Computational analysis of DNA gyrase action

Abstract

DNA gyrase introduces negative supercoiling into circular DNA by catalyzing the passage of one DNA segment through another. The efficiency of the reaction is many times higher than that of other topological transformations. We analyze, by a computer simulation, the reaction selectivity for a model of DNA gyrase action that assumes existence of a free loop between the G- and T- DNA segments participating in the reaction. A popular model of this type assumed that the selectivity can be provided by the conformation of the DNA segment wrapped around the enzyme into the right-handed helix turn (G-segment). We simulated the distribution of the reaction products for this model. Equilibrium sets of DNA conformations with one segment of the double helix wrapped around the enzyme were constructed. From these sets we selected conformations that had a second segment properly juxtaposed with the first one. Assuming that the juxtapositions result in the strand-passing reaction, we calculated the reaction products for all these conformations. The results show that different products have to be formed if the enzyme acts according to the model. This conclusion can be extended for any model with a free loop between the G- and T-segments. An alternative model that is consistent with the major experimental observations and the computational analysis, is suggested. © 2004 by the Biophysical Society.