Relating Structure to Function Through the Dominant Slow Modes of Motion of DNA Topoisomerase II

Type II DNA topoisomerases are enzymes capable of transporting one DNA duplex through another by performing a cycle of DNA cleavage, transport, and religation, coupled to ATP binding and hydrolysis. Here, we considered a coarse-grained model of the structure and investigated the motions within two structures, DNA topoisomerase II and DNA gyrase A. The coarse graining with only one point per residue means that motions in such large proteins can be thoroughly investigated. The overall motions are reflected in the crystallographic temperature factors, which are reproduced by the model. Also, with this approach, we can view the slowest, most cooperative, modes of motion, corresponding to the largest-scale correlated motions in the protein. These motions are nearly identical in the two proteins and are likely related to individual steps in the enzyme's complex mechanism of activity.