The key to understand a protein’s function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain ( n CaM) ( n CaM ) . In this model, two energy basins corresponding to the “closed” apo conformation and “open” holo conformation of n CaM n CaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EF β EF β -scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EF β EF β -scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in n CaM n CaM .
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Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin
Tripathi, Swarnendu
Follow The Journal of Chemical Physics
, Volume 128 (20)
American Institute of Physics – May 28, 2008
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