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 PM in water using coarse-grained molecular dynamics simulations. Nine independent 16 mu s 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 similar to 80 angstrom appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to similar to 15 angstrom away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and similar to 92% of the epitope is exposed to water molecules.