Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

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 (nCaM). In this model, tw...

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Vydáno v:The Journal of chemical physics Ročník 128; číslo 20; s. 205104
Hlavní autoři: Tripathi, Swarnendu, Portman, John J
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 28.05.2008
Témata:
Binding Sites
Calcium - metabolism
Calmodulin - chemistry
Calmodulin - metabolism
Kinetics
Methionine
Microcomputers
Models, Molecular
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
Thermodynamics
Time Factors
ISSN:1089-7690, 1089-7690
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Shrnutí: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 (nCaM). In this model, two energy basins corresponding to the "closed" apo conformation and "open" holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EFbeta-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 EFbeta-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 nCaM.
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ISSN:1089-7690
1089-7690
DOI:10.1063/1.2928634