Biological membranes are highly complex molecular systems, with a backbone that consist of a variety of lipid molecules, assembled in a bilayer. The lipid bilayer comprises a multitude of lipid species and serves as a matrix, providing an appropriate environment for the wide variety of membrane proteins. A number of vital cell processes are performed by the membrane proteins, incorporated in the membrane. They serve as an active interface between the cell and the environment, providing mass transport between the cell and surrounding, signal transduction and specific recognition. Lipids and proteins are not homogeneously distributed throughout the membrane and could form assemblies with a specific composition, such as lipid domains, and this further increases the level of complexity of the membrane. The importance of the membrane as a vital part of the cell inspired many studies, including this thesis. Here we used Atomic Force Microscopy (AFM) as an imaging and force measuring device on a variety of membrane mimicking systems. We studied processes of phase separation and domain formation in model membrane systems, peptide aggregation within lipid bilayers and lipid/lipid and lipid/peptide interactions. \ud After an introduction in the filed of biological membranes and AFM technique, presented in Chapter 1, in Chapter 2 the behaviour of the model WALP peptide, which resembles the transmembrane part of integral membrane proteins, and its ability to form a specific ordered domains in lipid bilayers of different compositions is studied. In Chapter 3 we studied further the behaviour of WALP in lipid bilayers and investigated the strength of integration of this transmembrane peptide, using the force measuring possibilities of the AFM. Data analysis according to the described theory gives insight in the factors, governing the stability of integration of transmembrane proteins. Another example for possibilities of the AFM as a manipulating tool is presented in Chapter 4, where Lipid II - an important biological molecule, is studied and size and orientation of its head group, when the molecule is incorporated in a bilayer, was obtained. The thesis finishes with a summary and perspectives in Chapter 5
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