Functionally important correlated motions in the single-stranded DNA binding protein encoded by filamentous phage Pf3

To elucidate the interplay between different parts of dimeric single-strand ed DNA-binding proteins we have studied the correlated motions in the prote in encoded by filamentous phage Pf3 via the combined use of N-15-NMR relaxa tion experiments, molecular dynamics simulations and essential dynamics cal culations. These studies provide insight into the mechanism underlying the protein-DNA binding reaction. The most important motions can be described b y a few essential modes. Most outstanding is the correlated symmetric motio n of the DNA-binding wings, which are far apart in the structure. This moti on determines the access of DNA to the DNA-binding domain. A correlation be tween the motion of the DNA-binding wing and the complex loop is indicated to play a role in the cooperative binding of the protein to DNA. These moti ons are in the nanosecond regime in correspondence with the 15N-NMR relaxat ion experiments. (C) 1999 Academic Press.