Geometric analysis of cross-linkability for protein fold discrimination.
Protein structure provides insight into the evolutionary origins, functions, and mechanisms of proteins. We are pursuing a minimalist approach to protein fold identification that characterizes possible folds in terms of consistency of their geometric features with restraints derived from relatively cheap, high-throughput experiments. One such experiment is residue-specific cross-linking analyzed by mass spectrometry. This paper presents a suite of novel lower- and upper-bounding algorithms for analyzing the distance between surface cross-link sites and thereby validating predicted models against experimental cross-linking results. Through analysis and computational experiments, using simulated and published experimental data, we demonstrate that our algorithms enable effective model discrimination.
Potluri
S
S
Dept of Comp. Sci., Purdue Univ., West Lafayette, IN 47907, USA.
Khan
A A
AA
Kuzminykh
A
A
Bujnicki
J M
JM
Friedman
A M
AM
Bailey-Kellogg
C
C
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D003432:Cross-Linking Reagents; D013058:Mass Spectrometry; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry
D003432:Cross-Linking Reagents; D011506:Proteins