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Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs

Abstract

Proteins are inherently dynamic systems whose motions cover large ranges in both magnitude and timescale. Because of the omnipresence of motion, it is likely that dynamics have important roles in the function of biomolecules. For detailed understanding of a protein's function, the three-dimensional structure and description of its dynamics are therefore required. Structure determination methods are well established, and NMR-relaxation phenomena provide insights into local molecular dynamics; moreover, recently several attempts have been made to detect concerted motion. Here, we present an ensemble-based structure-determination protocol using ensemble-averaged distance restraints obtained from exact NOE rates. Application to the model protein GB3 establishes an ensemble of structures that reveals correlated motion across the β-sheet, concerted motion between the backbone and side chains localized in the structure core, and a lack of concerted conformational exchange between the β-sheet and the α-helix.

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Figure 1: Heavy-atom structural representations of GB3 following either the classical protocol with NOEs as experimental input, the classical protocol with eNOEs or the ensemble-based protocol with eNOEs.
Figure 2: Target-function (TF) values of various ensemble-based structure calculations of GB3, highlighting the importance of the ensemble-based structure calculation (left) and the self-consistency of the data by cross-validations (right).
Figure 3: Structural space coverage of the ensemble-based structure of GB3.
Figure 4: Structural representation of a three-state ensemble of GB3.

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Acknowledgements

We thank L. Wang (Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Zürich) for the preparation of the GB3 NMR sample. P.G. gratefully acknowledges financial support from the Lichtenberg program of the Volkswagen Foundation.

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B.V., P.G. and R.R. designed the study; B.V. conducted measurements; P.G. did the software programming; B.V., P.G., S.K. and R.R. analyzed the data.

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Correspondence to Roland Riek.

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The authors declare no competing financial interests.

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Supplementary Tables 1 and 2 (DOC 1442 kb)

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Vögeli, B., Kazemi, S., Güntert, P. et al. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs. Nat Struct Mol Biol 19, 1053–1057 (2012). https://doi.org/10.1038/nsmb.2355

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