The aqueous interface between biomolecules and inorganic substrates is of interest to many cross-disciplinary areas of science, ranging from fundamental biological research into biomineralisation processes, to the more application-driven fields of nanotechnology and biomimetic materials synthesis. In particular, by harnessing the selectivity observed in Nature, proteins and peptides make ideal candidates for directing the assembly of nanoparticles into nanostructured, multifunctional materials with pre-defined physical properties. The rational design of peptide sequences with tunable affinities either for a substrate of a specific composition, or for a specific crystallographic plane of a given material, would mark an important step towards realising these goals. Before this is possible, however, the fundamental mechanisms involved in peptide substrate binding under aqueous conditions must be understood. Molecular simulation, used throughout this thesis, is well suited for studying biointerfacial systems at the level of detail needed to advance research. The work presented herein is primarily focused on answering the question of whether facet-selective peptide adsorption is indeed possible at the aqueous quartz and gold interfaces. A range of different simulation techniques, all based on atomistic molecular dynamics, are employed. As part of the study, two of the ‘grand challenges’ currently facing biointerfacial simulation–the deviation of force-fields suitable for the interfacial environment, and enhancing conformational sampling of an adsorbed biomolecule–are addressed. Potential of Mean constraint Force free energy of adsorption calculations show that, out of the amino-acid analogues tested, all display energetic and/or spatial selectivity between the (100), (001) and (011) surfaces, on adsorption to Quartz. Facet specificity in binding, for the building blocks from which peptides are comprised, is highly suggestive of the biomolecules themselves displaying similar characteristics. The general trend in small molecule adsorption strength–non-polar aromatic > negatively-charged > non-polar aliphatic > positively-charged–is common to all three aqueous Quartz interfaces. The propensity for negatively-charged ethanoate to bind more strongly to the aqueous, fully hydroxylated (100) a-Quartz surface than positively-charged ammonium is confirmed by first-principles simulations. Selectivity between the Au(111), Au(100)(1×1) and Au(100)(5×1) surfaces is also observed when the gold-binding peptide AuBP-1 [Hnilova et al. [2008]] adsorbs to gold under aqueous conditions. Metadynamics, in combination with the advanced sampling technique Replica Exchange with Solute Tempering, is used to study this system. The impact of Au(100) reconstruction on peptide binding is considered here for the first time. This aspect of gold binding was made possible by a suite of force-fields derived within this work, GolP-CHARMM, for modelling the interactions between proteins and peptides and gold.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:606196 |
| Date | January 2014 |
| Creators | Wright, Louise B. |
| Publisher | University of Warwick |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://wrap.warwick.ac.uk/61709/ |
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