Two publications are currently being written based on results discussed in this blog:
- Publication 1: Towards atomistic resolution structure of phosphatidylcholine glycerol backbone and choline headgroup at different ambient conditions. The core content of the publication is pretty much complete. Some figures and minor issues are still to be improved. The discussion concerning submission to a journal has begun.
- Publication 2: Ion-lipid interactions. Writing is in progress, and the first draft was already posted on the 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 Tjörnhammar 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 Tjörnhammar14 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.