title: Modeling the self-assembly of peptide amphiphiles into fibers using coarse-grained molecular dynamics.
abstract: 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.
authors.affiliation: Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.
authors.forename: One-Sun
authors.initials: OS
authors.lastname: Lee
authors.forename: Vince
authors.initials: V
authors.lastname: Cho
authors.forename: George C
authors.initials: GC
authors.lastname: Schatz
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D019281:Dimerization; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D014867:Water