This thesis describes the combination of experimental (E-ray and neutron diffraction) and computational techniques (molecular dynamics simulations) to investigate membrane peptide interactions. Initially, a computational model for a dioleylphosphatidyl choline (DOPC) bilayer was constructed. This bilayer had been verified with experimental data (namely area per headgroup, volume per lipid, order parameter of the oleyl chains and electron density profile). A mixed bilayer of DOPC and diolelylphopshatidyl glycerol (DOPG) was then constructed. The mixer bilayer was verified in the same manner. A peptide (adenosine diphosphate ribosylation factor-1 (pARF-1)) was then inserted into the pre-equilibrated mixed bilayer. The orientation of this peptide with respect to the membrane was based on previous neutron diffraction studies, carried out by other group members. Four possible orientations had resulted from analysis of the neutron data. The four orientations of a pARF-1 were then subjected to molecular dynamics simulations. The time course of these simulations was 4 ns. The simulations’ trajectories were analysed for each of the four models. Particular emphasis was placed upon the positional changes of the phenylalanine label positions that were derived from the neutron data. It was concluded that model A was the most likely orientation of pARF-1 in relation to the bilayer. Having established the technique, and confirmed that the most likely orientation of the peptide was what was originally proposed, another peptide, the fusion peptide of simian immunodeficiency virus (SIV) was placed into a previously equilibrated DOPC bilayer. In this case, only the proposed orientation of the SIV fusion peptide in relation to the bilayer was studied utilizing molecular dynamics simulations. The results are interpreted in relation to the actions of SIV fusion peptide upon the membrane, with particular emphasis on the disruption of oleyl chain order parameters.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:641239 |
| Date | January 2005 |
| Creators | Balali-Mood, Kia |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/29054 |
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