Modeling the self-assembly of peptide amphiphiles into fibers using coarse-grained molecular dynamics

We have studied the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber starting from a homogeneous mixture of PAs in water using coarse-grained molecular dynamics simulations. Nine independent 16 μs runs all show spontaneous fiber formation in which the PA molecules first form spherical micelles, and then micelles form a three-dimensional network via van der Waals interactions. As the hydrophobic core belonging to the different micelles merge, the three-dimensional network disappears and a fiber having a diameter of ∼80 Å appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to ∼15 Å away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and ∼92% of the epitope is exposed to water molecules.