Paper Citing NAMD - Abstract
Feng, Jie; Slocik, Joseph M.; Sarikaya, Mehmet; Naik, Rajesh R.; Farmer, Barry L.; Heinz, Hendrik
Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution
SMALL, 8:1049-1059, APR 10 2012
Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr12, Ser12, A3, Flg-Na3) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (20 to 60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (15 to 25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often beta-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures.
