Nanomechanical response of peptide-bound DNA as a model molecular bio-nanocomposite: a steered molecular dynamics...

This study presents an atomistic nanomechanical investigation of peptide-bound DNA systems treated as model molecular bio-nanocomposites (BNCs). Octa-arginine (R8) and octa-lysine (K8) peptides were comparatively examined as cationic molecular components interacting with a short DNA duplex. The results indicate that DNA-R8 forms more persistent peptide-DNA contacts than DNA-K8, mainly due to the guanidinium side-chain chemistry of arginine. Mechanical analysis based on stress-strain behavior showed that the DNA-R8 BNC model exhibited the highest apparent Young's modulus (0.253 ± 0.007 GPa), corresponding to an increase of approximately 70% relative to DNA alone (0.147 ± 0.009 GPa) and approximately 40% relative to DNA-K8 (0.175 ± 0.008 GPa). DNA-K8 showed a moderate increase of approximately 20% relative to DNA alone. The mechanical properties obtained for DNA alone were within the range of representative reported values, supporting the use of the present protocol for relative comparative analysis. These findings highlight the role of peptide side-chain chemistry in modulating the apparent nanomechanical response of model DNA-peptide BNC systems under the present simulation conditions.

Molecular docking, classical molecular dynamics (MD), and steered molecular dynamics (SMD) simulations are employed to investigate the structural and mechanical behavior of DNA-peptide model molecular bio-nanocomposite (BNC) systems. Interaction energies and structural stability are evaluated using MD simulations, while apparent mechanical properties are derived from stress-strain curves obtained through SMD simulations. The simulations are performed using a consistent biomolecular force-field protocol, and all software and computational details are provided in the main manuscript.