Histone lysine methyltransferase SET7/9: Formation of a water channel precedes each methyl transfer

Molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have been carried out in an investigation of histone lysine methyltransferase (SET7/9). Proton dissociation (SET7/9 center dot Lys4-NH3+center dot AdoMet -> SET7/9 center dot Lys4-NH2 center dot AdoMet + H+) must be prior to the methylation by S-adenosylmethionine (AdoMet). We find that a water channel is formed to allow escape of the proton to solvent. The water channel appears in the presence of AdoMet, but is not present in the species SET7/9 center dot Lys4-NH3+ or SET7/9 center dot Lys4-N(Me)H-2(+)center dot AdoHcy. A water channel is not formed in the ground state of SET7/9 center dot Lys4-N(Me)H-2(+)center dot AdoMet, and the second methyl transfer does not occur. The structure of SET7/9 center dot Lys4-N(Me)H-2(+)center dot AdoMet includes a greater distance (6.1 +/- 0.3 angstrom) between C gamma(AdoMet) and N(MeLys4) than is present in SET7/9 center dot Lys4-NH3+center dot AdoAMet (5.7 +/- 0.2 angstrom)The electrostatic interactions between the positive charges on AdoMet and SET7/9 center dot Ly4-NH3+ decrease the pK(a) of the latter from 10.9 +/- 0.4 to 8.2 +/- 0.6, and this is not seen in the SET7/9 center dot Lys4-N(Me)H-2(+)center dot AdoMet species. The formation, or not, of a water channel, the distance between S delta(AdoMet) and N(Lys4), and the angle S delta(AdoMet)-C gamma(AdoMet)-N(Lys4) determine whether methyl transfer can occur. By QM/MM, the calculated free energy barrier of the methyl transfer reaction in the SET7/9 [Lys4-NH2 + AdoMet -> Lys4-N(Me)H-2(+) + AdoHcy] complex is Delta G(not equal) = 19.0 1.6 kcal/mol. This Delta G(not equal) is in agreement with the value of 20.9 kcal/mol calculated from the experimental rate constant (0.24 min(-1)).