THE ESSENTIAL DYNAMICS OF CU, ZN SUPEROXIDE-DISMUTASE - SUGGESTION OFINTERSUBUNIT COMMUNICATION

A 300-ps molecular dynamics simulation of the whole Cu, Zn superoxide dismutase dimer has been carried out in water, and the trajectory has been analyzed by the essential dynamics method. The results indicate t hat the motion is defined by few preferred directions identified by th e first four to six eigenvectors and that the motion of the two monome rs at each instant is not symmetrical. The vectors symmetrical to the eigenvectors are significantly sampled, suggesting that, on average, t he motions of the two subunits will exchange. Large intra- and intersu bunit motions involving different subdomains of the protein are observ ed. A mechanical coupling between the two subunits is also suggested, because displacements of the loops surrounding the active site in one monomer are correlated with the motion of parts of the second toward t he intersubunit interface.