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.