Studies on the structure and stability of cyclic peptide based nanotubes using oligomeric approach: a computational chemistry investigation

Abstract

In this study, an attempt has been made to investigate the structure, dynamics, and stability of cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) using classical molecular dynamics (MD) simulation and semiempirical quantum chemistry calculation employing PM6 Hamiltonian with the dispersion correction and hydrogen-bonding interaction (DH2). The structure and energetics of monomer and various oligomeric CPNTs have been investigated by considering the (cyclo-[(D-Ala-l-Ala)₄]) peptide as the model for CP. Although the formation of CPNTs has been intensively studied, the present study adds valuable information to the de novo design of CPNTs. Various geometrical parameters extracted from the MD simulation reveal that the terminal residues are loosely hydrogen bonded to the inner subunits regardless of degree of oligomerization. The hydrogen bonds present in the inner core regions are stronger than the terminal residues. As the degree of oligomerization increases, the stability of the tube increases due to the hydrogen-bonding and stacking interactions between the subunits. The results show that the binding free energy increases with the extent of oligomerization and reaches saturation beyond pentamer CPNT. In addition, hydrophobic and electrostatic interactions play crucial roles in the formation of CPNTs. Analysis of both structure and energetics of the formation of CPNTs unveils that the self-assembly of dimer, trimer, and tetramer CPNTs are the essential steps in the growth of CPNTs.