Molecular Dynamics Simulation Study on Binding Affinity of Integrin and RGD-QWNT for Enhanced Biosensor Performance

This study is a molecular dynamics (MD) simulation investigation analyzing the binding affinity between integrin and RGD-QWNT to enhance the performance of protein detection sensors. When a sp3 quantum defect is induced in a semiconducting (6,5) single-walled carbon nanotube (SWCNT), a new energy level is formed within the band gap, significantly improving its fluorescence emission performance. By attaching the target-specific receptor, an RGD peptide, to this quantum defect carbon nanotube (QWNT), integrin can be selectively and precisely detected. This study conducted MD simulations to examine the mechanism of the enhanced integrin target detection performance at the molecular level upon RGD attachment.
To compare the interactions of the integrin protein with pristine QWNT and RGD-QWNT complexes, the binding energy, contact interfaces, and structural dynamics were analyzed. Through energetic analysis, the primary driving forces of binding were identified by calculating electrostatic attractions and van der Waals forces. In addition, the atomic contact frequencies on the protein surface were analyzed to identify key binding hotspots. Furthermore, the stability of specific binding due to RGD attachment was verified by comparatively analyzing the persistence of hydrogen bonds, the dynamic behavior of the nanomaterial, and the changes in flexibility (RMSF) of the core protein loops.
Based on these binding conformations, Steered Molecular Dynamics (SMD) and Umbrella Sampling were performed to gradually detach the nanomaterial from the integrin, deriving the Potential of Mean Force (PMF) and the final binding energy. This study quantitatively demonstrates the enhanced target binding affinity of RGD-QWNT through MD simulations, providing a structural basis for the design of high-performance nano-biosensors.