Use of Steered Molecular Dynamics to Explore the Conformational Changes of SNARE Proteins.

Steered Molecular Dynamics (SMD) simulation is a powerful computational simulation technique that enables the controlled manipulation of molecular systems by applying external forces. This method is frequently utilized to investigate the slow processes of biomolecular systems that occur within sub-second to second time scales, achieved through SMD simulations that only span nanoseconds. SMD simulation can be utilized to study the detailed mechanism of protein conformational changes, protein unfolding, and ligand dissociation, etc. Here, we introduce the application of SMD in the study of intra-molecular interactions and regulatory mechanisms in SNAREs by analyzing their conformational change pathways.