Structural basis for the role of LYS220 as proton donor for nucleotidyl transfer in HIV-1 Reverse transcriptase

Servaas Michielssens (1) , Samuel L.C. Moors (1) , Mathy Froeyen (1) , Piet Herdewijn (1) , Arnout Ceulemans (1)

1 KU Leuven - Catholic University of Leuven = Katholieke Universiteit Leuven

Biochemical studies by Castro have recently revealed a crucial role for a general acid in the catalysis of nucleic acid transfer in distinct classes of polymerases. For HIV-RT LYS220 was identified as proton donor. This was unanticipated from a structural point of view, since in all ternary crystal structures of HIV-RT LYS220 is too distant from the active site to fulfill this role. In this work molecular dynamics simulations were used to reveal the dynamics of HIV-RT and to provide structural evidence for the role of LYS220. During a 1 molecular dynamics simulation LYS220 migrates toward the active site and occupies several positions enabling direct and water mediated proton transfer towards pyrophosphate. A combination of quantum mechanical and molecular mechanics methods was used to validate the different modes of interaction.

Mots clés: HIV reverse transcriptase; QM/MM; Molecular Dynamics; Protein dynamics; Enzymatic catalysis

Domaines: Chimie-Physique [physics.chem-ph]

Servaas Michielssens, Samuel L.C. Moors, Mathy Froeyen, Piet Herdewijn, Arnout Ceulemans. Structural basis for the role of LYS220 as proton donor for nucleotidyl transfer in HIV-1 Reverse transcriptase. Biophysical Chemistry, 2011, ⟨10.1016/j.bpc.2011.03.009⟩. ⟨hal-00759072⟩