Figure 1.
Proposed catalytic mechanism for GCN5/H3/AcCoA complex, (a) Three processes involved in the whole reaction, deprotonation, intermediate and production; (b) detailed mechanism for transition state and intermediate formation, critical atoms are numeric labeled for clarity.
Figure 2.
Time dependencies of the weighted root-mean-square deviations (wRMSDs) for the backbone atoms of GCN5/H3/AcCoA complex, AcCoA, H3 and GCN5 from their initial positions during the 20 ns simulation.
Figure 3.
Residue fluctuations obtained by average residual fluctuations over the 20 ns simulation are illustrated in dashed lines, while the solid lines stands for the experimental results calculated from B factors of hGCN5 (PDB code: 1Z4R) crystal structure.
Figure 4.
Conformation changes of AcCoA among original crystal structure, modeling structure and structure after MD simulation.
The rectangle region corresponds to the 3′-phosphate ADP part of AcCoA, which implies the most different part among the three structures, indicating to transform into the appropriate conformation to provide the proper interactions with substrate H3.
Figure 5.
Number of average hbonds during 20 ns simulation.
Figure 6.
Time dependencies of hbond analysis for the whole H3 peptide showing critical residues for H3 tail binding and strong hbonds network for acetylation reaction center.
Figure 7.
Residues involved in hbonds with AcCoA along the 20 ns simulation. Labels are listed for clarity.
Figure 8.
Time dependencies of hydrophobic analysis for the whole H3 peptide, suggesting the recognition of G-K-X-P sequence (Gly170-Pro173) and the importance of loop α1-α2 (Arg38 and Met39, in gray regions of Gly170, Lys171, Ala172 and Arg174), α2 helix (Glu42 and Tyr43, in gray regions of Lys166 and Gly169) and loop α1-β7 (Lys148 and Tyr150, in gray regions of Thr168, Gly169 and Gly170) for substrate binding.
Figure 9.
Residues in hydrophobic interactions with AcCoA along the 20 ns simulation time series.
Labels are listed for clarity.
Figure 10.
The potential energy surface (PES) of reaction pathway for GCN5/H3/AcCoA complex.
(A) Energy barriers of transition state (TS1) of addition process and intermediate production (INTMED) are marked along the defined reaction coordinates. (B) Contour plot of the PES corresponding to (A). The pink triangle line represents the lowest energy path according to the calculation of PES, positions of reactant (R), transition state 1 (TS1) and intermediate product (INTMED) are also displayed. (C) Critical structures along the reaction coordinate. Information of bonds formation and rupture is displayed and labeled in yellow dashed lines.
Figure 11.
Whole relative energy profile along the reaction coordinate, reactant (R), transition state 1 (TS1), intermediate product (INTMED), transition state 2 (TS2) and final product (P).
Relative energy barriers are labeled for each state.
Figure 12.
Overall structure of GCN5/H3/AcCoA complex and the interactions.
Two important loops involved in H3 binding, α1-α2 loop and α1-β7 loop are illustrated. Hbond interactions indicate those residues in hydrogen bonds with H3, which are displayed in yellow dashed lines in left enlarged figure; hydrophobic interactions presented in right enlarged figure indicate those residues forming hydrophobic interactions with H3 to provide appropriate reaction environment.
Figure 13.
Critical residues (atoms) for QM region in QM/MM calculation.
Hbonds involved in deprotonation and acetylation reaction paths are labeled in yellow dashed lines.