Computer Simulations of Lipid Bilayers and Proteins

Jacob Sonne

Research output: Book/ReportPh.D. thesisResearch

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The importance of computer simulations in lipid bilayer research has become more prominent for the last couple of decades and as computers get even faster, simulations will play an increasingly important part of understanding the processes that take place in and across cell membranes. This thesis entitled Computer simulations of lipid bilayers and proteins describes two molecular dynamics (MD) simulation studies of pure lipid bilayers as well as a study of a transmembrane protein embedded in a lipid bilayer matrix. Below follows a brief overview of the thesis. Chapter 1. This chapter is a short introduction, where I briefly describe the basic biological background for the systems studied in Chapters 3, 4 and 5. This is done in a non-technical way to allow the general interested reader to get an impression of the work. Chapter 2, Methods: In this chapter the background for the methods used in the succeeding chapters is presented. Details on system setups, simulation parameters and other technicalities can be found in the relevant chapters. Chapter 3, DPPC lipid parameters: The quality of MD simulations is intimately dependent on the empirical potential energy function and its parameters, i.e., the force field. The commonly employed CHARMM27 force field reproduces fluid phase bilayer properties only when a tension is applied in the simulations. Without this tension the simulated bilayers become too ordered. To allow for more realistic lipid bilayer simulations in the tensionless isothermal-isobaric (NPT) ensemble, we reparameterized a part of the CHARMM27 force field by assigning new partial charges to the lipid head group atoms. Our modified CHARMM27 force field was tested in lipid bilayer MD simulations and was found to improve the phase properties of the simulated bilayers significantly. Thus, the improved force field makes it possible to simulate the biologically relevant fluid ($L_{\alpha}$) phase in an NPT ensemble, which is an important prerequisite for taking full advantage of the predictive power of MD simulations since the area per lipid need not be known prior to simulation. Chapter 4, Pressure profile calculations in lipid bilayers: A lipid bilayer is merely $\sim$5~nm thick, but the lateral pressure (parallel to the bilayer plane) varies several hundred bar on this short distance (normal to the bilayer). These variations in the lateral pressure are commonly referred to as the pressure profile. The pressure profile changes when small molecules partition into the bilayer and it has previously been suggested that such changes may be related to general anesthesia. MD simulations play an important role when studying the possible coupling between general anesthesia and changes in the pressure profile since the pressure profile cannot be measured in traditional experiments. Even so, pressure profile calculations from MD simulations are not trivial due to both fundamental and technical issues. We addressed two such issues namely the uniqueness of the pressure profile and the effect of neglecting pressure contributions from long range electrostatic interactions. The first issue is addressed by comparing two methods for calculating pressure profiles, and judged by the similar results obtained by these two methods the pressure profile appears to be well-defined for fluid phase lipid bilayers. For the second issue, we developed a method that allows pressure contributions from long range electrostatic interactions to be included in pressure profile calculations. Chapter 5, Structural transitions in the ABC transporter BtuCD: In this chapter, we present a study of the transmembrane protein BtuCD. BtuCD belongs to the adonesine triphosphate (ATP) binding cassette (ABC) transporter family that use ATP to drive active transport of a wide variety of compounds across cell membranes. BtuCD accounts for vitamin B12 import into Escherichia coli and is one of the only ABC transporters for which a reliable crystal structure of the whole transporter has been determined. The (dys)function of ABC transporters accounts for cystic fibrosis and multi-drug resistance, for example tumor cell resistance to anticancer drugs. Hence, the mechanism facilitating substrate translocation in ABC transporters is of both fundamental and medical interest. It is commonly accepted that substrate translocation relies on binding and hydrolysis of ATP and maybe also on the release of hydrolysis products; however, the global structural rearrangements induced by these events remain largely unknown. To investigate these structural rearrangements in BtuCD we employed perturbed elastic network calculations and biased MD simulations. Comparing the results of these calculations with two transport models proposed in the literature, we are able to favor one over the other. Our observations for BtuCD may be relevant for all ABC transporters, owing to the conservation of ATP binding domains Chapter 5: This chapter contains a more technical summary of the thesis and some general conclusions. Chapter 7: This chapter contains a compilation of supplementary material relating to the subjects discussed in the preceding chapters. pressure profile calculations.
Original languageEnglish
Number of pages114
ISBN (Print)87-91233-14-3
Publication statusPublished - Jul 2006


  • abc transporter
  • bilayer
  • parameter
  • reparmeterization
  • md
  • pressure profile
  • lipid
  • btucd
  • molecular dynamics
  • dppc

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