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Floating stereospecific assignment revisited: Application to an 18 kDa protein and comparison with J-coupling data (1997)

Folmer, Rutger H.A. ; Hilbers, Cornelis W. ; Konings, Ruud N.H. ; [et al.]

Springer

Journal of biomolecular NMR 9 (1997), S. 245-258

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ISSN: 1573-5001

Keywords: Structure calculation ; Floating chirality ; Stereospecific assignment ; Simulated annealing ; ssDNA binding protein

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Abstract We report a floating chirality procedure to treat nonstereospecifically assigned methylene orisopropyl groups in the calculation of protein structures from NMR data using restrainedmolecular dynamics and simulated annealing. The protocol makes use of two strategies toinduce the proper conformation of the prochiral centres: explicit atom ‘swapping’ followingan evaluation of the NOE energy term, and atom ‘floating’ by reducing the angle andimproper force constants that enforce a defined chirality at the prochiral centre. The individualcontributions of both approaches have been investigated. In addition, the effects of accuracyand precision of the interproton distance restraints were studied. The model system employedis the 18 kDa single-stranded DNA binding protein encoded by Pseudomonas bacteriophagePf3. Floating chirality was applied to all methylene and isopropyl groups that give rise to non-degenerate NMR signals, and the results for 34 of these groups were compared to J-couplingdata. We conclude that floating stereospecific assignment is a reliable tool in protein structurecalculation. Its use is beneficial because it allows the distance restraints to be extracteddirectly from the measured peak volumes without the need for averaging or addingpseudoatom corrections. As a result, the calculated structures are of a quality almostcomparable to that obtained with stereospecific assignments. As floating chirality furthermoreis the only approach treating prochiral centres that ensures a consistent assignment of the twoproton frequencies in a single structure, it seems to be preferable over using pseudoatoms or(R-6) averaging.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1018670623695

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1H-Nmr stereospecific assignments by conformational data-base searches (1990)

Nilges, Michael ; Clore, G. Marius ; Gronenborn, Angela M.

New York : Wiley-Blackwell

Biopolymers 29 (1990), S. 813-822

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ISSN: 0006-3525

Keywords: Chemistry ; Polymer and Materials Science

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Notes: A search procedure is described for making stereospecific assignments at prochiral centers in proteins on the basis of nuclear Overhauser enhancement and coupling constant data derived from nmr experiments. A data base comprising torsion angles, associated 1H-1H coupling constants and interproton distances is searched by a computer algorithm for sets of values that match the experimental data within specified error limits. Two different data bases are used. The first is a crystallographic data base derived from 34 well-refined crystal structures; the second is a systematic data base derived from conformations of a short peptide fragment with idealized geometry by systematically varying the φ,ψ, and χ1 torsion angles. Both approaches are tested for β-methylene groups with model data obtained from 20 crystal structures. The results for the two methods are similar though not identical, so that a combination of the two methods appears to be useful. With an appropriate choice of error estimates, around 80% of the β-methylene groups could be assigned in the test calculations. In addition, results with experimental nmr data indicate that a similar percentage of stereospecific assignments can be made in practical situations.

Additional Material: 3 Tab.