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

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

Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.

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

Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.