Rapid evaluation of the binding energies between peptide amide and DNA base

Abstract

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen-bonded amide-base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N-H···N, N-H···O=C, C-H···N, and C-H···O=C dipole-dipole attractive interaction energies and C=O···O=C, N-H···H-N, and N-H···H-C dipole-dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6-311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6-311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6-311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base-peptide amide systems involving amino acid side chain and β-sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen-bonded peptide amide-DNA base dimers quickly and accurately.