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.
| Identifer | oai:union.ndltd.org:oulo.fi/oai:oulu.fi:isbn951-42-5943-2 |
| Date | 21 March 2001 |
| Creators | Hyvönen, M. (Marja) |
| Publisher | University of Oulu |
| Source Sets | University of Oulu |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/doctoralThesis, info:eu-repo/semantics/publishedVersion |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess, © University of Oulu, 2001 |
| Relation | info:eu-repo/semantics/altIdentifier/pissn/0355-3191, info:eu-repo/semantics/altIdentifier/eissn/1796-220X |
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