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.Lys4-NH3+.AdoMet --> SET7/9.Lys4-NH2.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.Lys4-NH3+ or SET7/9.Lys4-N(Me)H2+.AdoHcy. A water channel is not formed in the ground state of SET7/9.Lys4-N(Me)H2+.AdoMet, and the second methyl transfer does not occur. The structure of SET7/9.Lys4-N(Me)H2+.AdoMet includes a greater distance (6.1 +/- 0.3 A) between Cgamma(AdoMet) and N(MeLys4) than is present in SET7/9.Lys4-NH3+.AdoMet (5.7 +/- 0.2 A). The electrostatic interactions between the positive charges on AdoMet and SET7/9.Lys4-NH3+ decrease the pKa of the latter from 10.9 +/- 0.4 to 8.2 +/- 0.6, and this is not seen in the SET7/9.Lys4-N(Me)H2+.AdoMet species. The formation, or not, of a water channel, the distance between Sdelta(AdoMet) and N(Lys4), and the angle Sdelta(AdoMet)-Cgamma(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)H2+ + AdoHcy] complex is DeltaG++ = 19.0 +/- 1.6 kcal/mol. This DeltaG++ is in agreement with the value of 20.9 kcal/mol calculated from the experimental rate constant (0.24 min(-1)).