A random graph approach to NMR sequential assignment.
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding connectivity (e.g., through-bond atomic interactions) and amino acid type, typically using the former to determine strings of connected residues and the latter to map those strings to positions in the primary sequence. Significant ambiguity exists in both connectivity and amino acid type information. This paper focuses on the information content available in connectivity alone and develops a novel random-graph theoretic framework and algorithm for connectivity-driven NMR sequential assignment. Our random graph model captures the structure of chemical shift degeneracy, a key source of connectivity ambiguity. We then give a simple and natural randomized algorithm for finding optimal assignments as sets of connected fragments in NMR graphs. The algorithm naturally and efficiently reuses substrings while exploring connectivity choices; it overcomes local ambiguity by enforcing global consistency of all choices. By analyzing our algorithm under our random graph model, we show that it can provably tolerate relatively large ambiguity while still giving expected optimal performance in polynomial time. We present results from practical applications of the algorithm to experimental datasets from a variety of proteins and experimental set-ups. We demonstrate that our approach is able to overcome significant noise and local ambiguity in identifying significant fragments of sequential assignments.
Bailey-Kellogg
Chris
C
Department of Computer Science, Dartmouth College, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA. cbk@cs.dartmouth.edu
Chainraj
Sheetal
S
Pandurangan
Gopal
G
D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins