Binding Affinities of Amino Acids on Graphene: Assessment of Force Fields

Graphene–protein interactions are central to understanding the biocompatibility of graphene (GRA). Understanding these interactions is important for many diverse applications such as biosensors, theranostics, cosmetics and electronics. The mechanisms and driving forces that govern protein and peptide interactions with GRA are not completely understood. Recent experimental and simulation studies indicate a dominance of aromatic amino acids and arginine in mediating the GRA–peptide interactions. However, in our previous combined experimental and simulation study of albumin adsorption on GRA, we observed no such dominant effect from any of the amino acids.[1]

Furthermore, recently reported binding strengths for these amino acids on GRA have been inconsistent. In general, most of the force fields employed are developed to represent proteins in aqueous media but not at material interfaces, such as graphene and self-assembled monolayers. In a recent study, the free energy of adsorption of peptides on silica surfaces using CHARMM force field was observed to deviate as large as 5-9 kcal/mol with the experimental data. This highlights the need to carefully evaluate the different force-fields available to describe protein systems in the context of GRA-protein interactions. To this end, we have performed extensive simulations to calculate the free energy of adsorption of amino acids on GRA. Specifically, we have used umbrella sampling method to determine the potential of mean force of all twenty amino acids using three of the widely employed force fields–—Amberff99SB-ILDN, CHARMM-36 and OPLS-AA/M in explicit water. We compare the calculated free energy of adsorption with the available experimental data. In our talk, we will present these detailed results discussing the trends and their implications in understanding GRA–peptide interactions.

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[1]

Sengupta, Bishwambhar, Wren E. Gregory, Jingyi Zhu, Siva Dasetty, Mehmet Karakaya, Jared M. Brown, Apparao M. Rao, John K. Barrows, Sapna Sarupria, and Ramakrishna Podila. "Influence of carbon nanomaterial defects on the formation of protein corona." RSC Advances 5, no. 100 (2015): 82395-82402.

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See more of this Session: Molecular Simulation of Protein Adsorption and Molecular Recognition Processes
See more of this Group/Topical: Computational Molecular Science and Engineering Forum