Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation

Figures & data

Figure 1 Representative snapshots of insertion of the HA-FD-13 peptide into an armchair (20,20) CNT at various times. For clarity, molecules of water have not been shown.

Figure 2 Representative snapshots of insertion of HA-FD-13 into an armchair (20,20) HCNT at various times. For clarity, molecules of water have not been shown.

Figure 3 Center of mass (CoM) distance between (A) HA-FD-13 and the CNT; (B) HA-FD-13 and the HCNTs as a function of simulation time; vdW interaction between (C) HA-FD-13 and the CNT (20,20); (D) HA-FD-13 and the HCNT (20,20); (E) coulombic interaction between HA-FD-13 and the HCNT (20,20) as a function of simulation time.

Figure 4 Potential of mean force (PMF) for systems of (A) CNT–peptide and (B) HCNT–peptide complexes computed from ten pullings through the MD simulation. The images represent the positions of HA-FD-13 corresponding to the z-coordinate along the (A) CNT and (B) HCNT at key positions.

Table 1 Energy contributions (kcal.Mol⁻¹) in the spontaneous encapsulation of HA-FD-13 inside CNTs (20,20). : Free energy variation of the whole system in the encapsulation process. : Entropy variation of the whole system. : Enthalpy variation of the whole system. : Kinetic energy variation of the system in the encapsulation process. : Multiplication of the volume of the system and pressure change of the whole system, : Potential energy variation of the system, composed of vdW energy change (), Elec energy change (), and bonded-atom energy change ()

–43.91
2,949.62	–2,993.53
	–2,576.543	11.273	–428.26
			–310.5	–198.28	80.52

Table 2 Energy contributions (kcal.Mol⁻¹) in the spontaneous encapsulation of HA-FD-13 inside the HCNT (20,20). : Free energy variation of the whole system in the encapsulation process. : Entropy variation of the whole system. : Enthalpy variation of the whole system. : Kinetic energy variation of the system in the encapsulation process. : Multiplication of the volume of the system and the pressure change of the whole system. : Potential energy variation of the system, composed of vdW energy change (), Elec energy change (), and bonded-atom energy change ()

–69.2
1,648.42	–1,717.62
	–1,257.71	180.96	–640.87
			–7.176	–677.46	43.766

Figure 5 (A) Axial views of HA-FD-13 at 0 and 15 ns in the MD simulation. For the sake of clarity, molecules of water have not been shown. (B) Root mean square deviation (RMSD) of HA-FD-13 as a function of simulation time. (C) Radius gyration of HA-FD-13 as a function of simulation time in the CNT– HA-FD-13 complex.

Figure 6 (A) Axial views of HA-FD-13 at 0 and 15 ns in the MD simulation. For the sake of clarity, molecules of water have not been shown. (B) Root mean square deviation (RMSD) of HA-FD-13 as a function of simulation time. (C) Radius gyration of HA-FD-13 as a function of simulation time in the HCNT–peptide complex.

Figure 7 Distance between the center of mass (CoM) of HA-FD-13 and the central axis of (A) the CNT and (B) HCNT as a function of simulation time. Potential energy of HA-FD-13 in the (C) CNT–peptide complex and (D) HCNT–peptide as a function of simulation time.