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Journal of Biomolecular NMR

, Volume 57, Issue 3, pp 211–218 | Cite as

Stereospecific assignments in proteins using exact NOEs

  • Julien Orts
  • Beat Vögeli
  • Roland Riek
  • Peter Güntert
Article

Abstract

Recently developed methods to measure distances in proteins with high accuracy by “exact” nuclear Overhauser effects (eNOEs) make it possible to determine stereospecific assignments, which are particularly important to fully exploit the accuracy of the eNOE distance measurements. Stereospecific assignments are determined by comparing the eNOE-derived distances to protein structure bundles calculated without stereospecific assignments, or an independently determined crystal structure. The absolute and relative CYANA target function difference upon swapping the stereospecific assignment of a diastereotopic group yields the respective stereospecific assignment. We applied the method to the eNOE data set that has recently been obtained for the third immunoglobulin-binding domain of protein G (GB3). The 884 eNOEs provide relevant data for 47 of the total of 75 diastereotopic groups. Stereospecific assignments could be established for 45 diastereotopic groups (96 %) using the X-ray structure, or for 27 diastereotopic groups (57 %) using structures calculated with the eNOE data set without stereospecific assignments, all of which are in agreement with those determined previously. The latter case is relevant for structure determinations based on eNOEs. The accuracy of the eNOE distance measurements is crucial for making stereospecific assignments because applying the same method to the traditional NOE data set for GB3 with imprecise upper distance bounds yields only 13 correct stereospecific assignments using the X-ray structure or 2 correct stereospecific assignments using NMR structures calculated without stereospecific assignments.

Keywords

Stereospecific assignment NOE Distance restraint Protein structure CYANA 

Notes

Acknowledgments

This work was financially supported by the Swiss National Science Foundation (Grant 140214 to B.V.), the Federation of the European Biochemical Societies (FEBS long-term fellowship to J.O.), and the Eidgenössische Technische Hochschule Zürich. P.G. gratefully acknowledges financial support by the Lichtenberg program of the Volkswagen Foundation, the Japan Society for the Promotion of Science (JSPS), and the Deutsche Forschungsgemeinschaft (DFG).

Supplementary material

10858_2013_9780_MOESM1_ESM.pdf (1.6 mb)
Supplementary material 1 (PDF 1597 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Laboratory of Physical ChemistrySwiss Federal Institute of TechnologyZurichSwitzerland
  2. 2.Center for Biomolecular Magnetic Resonance, Institute of Biophysical ChemistryGoethe University Frankfurt am MainFrankfurt am MainGermany
  3. 3.Frankfurt Institute for Advanced StudiesGoethe University Frankfurt am MainFrankfurt am MainGermany
  4. 4.Graduate School of Science and EngineeringTokyo Metropolitan UniversityHachiojiJapan

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