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Characterisation of the structure and self-assembly of a small cyclic peptide: an analysis using NMR spectroscopy, diffusion and heteronuclear relaxation measurements

Boek - Dissertatie

Pseudodesmin A, a member of the viscosin group, is a cyclic lipodepsipeptide (CLP) consisting out of an oligopeptide that is cyclised through a lactone bond between its C-terminal carboxyl group and the hydroxyl group of a threonine side chain and a 3-hydroxydecanoic acid moiety bonded to the N-terminal end of the peptide. It is found to self-assemble in apolar organic solvents, which is reminiscent of its expected ability of forming ion pores in cellular membranes. The goal of this dissertation is to investigate the self-assembly in organic solvents and the structure of the assemblies formed mainly by translational diffusion and heteronuclear relaxation NMR measurements.After covering some theory and background concerning diffusion, translational diffusion NMR, NMR relaxation, and CLPs, the elucidation of the pseudodesmin A conformation – by both X-ray diffraction and NMR – will be discussed. Next, the self-assembly is studied by translational diffusion measurements at different concentrations in chloroform and acetonitrile/chloroform mixtures. Using these results, a model is proposed for the supramolecular assembly that explains the selective self-assembly in non-polar environment, the limitless nature of the assembly and the biological function of the ion pore. This model, confirmed by the detection of intermolecular rOe contacts, encompasses a side by side aggregation of the amphipathic monomer alpha-helical units followed by a stacking of these aggregates – along a direction closely parallel to the alpha-helix – to cylindrically shaped structures. Heteronuclear 13C-alpha relaxation is then used to gain more insight in the organisation of the supramolecular structure and to confirm some aspects of the proposed model. The dependence of the 13C-alpha R1 and R2 relaxation rate constants on the 13C-1H bond vector orientation within a molecular structure is used to obtain information concerning the rotational diffusion properties of the assembly and the orientation of the monomer within the supramolecular assembly. This is used to acquire the shape and average dimensions of the supramolecular assembly, which confirm the model of cylindrical assemblies that grow in only one dimension, nearly parallel with the helix structure. Finally, a theoretical simulation is performed to assess the impact of the self-association equilibria on the relaxation rate constants.
Pagina's: XXIV, 334 p.
Jaar van publicatie:2010