QM/MM MD Simulations on the Enzymatic Pathway of the Human Flap Endonuclease (hFEN1) Elucidating Common Cleavage Pathways to RNase H Enzymes

摘要: Flap endonucleases (FENs) are nucleic acid hydrolyzing enzymes in charge of excising 5′-small DNA and RNA fragments (flaps) protruding from structures during the lagging strand replication or long-patch base excision repair (LP-BER) processes. In this work we report, for first time, an atomistic energetic rendering enzymatic catalysis promoted by human FEN1. After reconstruction a reactive hFEN/double (ds) adduct employed mixed quantum-classical (QM/MM) metadynamics umbrella sampling free energy calculations, with QM part treated AM1/d-PhoT Hamiltonian, to perform extensive characterization all possible reaction pathways underlying cycle. Our investigation points most likely pathway very similar that recently proposed ribonuclease H, which rate-determining step is nucleophilic attack water scissile phosphate, occurs concomitantly its activation t...