Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Alexander Lemak, Carlos A. Steren, Cheryl H. Arrowsmith and Miguel Llinás
Journal of Biomolecular NMR; 2008; 41(1); pp 29 - 41
Abstract:
ABACUS [Grishaev et al. (2005) Proteins 61:36–43] is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic search. Here, we report further development of the two main algorithms that increase the flexibility and robustness of the method. Performance of the BACUS [Grishaev and Llinás (2004) J Biomol NMR 28:1–101] algorithm was significantly improved through use of sequential connectivities available from through-bond correlated 3D-NMR experiments, and a new set of likelihood probabilities derived from a database of 56 ultra high resolution X-ray structures. A Multicanonical Monte Carlo procedure, Fragment Monte Carlo (FMC), was developed for sequence-specific assignment of spin-systems. It relies on an enhanced assignment sampling and provides the uncertainty of assignments in a quantitative manner. The efficiency of the protocol was validated on data from four proteins of between 68–116 residues, yielding 100% accuracy in sequence specific assignment of backbone and side chain resonances.