Computer simulation of biological membranes and membrane bound proteins

Whitehead, Lewis (1999) Computer simulation of biological membranes and membrane bound proteins. University of Southampton, Doctoral Thesis.

Abstract

Biological membranes are vital for many biochemical functions in the body, and therefore obtaining an increased knowledge and understanding of membrane structure and function is essential. In this thesis, the results of molecular dynamics computer simulations of biological membrane models are presented. Their performance as reliable membrane computer models is assessed by extensive comparison to the experimental data.

In chapter 3, simulations of hydrated phospholipid bilayers are presented. These simulations proved to be an unsatisfactory model for lipid structure and dynamics, attributed to the application of the ambitious simulation protocols.

Chapters 4 and 5 concentrate on the modelling of a membrane bound peptide in hydrated phospholipid environments. These chapters explore the dynamics of the peptide in the bilayer environment in depth. The results generated for the peptide are in excellent agreement with the available experimental data. The effect of the presence of the peptide in these simulations on the lipid dynamics is also characterised with a great deal of success.

In response to the enormous computational resources necessary to generate the simulations outlined in chapters 3 and 5, chapter 6 describes the successful development of a reduced representation model for the hydrocarbon region of the phospholipid membrane using a commonly used potential for the modelling of liquid crystalline mesophases. This model proved successful in modelling the characteristic phase behaviour of lipid bilayer systems and promises a great deal of potential as a reliable membrane model.

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