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Science 13 June 2008:
Vol. 320. no. 5882, pp. 1471 - 1475
DOI: 10.1126/science.1157092
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Research Articles

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

Oliver F. Lange,1* Nils-Alexander Lakomek,2* Christophe Farès,2 Gunnar F. Schröder,1 Korvin F. A. Walter,2 Stefan Becker,2 Jens Meiler,3 Helmut Grubmüller,1 Christian Griesinger,2{dagger} Bert L. de Groot1{dagger}

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.

1 Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
2 Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
3 Vanderbilt University Center for Structural Biology, Nashville, TN 37212, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: cigr{at}nmr.mpibpc.mpg.de (C.G.); bgroot{at}gwdg.de (B.L.dG.)

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Science. ISSN 0036-8075 (print), 1095-9203 (online)