A Computational Study of the Promiscuity of the SAM-Dependent Methyltransferase AtHTMT1

Abstract

A two-pronged computational approach was taken to study the promiscuity of the SAM + -dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl – , Br – , I – , NCO – , NCS – ). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico . The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H 2 O molecules at the reactive site favors the reaction of NCS – over Cl – and Br – in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H 2 O molecules to the N terminus of NCS – greatly increases its reactivity, while H 2 O molecules attached to Cl – slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.

Structural and Transport Properties of Norbornene-Functionalized Poly(vinyl alcohol) “Click” Hydrogel: A Molecular Dynamics Study

“…The Amber14SB force field is used to correlate the bonded and nonbonded interactions. The Amber14SB force field is an updated version of the AMBER99SB force field, which has wider applications in macromolecule simulation. – Time-resolved trajectory through MD simulations has been performed in the GROMACS-2022.3 package . The functional form of the Amber14SB force field is given by eq . where V total represents the total potential energy which is represented as the sum of bond stretching energy, angle bending energy, torsional energy for proper dihedral and improper dihedrals, van der Waal interaction energy, and Coulombic interaction energy.…”

“…The Amber14SB force field is used to correlate the bonded and nonbonded interactions. The Amber14SB force field is an updated version of the AMBER99SB force field, which has wider applications in macromolecule simulation. – Time-resolved trajectory through MD simulations has been performed in the GROMACS-2022.3 package . The functional form of the Amber14SB force field is given by eq . .25ex2ex V normalt normalo normalt normala normall = ∑ b o n d s k b false( r − r 0 false) 2 + ∑ a n g l e s k θ false( θ − θ 0 false) 2 + ∑ d i h e d r a l s k χ [ 1 + cos false( n χ − δ χ false) ] infix+ ∑ i m p r o p e r k…”

Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering

“…[328] Although most Mtases are highly specific, a few more promiscuous variants form a promising starting point for the methylation of a variety of compounds, [325] and the origin of their promiscuity was studied via QM/MM and MD simulations. [329] One promiscuous Mtase was engineered to produce cis-α-irone, an important fragrance compound. To increase specificity, a combination of MD and energy calculations was combined with experimental screening to find mutants with an impressive > 10,000-fold and > 1000-fold improvement in cis-α-irone activity and selectivity, respectively.…”

“…While a lot of insight was gained from the computational study of Mtases from pathogens such as SARS‐CoV 2, [326–327] these enzymes can also be employed in the synthetic methylation of pharmaceuticals, which can vastly increase a drug's potency (the “magic methyl effect”) [328] . Although most Mtases are highly specific, a few more promiscuous variants form a promising starting point for the methylation of a variety of compounds, [325] and the origin of their promiscuity was studied via QM/MM and MD simulations [329] . One promiscuous Mtase was engineered to produce cis‐α‐irone, an important fragrance compound.…”