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. 2012 May 18;7(5):e37674. doi: 10.1371/journal.pone.0037674

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Chu et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) A representative active-site structure along with the average values of some structural parameters of the reactant complex for the first methyl transfer. GLP is shown in balls and sticks, and AdoMet and the H3K9 sidechain are in sticks. Hydrogen atoms are not shown for clarity except for those on N_ζ and transferable methyl group. Hydrogen bonds are indicated by red dotted lines, and the distances related to the reactant coordinate are also shown. (B) Left: the two-dimensional plot of r(C_M…N_ζ) and θ distributions based on the 1.5-ns simulations of the reactant complex for the first methyl transfer; Middle: the free-energy change as a function of r(C_M…N_ξ) obtained from the distributions; Right: the free-energy change as a function of θ obtained from the distributions. (C) The active-site structure along with the average values of some structural parameters of the reactant complex for the second methyl transfer. (D) Left: the two-dimensional plot of r(C_M…N_ζ) and θ distributions of the reactant complex for the second methyl transfer; Middle: the free-energy change as a function of r(C_M…N_ξ) obtained from the distributions; Right: the free-energy change as a function of θ obtained from the distributions. (E) The structure of the reactant complex for the third methyl transfer. (F) Left: the two-dimensional plot of r(C_M…N_ζ) and θ distributions of the reactant complex for the third methyl transfer; Middle: the free-energy change as a function of r(C_M…N_ξ) obtained from the distributions; Right: the free-energy change as a function of θ obtained from the distributions. (G) A representative active-site structure along with the average values of some structural parameters near the transition state for the first methyl transfer obtained from the free energy (potential of mean force) simulations. (H) The structure along with the average values of some structural parameters near the transition state for the second methyl transfer. (I) The structure near the transition state for the third methyl transfer. All images were made by VMD [38]. The distances shown on the structures are the calculated average distances from the trajectories over the 50-ps production runs in the corresponding window.