Comparing X-RAY and NMR Protein Structures Using Computational Geometry

Abstract

X-ray crystallography is widely used to solve high resolution protein structures, but only when the protein can be crystalized. NMR spectroscopy can be performed in solution, which is much more similar to the natural protein environment in a 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 in the cells. Computational geometry analysis of nearest neighbor residues in different conformations of NMR ensemble 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 simplex, and type of simplex (based on sequence).