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KNOWLEDGE-BASED VERSUS EXPERIMENTALLY ACQUIRED DISTANCE AND ANGLE CONSTRAINTS FOR NMR STRUCTURE REFINEMENT

FENG CUI

Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

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ROBERT JERNIGAN

Program on Bioinformatics and Computational Biology, Iowa State University, Ames, IO 50011, USA

Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IO 50011, USA

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and

ZHIJUN WU

Program on Bioinformatics and Computational Biology, Iowa State University, Ames, IO 50011, USA

Department of Mathematics, Iowa State University, Ames, IO 50011, USA

Corresponding author.

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https://doi.org/10.1142/S0219720008003448Cited by:0

Abstract

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

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Vol. 06, No. 02

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History

Received 16 July 2007

Revised 30 October 2007

Accepted 17 November 2007

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KNOWLEDGE-BASED VERSUS EXPERIMENTALLY ACQUIRED DISTANCE AND ANGLE CONSTRAINTS FOR NMR STRUCTURE REFINEMENT

Abstract

References

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