Abstract

The antimicrobial peptide alamethicin (Alm) is well known to form ion channels (peptide bundles) in lipid membranes. Due to its simple chemical structure and complex electrical properties, Alm serves as a model for describing intrinsic ion channels in mammalian systems. In this thesis we investigated the supramolecular organization of Alm in fluid lipid model membranes by using x-ray scattering.

Oriented multilayer samples of Alm/lipid mixtures are used in this thesis. When the hydration level is sufficiently high, the interactions between the peptide bundles in different layers are negligible. Bragg rod shaped in-plane scattering side peaks caused by Alm bundles are obtained. To account for the positional correlations between the peptide bundles in a single bilayer, a hard disk model with and without long distance interactions is considered. The q_r dependence of the form factor, which is the Fourier transform of the electron density distribution of the peptide bundle, is modeled in two ways. One approximates the bundle as a cylinder (solid bundle) and the other uses the bundle structure from molecular dynamics simulations (MD bundle). The lateral in-plane scattering intensity is fit by the product of the structure factor and the form factor. The fitting results indicate that the number N of peptides per bundle is 6 in DOPC and N≥8 in diC22:1PC. The difference is well described by the hydrophobic matching mechanism.

When the Aim/lipid sample is progressively dehydrated, the maximum position of the side peaks shifts away from the equator (q_z=0). This is consistent with repulsive interactions at short distances between peptide bundles in different layers. The observed shifting is demonstrated by two types of correlations between neighboring layers, a hard disk correlation and a Lennard-Jones type correlation. Crystal like scattering peaks are obtained by removing most of the water molecules from the sample. The scattering pattern does not fit the proposed hexagonal close-packed or the rhombohedral structure. The pattern was better fit by the body centered tetragonal and the monoclinic structure.

A second diffuse peak located at q_r ∼0.7 Å ^-1 is obtained in well-hydrated samples of both DOPC and diC22:1PC at all peptide concentrations. A phase separated 2-D hexagonal packing cluster model in equilibrium with Alm bundles is proposed.