Abstract

Phospholipids are the main components of cell membranes, lipoproteins and other membrane structures in living organisms. Properties of lipid molecules are important to the overall behaviour and interactions of membranes. Furthermore, characteristics of the biological membranes act as important regulators of membrane functions. Molecular dynamics (MD) simulations were applied in this thesis to study properties of biological membranes. A certain degree of acyl chain polyunsaturation is essential for the proper functioning of membranes, but earlier MD simulations had not addressed the effects of polyunsaturation. Therefore a solvated all-atom bilayer model consisting of diunsaturated 1-palmitoyl-2-linoleoyl-3-phosphatidylcholine (PLPC) molecules was simulated. The analysis of the simulation data was focused on the effects of double bonds on a membrane structure.

Self-organising neural networks were applied to the analysis of the conformational data from the 1-ns simulation of PLPC membrane. Mapping of 1.44 million molecular conformations to a two-dimensional array of neurons revealed, without human intervention or requirement of a priori knowledge, the main conformational features. This method provides a powerful tool for gaining insight into the main molecular conformations of any simulated molecular assembly.

Furthermore, an application of MD simulations in the comparative analysis of the effects of lipid hydrolysis products on the membrane structure was introduced. The hydrolysis products of the phospholipase A₂ (PLA₂) enzyme are known to have a role in a variety of physiological processes and the membrane itself acts as an important regulator of this enzyme. The simulations revealed differences in the bilayer properties between the original and hydrolysed phospholipid membranes. This study provides further evidence that MD simulations on biomembranes are able to provide information on the properties of biologically and biochemically important lipid systems at the molecular level.