets. Current efforts for determining protein structures are centered on novel high-throughput (HT) approaches. These include high throughput (HT) crystallization efforts and global structure prediction efforts monitored through the Critical Assessment of Structure Prediction (CASP) experiments where progress has been incremental at best. Protein structure analysis of conformational changes and protein-proteins interactions can be monitored by biophysical methods which include fluorescence spectroscopy, differential scanning calorimetry, circular dichroism and ultra centrifugation. These methods provide adequate low resolution information on global changes in secondary and tertiary structure but are limited in providing detailed information on protein structure, protein conformational changes and protein- protein interactions. Therefore, there is a great need for improvements in the speed and ease of determining and analyzing protein structures and protein dynamics. Hydrogen/Deuterium (H/D) exchange rates are highly dependent on protein structure and amide hydrogen solvent accessibility. Exchange rates can report structure stability at the individual amino acid scale and provide important information on the secondary and tertiary structure. The dissertation is arranged as follows: Chapter 1 is an introduction to Hydrogen/Deuterium exchange mass spectrometry and also reports my studies on the thrombin-Lepirudin complex. Chapter 2 is in preparation for submission and reports the application of DXMS for characterizing the molecular dynamics of spectrin. It also presents the development and validation studies for a computational method for generating amide exchange rate maps from DXMS data, a critical component of the structure determination method described in Chapters six and seven. Chapter 3 reports the application of DXMS for structural analysis of drug-protein interactions. Chapter 4 reports methods for using DXMS to improve the crystallizability of protein constructs for 3D structure determination by x ray crystallography. Chapter 5 reports the detailed 3-D structures of the first two proteins that were successfully studied with the DXMS- guided construct design method. Chapter 6 outlines the development of a hybrid computational-experimental method for high- throughput protein 3-D structure determination: DXMS- Rosetta-COREX engine. Chapter 7 summarizes my conclusions from the foregoing studies and outlines future directions of these studies