Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution

Abstract

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 (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) 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 β-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.

From the Lindlar Catalyst to Supported Ligand‐Modified Palladium Nanoparticles: Selectivity Patterns and Accessibility Constraints in the Continuous‐Flow Three‐Phase Hydrogenation of Acetylenic Compounds

“…Particularly, the generalized AMBER force field61, 62 for the HHDMA molecule and METAL63 for palladium. This combination has been previously validated by Heinz and co‐workers 64. 65 The equilibration period was 0.1 ns in the NVT ensemble.…”

Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution

“…Similar diversity of surface environments is also expected for other oxides such as titania and apatites, however, not for precious metals that are of simple chemistry and attract similar peptide sequences. [77][78][79][80][81][82][83] Two major factors play a role for the construction of a silica surface model. One is the type of substrate that determines the area density of silanol groups; the other is the degree of ionization ( as a function of pH and ionic strength.…”

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

“…To underscore this hypothesis, we performed two types of test using a force-field that has been previously used to model biomolecule adsorption to faceted aqueous NMNPs, 11,27,35 CHARMM-METAL, 80 to probe the interaction between our Au 147 NP and water. In the first test, we investigated the in-vacuo adsorption of a single water molecule on the Au 147 NP using CHARMM-METAL.…”

“…Even in those instances when the adsorption to stepped noble metal surfaces or actual NMNP surfaces was investigated, the FFs employed in these studies were designed for use with infinite planar surfaces without the presence of low-coordinated metal atom sites. 11,27,35 Here, we have rigourously investigated and determined the non-covalent adsorption energies and minimum energy configurations of a variety of different small organic molecules containing the same functional groups present in the side-chains of amino acids, as well as water, to various sites (facets, edges and vertices) located on cuboctahedral Au 147 and Pt 147 , using PW-DFT calculations with the revPBE-vdW-DF functional. Our set of adsorbates covers a range of amino acid physicochemical properties including non-polar molecules, polar molecules and aromatic molecules.…”

“…13,[24][25][26][27][28][29][30][31][32][33][34] However, the majority of these studies modelled the adsorption of peptides at periodic planar interfaces as an approximation to the NMNP surface. Even in those instances when the adsorption to stepped noble metal surfaces or actual NMNP surfaces was investigated, the FFs employed in these studies were designed for use with infinite planar surfaces without the presence of low-coordinated metal atom sites.…”