The hydrolysis of RNase H: Insight into the molecular mechanism via high level 1st principle QM simulation

点击翻译按钮获取中文摘要

In our study we will complete our present investigation on the hydrolysis of the phosphodiester linkages between two nucleotides of RNA chains by human RNase H, an enzyme that binds RNA/DNA hybrid duplex substrates. In the course of our previous studies we have already identified a possible pathway for this hydrolysis, however, with energy barriers presumably too high for an enzymatic reac-tion. Just recently, we have now compiled a very promising alternative, which differs from our original hypothesis by simplifying the reaction to a 2 step mechanism. To investigate this reaction pathway in detail we will continue using a DFT based comprehensive QM/MM theoretical method and the well established nudged elastic bend (NEB) calculations to designate the stationary points and to deter-mine the free energy profile of the reaction coordinates. Starting from the RNase H structure of the wild type protein generated from the X-ray structure of the mutated enzyme-substrate complex we are going to use a series of constrained and relaxation steps to model the product and intermediate states. This will be followed by performing transition state searches and energy barrier calculations over the entire reaction coordinates and the identification of the rate limiting step of the reaction.