The twin questions of how and why protein molecules fold into the specific topologies which enable them to fulfill their biological function have been the subject of continuous scientific investigation since the early twentieth century. Interactions between biological macromolecules and water are obviously crucial to both folding and function but attempts to gain understanding are impeded by the size and complexity of these systems. A useful approach is to consider much simpler model systems which capture some essential element of real biological systems but are experimentally and theoretically tractable. N-methylacetamide (NMA) is a minimal model of the peptide linkage which forms the backbone of protein molecules. Its behaviour in aqueous solution therefore captures the important competition between peptide - peptide and peptide - water hydrogen bonds which arises in protein hydration. In this thesis aqueous NMA solutions are studied across the full concentration range using classical molecular dynamics simulation. This gives access to the complete spectrum of behaviour between the two important limiting cases of dilute NMA in water and, conversely, dilute water in NMA. Water is now known to be an active player in biological interactions and the simple system studied here displays significant disruption of the structure and dynamics of pure water with the addition of only a small proportion of peptide groups. At dilute NMA concentrations water molecules continue to form system-size hydrogen bonded networks. Water molecules appear to optimise their local tetrahedral order by forming hydrogen bonds with a combination of NMA and water neighbours, rather than solely with members of their own species. NMA molecules hydrogen bond through the amide and carbonyl groups to form linear and branched chains in both the pure liquid and in the aqueous solutions. In the NMA rich region water molecules preferentially donate both hydrogens to chain-end or midchain carbonyl oxygens, forming bridges between NMA chains which resemble buried water configurations found in protein cavities. These bridge structures are thought to contribute to the observed slowing of the system dynamics at these concentrations. The investigation of dynamics by classical simulation is complemented by a quasielastic neutron scattering study of NMA in its liquid and aqueous phases.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:562070 |
| Date | January 2007 |
| Creators | Allison, Susan |
| Contributors | Bates, Simon |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/2427 |
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