There is a still growing interest in graphene interactions with proteins; both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding from amino acid composition is desirable. In this work we systematically studied the adsorption process of amino acids onto pristine graphene via rigurous free-energy calculations. We characterized the free energy, potential energy, and entropy of adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free-energy and the Solvent Accessible Surface Area change during adsorption(Δ SASA^ads). Free energies over pristine graphene were compared with adsorption onto graphene oxide (GO), finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with the Δ SASA^ads was used to successfully predict the free-energy of adsorption of penta-L-alanine in two different structural states. Due to the relative ease of calculating the Δ SASA^ads compared to free-energy calculations, it could prove a cost-effective predictor of the free-energy of adsorption for proteins onto non-polar surfaces.

• data: data used for figures, scripts and tables may reference these files
  • 5ala: PMF(ξ) of peptides
  • glutamic: analysis of gluamate intramolecular interactions
  • pmfs: PMF(ξ) for all amino acids over graphene
  • tables: .csv files for different energetic components
  • unbias: unbiased energies
• figures: For all figures
• gromos: Input files for GROMOS (1.4.0)
• paper: .tex files for the article
• scripts: any relevant script for the creation of figures (there is also a “copy files” script but it is only expected to work on my computer)