title: Self-assembly of cyclo-diphenylalanine peptides in vacuum.
abstract: The diphenylalanine (FF) peptide self-assembles into a variety of nanostructures, including hollow nanotubes that form in aqueous solution with an unusually high degree of hydrophilic surface area. In contrast, diphenylalanine can also be vapor-deposited in vacuum to produce rodlike assemblies that are extremely hydrophobic; in this process FF has been found to dehydrate and cyclize to cyclo-diphenylalanine (cyclo-FF). An earlier study used all-atom molecular dynamics (MD) simulations to understand the early stages of the self-assembly of linear-FF peptides in solution. Here, we examine the self-assembly of cyclo-FF peptides in vacuum and compare it to these previous results to understand the differences underlying the two cases. Using all-atom replica exchange MD simulations, we consider systems of 50 cyclo-FF peptides and examine free energies along various structural association coordinates. We find that cyclo-FF peptides form ladder-like structures connected by double hydrogen bonds, and that multiple such ladders linearly align in a cooperative manner to form larger-scale, elongated assemblies. Unlike linear-FFs which mainly assemble through the interplay between hydrophobic and hydrophilic interactions, the assembly of cyclo-FFs in vacuum is primarily driven by electrostatic interactions along the backbone that induce alignment at long-range, followed by van der Waals interactions between side chains that become important for close-range packing. While both solution and vacuum phase driving forces result in ladder-like structures, the clustering of ladders is opposite: linear-FF peptide ladders form assemblies with side-chains buried inward, while cyclo-FF ladders point outward.
authors.affiliation: Department of Chemical Engineering, University of California Santa Barbara , Santa Barbara, California 93106-5080, United States.
authors.forename: Joohyun
authors.initials: J
authors.lastname: Jeon
authors.forename: M Scott
authors.initials: MS
authors.lastname: Shell
mesh_terms: D004151:Dipeptides; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D010649:Phenylalanine / Q000031:analogs & derivatives* / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics; D014618:Vacuum
chemical_list: D004151:Dipeptides; D010455:Peptides; C026650:phenylalanylphenylalanine; D010649:Phenylalanine