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

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 are 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.

Research Highlights► One microsecond molecular dynamics simulation of HIV-RT in complex with DNA and a nucleotide is performed. ► A large movement of LYS220 occurs and provides a structural basis for its role in catalysis. ► The different states of interaction are optimized using QM/MM to validate the interaction. ► The structural variability in the domain containing LYS220 is also observed in the ensemble of crystal structures.