Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin

Biophys J. 2001 May;80(5):2082-92. doi: 10.1016/S0006-3495(01)76182-6.


Molecular dynamics studies of the N-domain (amino acids 1-77; CaM(1-77)) of Ca2+-loaded calmodulin (CaM) show that a solvent exposed hydrophobic cleft in the crystal structure of CaM exhibits transitions from an exposed (open) to a buried (closed) state over a time scale of nanoseconds. As a consequence of burying the hydrophobic cleft, the R(g) of the protein is reduced by 1.5 A. Based on this prediction, x-ray scattering experiments were conducted on this domain over a range of concentrations. Models built from the scattering data show that the R(g) and general shape is consistent with the simulation studies of CaM(1-77). Based on these observations we postulate a model in which the conformation of CaM fluctuates between two different states that expose and bury this hydrophobic cleft. In aqueous solution the closed state dominates the population, while in the presence of peptides, the open state dominates. This inherent flexibility of CaM may be the key to its versatility in recognizing structurally distinct peptide sequences. This model conflicts with the currently accepted hypothesis based on observations in the crystal structure, where upon Ca2+ binding the hydrophobic cleft is exposed to solvent. We postulate that crystal packing forces stabilize the protein conformation toward the open configuration.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Biophysical Phenomena
  • Biophysics
  • Calcium / chemistry
  • Calcium / metabolism
  • Calmodulin / chemistry*
  • Computer Simulation
  • Crystallography, X-Ray
  • Dose-Response Relationship, Drug
  • Methionine / chemistry
  • Models, Molecular
  • Models, Theoretical
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Scattering, Radiation
  • Time Factors
  • Water / chemistry
  • Water / metabolism
  • X-Rays


  • Calmodulin
  • Water
  • Methionine
  • Calcium