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Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562

Brinkley, James F and Altman, R. B. and Duncan, B. S. and Buchanan, B. G. and Jardetzky, O. (1988) Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562. J. Chem. Inf. Comput. Sci. 28(4):pp. 194-210.

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Abstract

A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent computational intractability of this approach is reduced by assembling the protein in pieces, by considering the protein at several levels of abstraction, by utilizing constraint satisfaction methods to consider only a few atoms at a time, and by utilizing artificial intelligence methods of heuristic control to decide which actions will exclude the most conformations. Example results are presented for simulated NMR data from the known crystal structure of cytochrome b562 (103 residues). For 10 sample backbones an average root-mean-square deviation from the crystal of 4.1 A was found for all alpha-carbon atoms and 2.8 A for helix alpha-carbons alone. The 10 backbones define the family of all structures compatible with the data and provide nearly correct starting structures for adjustment by any of the current structure determination methods.

Item Type:Journal (Paginated)
Keywords:braincr96 kaz96 nihcv nmr spectroscopy proteins slisp95 structure prediction sig
Subjects:SIG Publications
ID Code:15
Deposited By:Hinshaw, Kevin
Deposited On:01 May 2003