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Roles of metal ions in the catalytic reaction of RNase H

Monday, October 24, 2011 — Poster Session I

Noon – 2:00 p.m.

Natcher Conference Center



* FARE Award Winner


  • E Rosta
  • G Hummer


Phosphate esters are essential to living systems. In a large number of enzymes, the phosphate ester hydrolysis is catalyzed by two bound divalent metal ions. We recently found that coupled proton transfer reactions emerge as central factors in the catalytic reaction, however, the exact roles of the two metal ions remains unclear. We carried out hybrid quantum-classical QM/MM free energy simulations of the catalytic reaction of the bacillus halodurans RNase H enzyme complexed with an RNA/DNA hybrid substrate. We find that the presence of both catalytic Mg-ions is an essential requirement for catalysis. Replacing either one of them with a Ca-ion abolishes the catalytic activity. Double Mn- or Ca-ion replacements have been characterized experimentally and our simulation results agree with measured catalytic activities. However, targeted single ion replacements have only been possible in our simulations. We identified that the main role of the metal ions is to decrease the pKa of the oxygen nucleophiles and, therefore, to decrease the barrier of the coupled proton transfer processes governing the catalytic reaction. Our proton transfer mechanism, together with the corresponding highly accurate transition state structure, represents an excellent target for structure-based drug design studies of novel HIV-specific inhibitors.

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