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

Nature Structural & Molecular Biology volume 19, pages 1053–1057 (2012)Cite this article

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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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References

  1. Clore, G.M. & Schwieters, C.D. How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J. Am. Chem. Soc. 126, 2923–2938 (2004).

    Article  CAS  Google Scholar 

  2. Clore, G.M. & Schwieters, C.D. Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43, 10678–10691 (2004).

    Article  CAS  Google Scholar 

  3. Lindorff-Larsen, K., Best, R.B., DePristo, M.A., Dobson, C.M. & Vendruscolo, M. Simultaneous determination of protein structure and dynamics. Nature 433, 128–132 (2005).

    Article  CAS  Google Scholar 

  4. Bouvignies, G. et al. Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. Proc. Natl. Acad. Sci. USA 102, 13885–13890 (2005).

    Article  CAS  Google Scholar 

  5. Clore, G.M. & Schwieters, C.D. Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α/β protein: a unified picture of high probability, fast atomic motions in proteins. J. Mol. Biol. 355, 879–886 (2006).

    Article  CAS  Google Scholar 

  6. Tang, C., Schwieters, C.D. & Clore, G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449, 1078–1082 (2007).

    Article  CAS  Google Scholar 

  7. Markwick, P.R.L., Bouvignies, G. & Blackledge, M. Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J. Am. Chem. Soc. 129, 4724–4730 (2007).

    Article  CAS  Google Scholar 

  8. Lange, O.F. et al. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. Science 320, 1471–1475 (2008).

    Article  CAS  Google Scholar 

  9. Baldwin, A.J. & Kay, L.E. NMR spectroscopy brings invisible protein states into focus. Nat. Chem. Biol. 5, 808–814 (2009).

    Article  CAS  Google Scholar 

  10. Markwick, P.R.L. et al. Toward a unified representation of protein structural dynamics in solution. J. Am. Chem. Soc. 131, 16968–16975 (2009).

    Article  CAS  Google Scholar 

  11. Bui, J.M., Gsponer, J., Vendruscolo, M. & Dobson, C.M. Analysis of sub-tc and supra-tc motions in protein Gb1 using molecular dynamics simulations. Biophys. J. 97, 2513–2520 (2009).

    Article  CAS  Google Scholar 

  12. Vögeli, B. & Yao, L. Correlated dynamics between HN and HC bonds observed by NMR cross relaxation. J. Am. Chem. Soc. 131, 3668–3678 (2009).

    Article  Google Scholar 

  13. Shaw, D.E. et al. Atomic-level characterization of the structural dynamics of proteins. Science 330, 341–346 (2010).

    Article  CAS  Google Scholar 

  14. Fenwick, R.B. et al. Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition. J. Am. Chem. Soc. 133, 10336–10339 (2011).

    Article  CAS  Google Scholar 

  15. Wüthrich, K. NMR of Proteins and Nucleic Acids (Wiley, 1986).

  16. Vögeli, B. et al. Exact distances and internal dynamics of perdeuterated ubiquitin form NOE buildups. J. Am. Chem. Soc. 131, 17215–17225 (2009).

    Article  Google Scholar 

  17. Vögeli, B., Friedmann, M., Leitz, D., Sobol, A. & Riek, R. Quantitative determination of NOE rates in perdeuterated and protonated proteins: practical and theoretical aspects. J. Magn. Reson. 204, 290–302 (2010).

    Article  Google Scholar 

  18. Olejniczak, E.T., Dobson, C.M., Karplus, M. & Levy, R.M. Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme. J. Am. Chem. Soc. 106, 1923–1930 (1984).

    Article  CAS  Google Scholar 

  19. Keepers, J.W. & James, T.L. A theoretical study of distance determinations from NMR. Two-dimensional nuclear Overhauser effect spectra. J. Magn. Reson. 57, 404–426 (1984).

    CAS  Google Scholar 

  20. Brüschweiler, R. et al. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J. Am. Chem. Soc. 114, 2289–2302 (1992).

    Article  Google Scholar 

  21. Leitz, D., Vögeli, B., Greenwald, J. & Riek, R. Temperature dependence of 1HN-1HN distances in ubiquitin as studied by exact measurements of NOEs. J. Phys. Chem. B 115, 7648–7660 (2011).

    Article  CAS  Google Scholar 

  22. Koning, T.M.G., Boelens, R. & Kaptein, R. Calculation of the nuclear Overhauser effect and the determination of proton-proton distances in the presence of internal motions. J. Magn. Reson. 90, 111–123 (1990).

    CAS  Google Scholar 

  23. Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298 (1997).

    Article  Google Scholar 

  24. Güntert, P. Automated structure determination from NMR spectra. Eur. Biophys. J. 38, 129–143 (2009).

    Article  Google Scholar 

  25. Derrick, J.P. & Wigley, D.B. The third IgG-binding domain from streptococcal protein G: an analysis by X-ray crystallography of the structure alone and in a complex with Fab. J. Mol. Biol. 243, 906–918 (1994).

    Article  CAS  Google Scholar 

  26. Yao, L., Vögeli, B., Torchia, D.A. & Bax, A. Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis. J. Phys. Chem. B 112, 6045–6056 (2008).

    Article  CAS  Google Scholar 

  27. Brüschweiler, R., Blackledge, M. & Ernst, R.R. Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide. J. Biomol. NMR 1, 3–11 (1991).

    Article  Google Scholar 

  28. Brünger, A.T., Clore, G.M., Gronenborn, A.M., Saffrich, R. & Nilges, M. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science 261, 328–331 (1993).

    Article  Google Scholar 

  29. Bonvin, A.M.J.J. & Brünger, A.T. Conformational variability of solution nuclear magnetic resonance structures. J. Mol. Biol. 250, 80–93 (1995).

    Article  CAS  Google Scholar 

  30. Chou, J.J., Case, D.A. & Bax, A. Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings. J. Am. Chem. Soc. 125, 8959–8966 (2003).

    Article  CAS  Google Scholar 

  31. Ulmer, T.S., Ramirez, B.E., Delaglio, F. & Bax, A. Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J. Am. Chem. Soc. 125, 9179–9191 (2003).

    Article  CAS  Google Scholar 

  32. Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277–293 (1995).

    Article  CAS  Google Scholar 

  33. Johnson, B.A. & Blevins, R.A. A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614 (1994).

    Article  CAS  Google Scholar 

  34. Bakan, A. & Bahar, I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl. Acad. Sci. USA 106, 14349–14354 (2009).

    Article  CAS  Google Scholar 

  35. Bakan, A., Meireles, L.M. & Bahar, I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27, 1575–1577 (2011).

    Article  CAS  Google Scholar 

  36. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    Article  CAS  Google Scholar 

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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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Authors and Affiliations

  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland

    Beat Vögeli & Roland Riek

  2. Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance and Frankfurt Institute for Advanced Studies, J.W. Goethe-Universität, Frankfurt am Main, Germany

    Sina Kazemi & Peter Güntert

  3. Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan

    Peter Güntert

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  1. Beat Vögeli
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  2. Sina Kazemi
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Contributions

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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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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