An Atomistic Molecular Dynamics Study of the Binding of Peptides onto Gold Surfaces

by Jing Yu

Institution: University of Akron
Department: Polymer Science
Degree: PhD
Year: 2012
Keywords: Chemistry; peptide; gold; adsorption; interfacial interaction
Record ID: 1962102
Full text PDF: http://rave.ohiolink.edu/etdc/view?acc_num=akron1340294273


The broad range of possible applications of gold nanoparticles (AuNPs) in the bio-sensing and bio-imaging fields has spurred a significant amount of scientific interest from both experimental and computational researchers. In particular, the binding of peptides to gold surfaces has attracted a significant amount of scientific interest recently. Our current knowledge indicates that peptides serve as protective agents for AuNPs surfaces and stabilize them against the formation of aggregates. However, a complete understanding of the adsorption behavior of gold-binding peptides and the connection between peptide adsorption and AuNP growth is still lacking, and is needed for the development of peptide-derived nanomaterials with controlled morphologies. Using Molecular Dynamics (MD) simulations we have studied the equilibrium structures and residue stabilities of the gold-binding peptide AYSSGAPPMPPF (A3) on spherical AuNPs of various sizes in order to investigate the adsorption strength at different growth stages. We have found the existence of a critical size corresponding to a maximum peptide stability which indicates a maximum binding strength. Furthermore, this result may explain how A3 controls the size of AuNPs via kinetic exchange. In order to clarify the role of the amino acid sequence during the binding process and in the equilibrium state after binding, we have designed a series of modified peptides by replacing or removing amino acid residues. A comparison of the binding process of peptide A3 obtained from five simulations started from different initial conformations showed the existence of several kinetic regimes, including one called anchoring, and identified Serine as an anchoring residue. A comparison of the adsorption behaviors of these modified peptides with the adsorption behavior of A3 helped clarify the functions of individual residues during the various binding stages. For example, we have found that Tyrosine, Methionine and Phenylalanine are strong binding residues, Serine serves as an effective anchoring residue, and Proline acts as a dynamic anchoring point while Glycine and Alanine provide flexibility to the peptide backbone. Afterward, we discovered that our findings also applied to unrelated phage-derived sequences that had been reported to facilitate AuNP synthesis. These results may facilitate a deeper understanding of the role that peptide adsorption plays in the control of AuNPs morphology. Moreover, our results identified the functions of individual amino acids in the adsorption of the peptide A3. This knowledge might aid in the design of new peptides for the synthesis of gold nanostructures with novel morphologies.