Metal ion binding of the alpha-gamma hybrid cyclic peptide nanotubes--a theoretical study based on the ONIOM method.
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.
Praveena
Gopalan
G
Department of Physics, Bharathiar University, Coimbatore 641046, India.
Kolandaivel
Ponmalai
P
D008670:Metals; D008958:Models, Molecular; D015233:Models, Statistical; D045333:Nanotubes, Peptide / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D011485:Protein Binding; D013816:Thermodynamics
D008670:Metals; D045333:Nanotubes, Peptide; D010456:Peptides, Cyclic