Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path-search algorithm

Branch migration of the Holliday junction takes place at the center of the RuvA tetramer. To elucidate how branch migration occurs, umbrella sampling simulations were performed for complexes of the RuvA tetramer and Holliday junction DNA. Although conventional umbrella sampling simulations set sampling points a priori, the umbrella sampling simulation in this study set the sampling points one by one in order to search for a realistic path of the branch migration during the simulations. Starting from the X-ray structure of the complex, in which the hydrogen bonds between two base-pairs were unformed, the hydrogen bonds between the next base-pairs of the shrinking stems were observed to start to disconnect. At the intermediate stage, three or four of the eight unpaired bases interacted closely with the acidic pins from RuvA. During the final stage, these bases moved away from the pins and formed the hydrogen bonds of the new base-pairs of the growing stems. The free-energy profile along this reaction path showed that the intermediate stage was a meta-stable state between two free-energy barriers of about 10 to 15 kcal/mol. These results imply that the pins play an important role in stabilizing the interactions between the pins and the unpaired base-pairs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010