Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules

Modeling and simulation of protein–surface interactions: achievements and challenges

“…Ideally, reconstruction of surfaces has to be taken into account in the simulation of adsorption (Ghiringhelli et al 2008): an enormous task in most cases. On the other hand, it has been reported in several studies that the reconstruction of some surfaces in certain conditions is negligible (Feng et al 2011;Raffaini & Ganazzoli, 2012;Wright et al 2013a). However, other experimental and computational studies show that large scale surface reconstruction may take place after adsorption of small molecules (Eralp et al 2011;Gibbs et al 1990;Lal et al 2004Lal et al , 2006.…”

“…However, for the adsorption of biomolecules with considerable dipole moments, including some peptides and proteins, the surface polarization contributes to the binding energy and influences the binding mode. Although studies have shown that, for water-metal surface systems, the energy due to polarization is less than 10% of the total binding energy (Feng et al 2011;Neves et al 2007;Siepmann & Sprik, 1995;Vila Verde et al 2009, for proteins, in particular, on Au (111) surfaces, the contribution from polarization has been estimated to be about 10-20% of the total binding energy . Further, on surfaces such as Au(100), where the van der Waals attraction is weaker, polarization was found to tune the adsorption of proteins ) and act as a major contributor to the adsorption of highly charged peptides .…”

“…Metal polarization is negligible for neutral adsorbates that do not have large dipoles and, since proteins usually have a relatively small total charge, it is often neglected in simulations (Braun et al 2002). Early studies of metal surfaces also showed that the effect of pure water on polarization of the metal is often negligible (Barabino & Marchesi, 1984;Shelley et al 1997;Spohr, 1995) and that charge-induced polarization does not cause any change in the structure of the water on the surface (Feng et al 2011). However, for the adsorption of biomolecules with considerable dipole moments, including some peptides and proteins, the surface polarization contributes to the binding energy and influences the binding mode.…”

“…The topographic characteristics of a surface or nanoparticle at the micro-to nanometer-scale are important determinants of protein adsorption properties, such as binding affinities and surface saturation values (Fenoglio et al 2011;Gagner et al 2011Gagner et al , 2012Roach et al 2006). The topography of a surface can be characterized by its exposed crystal planes, its roughness and its defects (due to locally varying chemical composition or the crystalline structure of the surface), as well as kinks, edges and steps that occur during the growth of a crystal.…”

Functional and Selective Bacterial Interfaces Using Cross-Scaffold Gold Binding Peptides

“…Although much of this work has been designed to isolate properties contributing to successful binding (e.g., flexibility, electrostatics, solvent interactions), it has remained difficult to distill this into a concise set of design principles. 36,53,54 In order to probe the origins of the predominance of hydroxyl-containing amino acids with gold surfaces, Calzolari et al 55 performed ab initio molecular dynamics (AIMD) of a hydroxyl containing b-sheet-forming peptide, and found that cooperativity between serine side chains and solvent molecules contributed to successful 57 suggested that Tyr, Met, and Phe are strong binders, while serine breaks through the hydration layer to form an anchor point. Verde et al 58 performed further molecular dynamics to study the role of flexibility and stability in adsorption of known gold-binding and non-gold-binding peptides.…”