Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution.

Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KF, Becker S, Meiler J, Grubmüller H, Griesinger C, de Groot BL
Science. 2008 320 (5882): 1471-5

PMID: 18556554 · DOI:10.1126/science.1157092

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.

MeSH Terms (16)

Amino Acid Motifs Animals Anisotropy Chemical Phenomena Chemistry, Physical Crystallography, X-Ray Entropy Kinetics Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Binding Protein Conformation Protein Structure, Tertiary Solutions Ubiquitin Xenopus laevis

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