Metal Ion Binding of the $\alpha$– $\gamma$ Hybrid Cyclic Peptide Nanotubes—A Theoretical Study Based on the ONIOM Method

Abstract

The quantum mechanics/molecular mechanics ONIOM calculations have been performed to study the structure and metal-ion binding properties of all-trans cyclo[1R-3S-gamma-Acc-Gly]3 hexapeptide nanotube (TAG)3PNT. The intersubunit distances and tube angle of (TAG)3PNT exhibited the sturdy nature of (TAG)3 stacks upon Li+ , K+ , Mg2+, and Zn2+ enclosure.The calculated dimer binding energies of (TAG)3PNT and its ionic complexes confirm that the building blocks are bound by C=O...H-N hydrogen bond interactions. The binding energy of (TAG)3PNT with ions interacting at the surface cavity exhibit the affinity of ions at the entrance of the channel and the many-body analysis for the ion interacting at the central region substantiates the major contribution of two-body interactions to the total binding energy. In general, the binding energies of (TAG)3PNT metal ion interacting complexes with well-maintained channel shows alpha-gamma hybrid cyclic peptides as the promising peptidic nanochannels of biological interests.