Dynamics and Catalytic Mechanism of Histone Demethylase PHF8

PHF8 is histone lysine demethylase that demethylates dimethylated lysine residues in H3 histone protein. The enzyme is involved in key events of the epigenetic regulation and has been linked to mental retardation and other pathologies. While success in understanding structure-function relationships of this enzyme was achieved using X-ray crystallographic, biochemical and mutagenic studies, so far there is no knowledge about its reaction mechanism and the effect of the conformational dynamics on the enzyme structure and functions. In order to provide understanding into this missing areas, we performed combination from molecular dynamics simulations (MD), Electronic Structure (ES) and Combined Quantum Mechanics and Molecular Mechanics (QM/MM) Calculations. The MD studies provided atomistic insights into the effects of the conformational dynamics and collective motions into enzyme structure, interactions with the co-substrates. The QM/MM studies revealed the mechanistic aspect of the oxygen activation processes as well the hydrogen abstraction (HAT) and rebound hydroxylation steps. Furthermore, HAT step is calculated to be the rate-limiting step. We explored the effects of conformational dynamics and effects of mutations on the HAT step. The results demonstrate the potential of multiscale computational methods to provide an insight that complement the experimental methods