Facet selectivity in gold binding peptides: exploiting interfacial water structure

Abstract

We demonstrate that surface hydration is a key factor in dictating the free energy of non-covalent peptide-materials recognition.

Aqueous Peptide–TiO2 Interfaces: Isoenergetic Binding via Either Entropically or Enthalpically Driven Mechanisms

“…[53][54] First, we implemented state-of-the-art REST+Metadynamics (REST+MetaD) simulations to obtain estimates of the free energy of peptide-titania adsorption; a quantity that is extremely challenging to capture using molecular simulation. 46 In addition, we performed RESTonly simulations to determine the conformational ensemble of each peptide in the adsorbed state, and to reveal the surface-contact preferences of each residue in each peptide. While in principle these data could be extracted from the REST+MetaD simulations, in practice, this is an extremely challenging task, and the outcomes of this analysis are not necessarily definitive; resolution of this issue remains for in future developments.…”

“…While in principle these data could be extracted from the REST+MetaD simulations, in practice, this is an extremely challenging task, and the outcomes of this analysis are not necessarily definitive; resolution of this issue remains for in future developments. 46 For both Ti-1 and Ti-2, we obtained the change in free energy as a function of the peptide-surface distance, from which the adsorption free energy was extracted and compared. This was accomplished via construction of symmetrized free energy profiles 46 (see 'Additional Computational Methodology' in the Supporting Information); see Figure 4 for an exemplar symmetrized free energy profile.…”

“…46 For both Ti-1 and Ti-2, we obtained the change in free energy as a function of the peptide-surface distance, from which the adsorption free energy was extracted and compared. This was accomplished via construction of symmetrized free energy profiles 46 (see 'Additional Computational Methodology' in the Supporting Information); see Figure 4 for an exemplar symmetrized free energy profile. The predicted free energy of adsorption for the two peptides was found to be -12.7±0.4 kJ mol -1 and -16.4±3.7 kJ mol -1 for Ti-1 and Ti-2 respectively.…”

“…45 Advanced molecular simulation approaches are capable of providing these molecular-level details, as was recently shown for the prediction and elucidation of the facet-selective binding preferences of peptides at aqueous Au interfaces. 46 Therefore, molecular simulation, when carefully performed, and done in close partnership with experimental approaches, can bring valuable insights into the structurebinding relationships inherent to these versatile and widely-used materials. 17,23,[47][48][49] Here, we have examined the binding behavior of two TiO2 binders, Ti-1 and Ti-2, previously used in the biomineralization of crystalline, sub-10 nm sized TiO2 nanoparticles from water (pH 7.4) or Tris buffer particles 37 (see Table 1 for peptide sequences).…”

Force fields for simulating the interaction of surfaces with biological molecules

“…It is implied that the fitting of enthalpic adsorption energies with model molecules (including water) will translate to an accurate thermodynamic treatment of the interface, and this is best tested with free energy simulations. Recent results measuring the free energy of adsorption of the gold-binding peptide AuBP1 on three different gold facets compare favourably with experimental data and also help explain facet selectivity and the role of water in binding [44]. Fitting the FF to the bulk material properties of the surface, by removing the fixed atom restraint on gold atoms, will also allow for validation using interfacial energies.…”