Thesis Defense Announcement
To: The George Mason University Community
Candidate: Steven R. Bowers
Program: M.S. in Bioinformatics & Computational Biology
Date: Thursday April 24, 2014
Time: 12:00 Noon
Place: George Mason University
Prince William Campus
Bull Run Hall, Room 253
Title: "Comparing Protein Structures Generated by X-Ray Crystallography to Structures Generated by NMR Spectroscopy Using Delaunay Tessellation to Determine the Nearest Neighbor"
Thesis Director: Dr. Iosif Vaisman
Thesis Committee: Dr. Dmitri Klimov, Dr. Alessandra Luchini
A copy of the thesis will be available in the Mercer Library. All are invited to attend the defense.
X-ray Crystallography is widely used to solve high resolution protein structures, but only when the protein can be crystallized. NMR spectroscopy can be performed in solution, which is more similar to the natural protein environment in the cell. X-ray and NMR structures of the same proteins, which are available from the Protein Data Bank, are largely similar, but not identical. By understanding the differences between NMR spectroscopy and X-ray crystallography structures, it may be possible to better understand the structure and function of proteins. Computational geometry analysis of nearest-neighbor residues in different conformations of NMR ensembles is first used to identify the consistent parts of NMR structures and the factors which affect this consistency. X-ray and NMR structures of the same protein are then compared to pinpoint the differences and the factors which affect these differences. A number of geometrical and topological factors were identified which are linked to the consistency of the simplexes across the conformations, including solvent accessibility, simplex residue content, secondary structure, shape of the simplex and the type of simplex based on sequence proximity of the residues.