title: Complex between human RNase HI and the phosphonate-DNA/RNA duplex: molecular dynamics study.
abstract: Our 200ns MD simulations show that even fully modified oligonucleotides bearing the 3'-O-P-CH2-O-5' (but not 3'-O-CH2-P-O-5') phosphonate linkages can be successfully attached to the surface of Human RNase H. It enables to explain that oligonucleotides consisting of the alternating 3'-O-P-CH2-O-5' phosphonate and phosphodiester linkages are capable to elicit the RNase H activity (while the 3'-O-CH2-P-O-5' phosphonates are completely inactive). Stability of the binuclear active site of Human RNase H was achieved using the one-atom model for Mg(2+) in conjunction with a polarized phosphate group of the scissile bond, which is wedged between both magnesium ions. The reference MD simulation (lasting for 1000ns), which was produced using a well-established seven-point (with dummy atoms) model for Mg(2+) led to essentially the same results. The MD run (lasting for 500ns) produced for the Thermus thermophilus Argonaute enzyme shows the transferability of our approach for the stabilization of a binuclear active site. Glu512 was bound in the T. thermophilus Argonaute active site to the 2'-OH of the nucleotide adjacent to the scissile phosphate and one of the two active-site divalent metal ions in exactly the same way as Glu186 in Human RNase H. Glu512 thus completes the catalytic tetrad of Argonaute.
authors.affiliation: Charles University, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, Prague 2 121 16, Czech Republic.
authors.forename: Kamil
authors.initials: K
authors.lastname: Maláč
authors.forename: Ivan
authors.initials: I
authors.lastname: Barvík
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry*; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D063065:Organophosphonates / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry*; D016914:Ribonuclease H / Q000737:chemistry*
chemical_list: D008024:Ligands; D063065:Organophosphonates; D012313:RNA; D004247:DNA; D016914:Ribonuclease H; C078856:ribonuclease HI
keywords: ACEMD; Antisense oligonucleotides; Argonaute; Molecular dynamics; Phosphonate; RNAi; RNase H