2-O'-Transesterifcation catalyzed by RNase A enzyem has been intensivly investigated via experiments and theoretical studies but the detailed mechanism is still not clear in the literature. Here we performed computational study to explore the mechansim of RNase A 2’-O-Transesterifcation reaction using a series of QM/MM umbrella sampling simulations. The computational results show that the possible mechanism is initiated by the rotation of the residue His12 and then the attack of O2' group to phosphorus atom, which forms an intermediate protonated and stablized by residue Lys41; the 5’O group leaves via a concerted mechanism as the rate-limiting step and a dianionic transition state, producing an acyclic phosphate and the molecule with the O5’ hydroxyl group. The predicted barrier is12.5 kcal/mol, which is in excellent agreement with the available experiment value. In this mechanism, the flip of His12 is investigated, which makes His12 toward O2' group with a right orientation for the attack and reduce the reaction barrier.

Catalytic mechanism of RNase A transphosphorylation

253rd National Meeting (2017)

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