Theoretical investigation of the binding free energies and key substrate-recognition components of the replication fidelity of human DNA polymerase β

We present a theoretical study of the selection of right/wrong dNTP substrates by DNA polymerases at the initial binding step. a major component of the DNA replication fidelity. Linear-response analysis (LRA) and molecular dynamics simulations are performed starting from the X-ray crystal structure of a ternary DNA polymerase beta . DNA . ddCTP complex. These simulations provide converged structures of ternary complexes containing all four Watson-Crick (W-C) pairs as well as 11 neutral mismatched dNTP-template base pairs in the anti-anti conformations. The signs and overall magnitudes of the calculated relative free energies for binding of each DNA polymerase beta . DNA complexes, which contain either correct or incorrect templating bases, agree with the observed universal preference of DNA polymerases for W-C base pairs. Overall, the binding free-energy differences of each dNTP to right versus wrong templates are found to be dominated by electrostatic interactions between templating and dNTP bases. However, about half of the electrostatic contribution can be attributed to the steric preorganization of the polymerase active site that was generated by the protein folding process. The preorganized site maintains optimal W-C pairing for matched bases while forcing mismatched pairs into configurations far from their ideal gas-phase geometries. Consequently, the preorganized site is responsible for large template contributions to fidelity. Individual additive contributions to fidelity are determined for active site residues. Interactions between incoming dNTPs and Asn279 and Tyr262 protein residues contribute significantly to the binding component of fidelity, with the Asn279 residue most effective in destabilizing each of the 15 nucleotide mispairs in neutral anti-anti conformations. Active site amino acids can also exert deleterious effects on fidelity. Tyr-262 enhances base substitution fidelity via mispair destabilization, but it also stabilizes slipped mispaired primer-template structures that are potential precursors for +1 frameshift mutations. The inclusion of an extra water molecule in the active cleft was found to stabilize several wobble base pairs. Calculations performed at this level of "fine" detail are used to predict the effects of amino acid substitutions on the fidelity for mutant forms of pol beta, thus providing a deeper understanding of the role of the polymerase active site in ensuring replication accuracy.