[NMR paper] Protein structure determination by conformational space annealing using NMR geometric restraints.

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Protein structure determination by conformational space annealing using NMR geometric restraints.

Related Articles Protein structure determination by conformational space annealing using NMR geometric restraints.

Proteins. 2015 Oct 10;

Authors: Joo K, Joung I, Lee J, Lee J, Lee W, Brooks B, Lee SJ, Lee J

Abstract
We have carried out numerical experiments to investigate the applicability of the global optimization method of conformational space annealing (CSA) to the enhanced NMR protein structure determination over existing PDB structures. The NMR protein structure determination is driven by the optimization of collective multiple restraints arising from experimental data and the basic stereo-chemical properties of a protein-like molecule. By rigorous and straightforward application of CSA to the identical NMR experimental data used to generate existing PDB structures, we re-determined 56 recent PDB protein structures starting from fully randomized structures. The quality of CSA-generated structures and existing PDB structures were assessed by multi-objective functions in terms of their consistencies with experimental data and the requirements of protein-like stereo-chemistry. In 54 out of 56 cases, CSA-generated structures were better than existing PDB structures in the Pareto-dominant manner, while in the remaining two cases, it was a tie with mixed results. As a whole, all structural features tested improved in a statistically meaningful manner. The most improved feature was the Ramachandran favored portion of backbone torsion angles with about 8.6% improvement from 88.9% to 97.5% (P-value < 10(- 17) ). We show that by straightforward application of CSA to the efficient global optimization of an energy function, NMR structures will be of better quality than existing PDB structures. This article is protected by copyright. All rights reserved.


PMID: 26454251 [PubMed - as supplied by publisher]



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