A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
J Mol Biol. 1999 Jan 29;285(4):1691-710
Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE
We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a limited set of long-range NMR distance constraints. The NMR data sets are derived from a realistic protocol involving completely deuterated 15N and 13C-labeled samples. A global optimization method, based upon a modification of the alphaBB (branch and bound) algorithm of Floudas and co-workers, is employed to minimize an objective function combining the NMR distance restraints with a residue-based protein folding potential containing hydrophobicity, excluded volume, and van der Waals interactions. To assess the efficacy of the new methodology, results are compared with benchmark calculations performed via the X-PLOR program of Brünger and co-workers using standard distance geometry/molecular dynamics (DGMD) calculations. Seven mixed alpha/beta proteins are examined, up to a size of 183 residues, which our methods are able to treat with a relatively modest computational effort, considering the size of the conformational space. In all cases, our new approach provides substantial improvement in root-mean-square deviation from the native structure over the DGMD results; in many cases, the DGMD results are qualitatively in error, whereas the new method uniformly produces high quality low-resolution structures. The DGMD structures, for example, are systematically non-compact, which probably results from the lack of a hydrophobic term in the X-PLOR energy function. These results are highly encouraging as to the possibility of developing computational/NMR protocols for accelerating structure determination in larger proteins, where data sets are often underconstrained.
PMID: 9917406 [PubMed - indexed for MEDLINE]
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PubMed