Willy Wriggers, Ernest Mehler, Felicia Pitici, Harel Weinstein, and Klaus Schulten. Structure and dynamics of calmodulin in solution. Biophysical Journal, 74:1622-1639, 1998.
To characterize the dynamic behavior of calmodulin in solution, we have carried out molecular dynamics (MD) simulations of the Ca²+-loaded structure. The crystal structure of calmodulin was placed in a solvent sphere of radius 44 Å, and 6 Cl- and 22 Na+ ions were included to neutralize the system and to model a 150 mM salt concentration. The total number of atoms was 32,867. During the 3 ns simulation the structure exhibits large conformational changes on the nanosecond time scale. The central alpha-helix, which has been shown to unwind locally upon binding of calmodulin to target proteins, bends and unwinds near residue Arg74. We interpret this result as a preparative step in the more extensive structural transition observed in the ``flexible linker'' region 74-82 of the central helix upon complex formation. The major structural change is a reorientation of the two Ca²+-binding domains with respect to each other and a rearrangement of alpha-helices in the N-terminus domain which make the hydrophobic target peptide binding site more accessible. This structural rearrangement brings the domains to a more favorable position for target binding, poised to achieve the orientation observed in the complex of calmodulin with myosin-light-chain-kinase. Analysis of solvent structure reveals an inhomogeneity in the mobility of water in the vicinity of the protein which is attributable to the hydrophobic effect exerted by calmodulin's binding sites for target peptides.
