title: Simulations of peptide-graphene interactions in explicit water.
abstract: The interaction of graphene with biomolecules has a variety of useful applications. In particular, graphitic surfaces decorated with peptides are being considered for high performance biochemical sensors. The interaction of peptides with graphene can also provide insight into the binding behavior of larger biomolecules. In this investigation, we have computed the binding enthalpies of a series of GXG tripeptides with graphene using classical molecular dynamics. Explicit water molecules were included to capture the effect of solvent. Of the twenty amino acid residues examined (X in GXG), arginine, glutamine, and asparagine exhibit the strongest interactions with graphene. Analysis of the trajectories shows that the presence of graphene affects the peptide conformation relative to its conformation in solution. We also find that the peptides favor the graphene interface predominantly due to the influence of the solvent, with hydrophilic residues binding more strongly than hydrophobic residues. These results demonstrate the need to include explicit solvent atoms when modeling peptide-graphene systems to mimic experimental conditions. Furthermore, the scheme outlined herein may be widely applicable for the determination and validation of surface interaction parameters for a host of molecular fragments using a variety of techniques, ranging from coarse-grained models to quantum mechanical methods.
authors: Air Force Research Laboratory, Materials & Manufacturing Directorate , 2941 Hobson Way, WPAFB, Ohio 45433, United States.
authors: Aerial N
authors: AN
authors: Camden
authors: Stephen A
authors: SA
authors: Barr
authors: Rajiv J
authors: RJ
authors: Berry
mesh_terms: D001120:Arginine / Q000737:chemistry; D001216:Asparagine / Q000737:chemistry; D003198:Computer Simulation; D005973:Glutamine / Q000737:chemistry; D006108:Graphite / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D014867:Water; D005973:Glutamine; D001216:Asparagine; D006108:Graphite; D001120:Arginine