Understanding the non-covalent adsorption of biomolecules on graphene is of fundamental importance towards addressing applications of graphene in biosensors and biomedicine. Since biological function depends not only on its primary sequence but also on its structural conformation which is influenced by the interacting surface and environment. Studies to understand the sequence-structure-function (SSF) relationship of peptides on surfaces are underway in several research groups. All-atom molecular dynamics (MD) simulation is a tool that provides a complementary means to study the SSF relationships. However, the adsorption-induced conformational change is usually a slow process taking microseconds or longer, which is beyond traditional MD simulation time-scales. To overcome this challenge, we report on a new strategy to obtain the conformational and kinetic information of peptides adsorbed onto graphene. In this strategy, intermediate conformations are generated from low resolution experimental data obtained from circular dichroism (CD) spectroscopy and scanning tunneling microscopy (STM) analysis. Starting with all possible distinguishable intermediate conformations, local equilibrium simulations are then conducted. The trajectories are analyzed using the geometrical clustering and kinetic grouping analysis. The adsorbed peptide conformation, the adsorption pathway and kinetic information can be extracted. This strategy is applied to a previously studied 15-mer peptide [D1-E2-L3-E4-R5-R6-I7-R8-E9-L10-E11-A12-R13-I14-K15], which is known to adsorb onto graphene. Experimental observations have shown that the peptide undergoes an a-helix to �-like sheet transition when adsorbed onto a graphene sheet. Using our methodology, we demonstrate that our computational approach recapitulates the conformational and associated kinetic transitions.

Computational studies on adsorption-induced structural and kinetic properties of peptides on graphene

248th National Meeting (2014)

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