Monday, March 9, 2015

Current and future activity

The project has expanded, and many things are going on. Here I go through the status of currently active topics, and present some new ideas on which to focus in the near future.

Two publications are currently being written based on results discussed in this blog:

One of the original goals of the project is still in progress:
  • Finding an atomistic (preferably united-atom) force field that correctly describes the glycerol backbone and choline headgroup structure in different conditions. This line of research was discussed mainly by me and Antti Lamberg until July 2014. After that, I have focused on writing the manuscripts on results already obtained. During this time I have learned some relevant details about the (dihedral angle distributions of the) structures, see especially Figs. 5 and 6, and related discussion, in the publication 1. Also, a new united atom model by Tj√∂rnhammar and Edholm, which seems to provide a better structure to start with, was published. I think that this line of research should be continued using the Tj√∂rnhammar14 model as a starting point.

There are several possibilities for the future directions of this project, and I believe that there is a huge potential also on a longer time span. The project will run for at least one more year from now. Further continuation of myself and Markus Miettinen as editors, as well as other long term future directions, depend on the success of our grant applications. For now, I will focus on these two topics that go beyond the original goals of the project:
  • Quantitative quality of lipid–cholesterol interactions in simulations based on x-ray scattering and NMR data. Lipid–cholesterol interactions have been widely studied with MD simulations in the recent years. Qualitatively, simulations reproduce the condensing effect, but it is not clear how accurate, quantitatively, the models are. This is crucial information to judge the credibility of the various simulation predictions. Directly comparing the simulations with different models (made available in Zenodo in this project) against x-ray scattering and NMR results, we can get a pretty clear picture of the quantitative quality of the models. The discussion on this is already going on in the blog with Peter Heftberger and Georg Pabst. I will soon write a blog post discussing this project in more detail.
  • Glycerol backbone and headgroup order parameters for other than phoshatidylcholine lipids (e.g., phophatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylserine (PS), glycolipids etc.). I have privately discussed the existence of order parameter data for these and other headgroups at many occasions. The bottom line is that a lot of published data exists, however, they seem to be quite poorly known and difficult to find. To my knowledge, these data have not been reviewed or collected anywhere (not even by Derek Marsh). I think we should, at minimum, collect the available data sets in an easily accessible format. This, with potentially some comparison to simulations, would teach us interesting lessons about the structural differences between headgroups, allowing us to expand on what has been discussed in the literature so far.

In addition, several issues have been shortly touched in the discussions of the blog, but are beyond both the original and the extended scopes of the project. I would be more than happy too see someone to progress, for example, these topics:
  • Temperature dependence of the glycerol backbone and choline order parameters. For example, Andrea Catte has reported interesting data on this and they have been discussed a bit already. There is also some temperature dependence in the data delivered by Fernando Favela.
  • Peter Heftberger shared a collection of x-ray scattering data for different systems. In addition to the lipid–cholesterol interactions mentioned above, there may be many other interesting issues to study with moderate effort by combining the simulation data now available in Zenodo with the scattering data shared in the blog.

2 comments:

  1. I just saw this paper recently which might be of interest: http://dx.doi.org/10.1021/jp510322t. It deals with the order parameter as a function of bilayer curvature (measured by 13C NMR). Maybe that goes beyond the scope of the blog, but it can be used at least as another source of experimental data for flat membranes.

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    1. Thanks for pointing this out. However, they do not directly measure order parameters. They measure dynamical parameters, assume a simple form of rotational correlation function and fit that one to the measured quantities to get order parameters. This procedure is used often for systems with isotropic rotation, like micelles or proteins in solution. However, for anisotropic liquid crystals the rotation correlation function and related analysis is more complicated. Also the order parameters can be measured directly. For more details see e.g. http://dx.doi.org/10.1063/1.4906274

      Thus, I think that their results cannot be considered in the same way as the direct order parameter measurements from dipolar or quadrupolar coupling.

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