Theoretical Insights into Catalytic Mechanism of Protein Arginine Methyltransferase 1

<div><p>Protein arginine methyltransferase 1 (PRMT1), the major arginine asymmetric dimethylation enzyme in mammals, is emerging as a potential drug target for cancer and cardiovascular disease. Understanding the catalytic mechanism of PRMT1 will facilitate inhibitor design. However, detailed mechanisms of the methyl transfer process and substrate deprotonation of PRMT1 remain unclear. In this study, we present a theoretical study on PRMT1 catalyzed arginine dimethylation by employing molecular dynamics (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) calculation. Ternary complex models, composed of PRMT1, peptide substrate, and S-adenosyl-methionine (AdoMet) as cofactor, were constructed and verified by 30-ns MD simulation. The snapshots selected from the MD trajectory were applied for the QM/MM calculation. The typical S_N2-favored transition states of the first and second methyl transfers were identified from the potential energy profile. Deprotonation of substrate arginine occurs immediately after methyl transfer, and the carboxylate group of E144 acts as proton acceptor. Furthermore, natural bond orbital analysis and electrostatic potential calculation showed that E144 facilitates the charge redistribution during the reaction and reduces the energy barrier. In this study, we propose the detailed mechanism of PRMT1-catalyzed asymmetric dimethylation, which increases insight on the small-molecule effectors design, and enables further investigations into the physiological function of this family. </p> </div

The potential energy surface (PES) of reaction pathway for GCN5/H3/AcCoA complex.

<p>(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.</p

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.

<p>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.</p

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.

<p>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.</p

Critical residues (atoms) for QM region in QM/MM calculation.

<p>Hbonds involved in deprotonation and acetylation reaction paths are labeled in yellow dashed lines.</p

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).

<p>Relative energy barriers are labeled for each state.</p

Residues in hydrophobic interactions with AcCoA along the 20 ns simulation time series.

<p>Labels are listed for clarity.</p

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.

<p>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.</p

Conformation changes of AcCoA among original crystal structure, modeling structure and structure after MD simulation.

<p>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.</p

Number of average hbonds during 20 ns simulation.

<p>Number of average hbonds during 20 ns simulation.</p