Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin

We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (C...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS Vol. 106; no. 7; p. 2104
Main Authors: Tripathi, Swarnendu, Portman, John J
Format: Journal Article
Language:English
Published: United States 17.02.2009
Subjects:
Allosteric Site
Amino Acid Motifs
Calcium - metabolism
Calmodulin - chemistry
EF Hand Motifs - genetics
Humans
Kinetics
Models, Molecular
Models, Statistical
Molecular Conformation
Pliability
Protein Conformation
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
ISSN:1091-6490, 1091-6490
Online Access:Get more information
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Summary:We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals "cracking" or local partial unfolding during the open/closed transition. This result is in harmony with the picture that cracking relieves local stresses caused by conformational deformations of a sufficiently rigid protein. We also compare the conformational transition in a recently studied even-odd paired fragment of CaM. Our results rationalize the different relative binding affinities of the EF-hands in the engineered fragment compared with the intact odd-even paired EF-hands (nCaM and cCaM) in terms of changes in flexibility along the transition route. Aside from elucidating general theoretical ideas about the cracking mechanism, these studies also emphasize how the remarkable intrinsic plasticity of CaM underlies conformational dynamics essential for its diverse functions.
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ISSN:1091-6490
1091-6490
DOI:10.1073/pnas.0806872106