Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents?

Abstract

A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.

Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme

“…Together, these choices resulted in models with a total charge of −1, and 153 and 156 atoms for architectures I and II, respectively, which satisfies the model size proven to be required for a reasonable representation of an active site. 53 Because of previous successes in modeling similar enzymatic systems, 67,68 the M06-2X 69 functional in conjunction with 6-31G(d,p) as implemented in Gaussian 09 (revision D.01) was used to characterize the pathways. 70 Relative Gibbs energies that include thermal corrections were determined using IEFPCM 71 -M06-2X/6-311+G(2df,p) with a dielectric constant of ε = 4 (see Table S1 for a comparison of relative energies with and without the thermal corrections).…”

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

“…Previous computational studies have examined nucleic acid phosphodiester bond hydrolysis using different DFT approaches, , including the widely used B3LYP − and M06-2X ,, functionals. Although rigorous testing of the accuracy of DFT methods compared to CCSD­(T)/CBS energetic data has been performed for the hydrolysis of dimethyl phosphate in the absence of a metal, it is not clear whether the same conclusions will hold for the reaction catalyzed by a single-metal-dependent nuclease.…”

“…Importantly, our data supports the use of standard functionals (M06-2X and B3LYP-D3) for these reactions, which have been widely used in literature to study other enzymatic mechanisms. 40,97,98 Regardless, the model used so far is minimal and larger cluster models must be considered to determine the impact of additional amino acids on the reaction mechanism and associated barriers.…”

Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I-PpoI

“…Since the inclusion of implicit solvent during optimizations has been shown to minimally impact the energetics of enzymecatalyzed reactions for cluster models larger than 100 atoms, 67,[73][74][75] each QM cluster RC was optimized in the gas phase using B3LYP-D3(BJ)/6-31G(d,p) calculations. Subsequently, a guess for a concerted TS was generated by constraining the key reaction parameters involved in the attack of nucleophilic water on the phosphorus reaction center (r(PÁ Á ÁO w ) = 1.9-2.2 Å) and cleavage of phosphodiester bond (r(P-O3 0 ) = 1.9-2.2 Å).…”