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

Vögeli, Beat; Kazemi, Sina; Güntert, Peter; Riek, Roland
October 2012
Nature Structural & Molecular Biology;Oct2012, Vol. 19 Issue 10, p1053
Academic Journal
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 ?-sheet, concerted motion between the backbone and side chains localized in the structure core, and a lack of concerted conformational exchange between the ?-sheet and the ?-helix.


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