Molecular Dynamics Simulations for Actin Monomers in Solution

Molecular dynamics simulations were performed for an actin monomer without Ca2+ and nucleotide for a period of 100 psec in order to study the stable structure and fluctuations of actin monomers in solution. For the initial structure for the molecular dynamics simulations, we used the X-ray structure of an actin monomer isolated from the actin: DNase I complex analyzed by Kabsch et al. (1990, Nature, Lond.347, 37-44). We found that the overall structure of the actin monomer obtained from the simulations was similar to the initial structure except for two parts. One was the α-helix of residues 223-230 and the other was the loop of residues 40-50, which corresponds to the contact site with DNase I. The latter large shift of about 7 Å from the X-ray structure was concluded to be due to the loss of DNase I from the complex.