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

Abstract

Abstract Biochemical studies by Castro et al. 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 μs 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.

Graphical abstract

Research highlights ►A structural explanation for the catalytic role of Lys220 in HIV-RT is offered using molecular dynamics simulations. QM/MM optimizations are used to asses the quality of the structures found on a quantum mechanical potential. The results are compared to the ensemble of available crystal structures of this protein.