Accelerating Peptoid-Surface Simulations: Peptoid Binding on Au(111) and Au(100)

Abstract

In nature, proteins and peptides are found to have specific binding on inorganic surface, especially on gold surface. However, the main challenge for synthesized proteins and peptides is their poor stability. Thus, sequence defined peptoids were found to mimic the natural behavior. F. Yan et al. recently discovered a method for designing peptoid that was able to change the morphology of the gold nanoparticles to star-shaped. However, no matter proteins, peptides or peptoids, the binding mechanism remains unknown due to difficult observation in conformational change from laboratory experiment. In our study, we used molecular dynamics simulation to investigate in atomic level for systems of peptoid on Au(111) and Au(100) surfaces, which are the most common structure for gold in nature. Combined with enhanced sampling method, we were able to obtain the binding free energy. In addition, to sample the strong binding systems, we introduced the two-step metadynamics method to accelerate the simulations.