A new constraint potential for the structure refinement of biomolecules in solution using experimental nuclear overhauser effect intensity

Stawarz, Bernard; Genest, Monique; Genest, D.

doi:10.1002/bip.360320606

Cited by 10 publications

(2 citation statements)

References 26 publications

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“…Often a quadratic potential is used (y = 2), directly with the NOE intensities (x = 1) (Yip and Case, 1989;Baleja et al, 1990;Bonvin et al, 1991;Mertz et al, 1991) or with their sixth-root (x TM 1/6) (Nilges et al, 1991) or inverse sixth-root (x = -1/6) (Stawarz et al, 1992), the last two definitions being closer to a standard distance-based potential. When averaging is introduced, the theoretical intensities A ~~ Instead of in Eq.…”

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confidence: 99%

Time- and ensemble-averaged direct NOE restraints

1994

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NMR data are collected as time- and ensemble-averaged quantities. Yet, in commonly used methods for structure determination of biomolecules, structures are required to satisfy simultaneously a large number of constrainsts. Recently, however, methods have been developed that allow a better fit of the experimental data by the use of time- or ensemble-averaged restraints. Thus far, these methods have been applied to structure refinement using distance and J-coupling restraints. In this paper, time and ensemble averaging is extended to the direct refinement with experimental NOE data. The implementation of time- and ensemble-averaged NOE restraints in DINOSAUR is described and illustrated with experimental NMR data for crambin, a 46-residue protein. Structure refinement with both time- and ensemble-averaged NOE restraints results in lower R-factors, indicating a better fit of the experimental NOE data.

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confidence: 99%

Time- and ensemble-averaged direct NOE restraints

1994

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“…A penalty function is then applied to minimize the differences in the ensemble-calculated volume and target volume. , Currently, a simple harmonic penalty term based on the difference in the volumes is utilized. The analytical function for the cross-peak volume with respect to the atomic coordinates will be incorporated soon .…”

Section: Experimental Methodsmentioning

confidence: 99%

Overlapping Ensemble Dynamics: A Method for Structure Calculations of Multiple Configurational Isomers

Mierke

1998

J. Am. Chem. Soc.

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A computational approach to utilize the overlapping NOE cross-peak intensities of multiple configurational isomers (e.g., cis/trans isomerization about substituted amide bonds in peptides or proteins) is illustrated. The method, overlap ensemble dynamics, utilizes an ensemble containing the appropriate ratio of the configurational isomers. The NOE intensities, containing contributions from different isomers, are then used as a constraining function to the entire ensemble. In this manner, NOE cross-peaks which before had to be ignored can now be readily used in the computation-based structural refinement. This method should find widespread use given the large number of small molecules of pharmaceutical and medicinal interest with substituted amides and multiple configurational isomers in their NMR spectra.

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