Atomic-Level Study of Adsorption, Conformational Change, and Dimerization of an α-Helical Peptide at Graphene Surface

Abstract

Recent circular dichroism spectroscopy and scanning tunneling microscopy study reported that a de novo designed α-helical peptide (with amino acid sequence DELERRIRELEARIK) would transform to β-sheet structure as well as random coil structure upon the addition of graphite particles to the peptide solution and aggregate into ordered β-sheet-rich assemblies at the graphite surface. However, the atomic-level information about the dynamics of early stage conformational transition at water-graphite interface and the driving force underlying the structural transition is largely unknown. In this study, we have investigated the conformational dynamics of two chains of the α-helical peptide in the absence and presence of a graphene sheet by performing all-atom molecular dynamic simulations in explicit solvent at 310 and 330 K. Our simulations show that consistent with the signal measured experimentally under physiological buffer conditions, two chains are mostly dimeric and keep α-helical structure in solution, whereas they unfold and assemble into an amorphous dimer at graphene surface. The β-sheet conformation is not observed in all MD runs within the 15-200 ns times scale, which indicates that the α-helix to β-sheet transition for this short peptide at graphite surface is a slow process, similar to the slow transition dynamics of globular protein reported experimentally. By analyzing all MD trajectories, we found that (1) the formation of α-helical dimer in solution is mostly driven by interpeptide hydrophobic interactions; (2) the adsorption and the α-helix unfolding of the peptide at graphene surface is initiated from the C-terminal region due to strong interactions between residues Arg13-Ile14-Lys15 and graphene surface; (3) the extent of helix unfolding strongly depends on the interaction strength between the peptide and graphene surface; and (4) the dimerization of two unfolded peptide chains at graphene surface results from the interplay between peptide-graphene and peptide-peptide interactions. This study would provide significant insight into the detailed mechanism of graphite-induced conformational transition and dimerization prior to the formation of β-sheet assemblies of this short synthetic α-helical peptide.