434114 Role of Protein Sequence in Driving Molecular Interactions Between Proteins and Carbon Nanomaterials: A Molecular Dynamics Study

Wednesday, November 11, 2015: 8:46 AM
255B (Salt Palace Convention Center)
Siva Dasetty, Chemical and Bimolecular Engineering, Clemson University, Clemson, SC and Sapna Sarupria, Chemical and Biomolecular Engineering, Clemson University, Clemson, SC

Carbon nanomaterials (CNM’s) are commonly used for biological applications, such as drug delivery, biosensors due to their high stability, large surface area and nanoscale dimensions. In order to engineer biologically safer CNMs it is important to understand the molecular interactions of CNMs with proteins which constitute a large part of the biological environment. In our recent combined experimental and molecular dynamics study we found that bovine serum albumin strongly interacts with one of the CNM, graphene nanoribbon (GNR) compared to graphene oxide nanoribbon (GONR). It is often postulated that the driving forces for this association are hydrophobic and van der waals interactions, primarily due to pi-pi stacking of aromatic amino acids of proteins and CNMs. However, there are other factors such as defects and curvature of CNMs, as well as the protein sequence that could have an impact on the protein-CNM interactions. To elucidate the effect of neighboring residues on protein-CNM interactions, we investigate the binding free energy of tripeptides to GNR using biased molecular dynamics simulations. We study X-PHE-GLY tripeptides, where X is a charged/uncharged residue and phenylalanine (PHE) is the chosen reference aromatic residue. In this context, it is expected that the (aromatic) interactions of the GNR with PHE will drive the tripeptide-GNR interactions. By using different residues in the X position we investigate how these driving forces are influenced by protein sequence. Specifically, we have calculated the potential of mean force between the tripeptide and GNR using umbrella sampling. Our results indicate that the strength of binding is influenced by the neighboring residues. Interestingly, the largest free energy of binding was observed for the GLY-PHE-GLY tripeptide. In our talk, we will present detailed results with various tripeptides and discuss the implications of our findings in understanding interactions of proteins with CNMs.

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