Abstract
K. Anton Feenstra, Herman J. C. Berendsen and Alan E. MarkHierarchical Motion in Small Proteins: Implications for Protein Folding
Extensive molecular dynamics simulations within a series of proteins have been used to identify elements which show highly concerted motion as well as below average internal mobility. Although secondary structure elements are frequently assumed to be comparatively rigid the motionally coherent elements identified often did not coincide with major secondary structure elements, within the proteins examined. A hierarchical organization of these motionally coherent elements was observed. This may be related to a hierarchy of folding with smaller elements being considered as possible protein folding nucleation sites or foldons.
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