About

This in an open scientific collaboration project to understand the atomistic resolution structures of lipid bilayers. The project is progressed through the comments in this blog and using the GitHub organization. The main results are also published in traditional peer reviewed scientific journals. The authorship in these publications is based on the self-assesment of the contributors, as defined in the beginning of the project.

People mainly interested on the open collaboration approach probably find these texts and discussions most interesting:

Our aim
On credits
Why not submit to a journal?
Towards first submission to journal

People mainly interested on the scientific content may find the list of separate ongoing projects helpful to outline our activity. Currently, there are five separate projects (to be reported in separate publications) either ongoing or already completed, see below.

NMRLipids I (journal article published): Headgroup and glycerol backbone structures of phosphatidylcholine (PC) lipids were studied with and without cholesterol, as well as in low hydrated conditions. We were able to identify force fields with most realistic structures and structural changes by comparing the C–H bond order parameters with experiments. The related files are available from the GitHub repository.

NMRLipids II (journal article published): Cation (Na\(^+\) and Ca\(^{2+}\)) binding affinity to phosphatidylcholine (PC) lipid bilayers was compared between NMR experiments and MD simulations using the headgroup C–H bond order parameters and the molecular electrometer concept. The comparison revealed that MD simulations generally overestimate the cation binding to PC lipid bilayers. The related files are available from GitHub.

NMRLipids III (manuscript in preparation): We aim to quantify lipid–cholesterol interactions in lipid bilayers using NMR, x-ray scattering, and MD simulation data. The approach should be applicable to intermolecular interactions also in other binary lipid mixtures. The manuscript status is discussed in a recent blog post and the related files are available at the GitHub repository.

NMRLipids IVa (manuscript in preparation): Headgroup and glycerol backbone structures of negatively charged phosphatidylserine (PS) lipids are studied with and without salt. The most realistic MD simulations suggest that the serine headgroup does not rotate freely. Improvements in force fields are required to interpret the cation binding details to bilayers containing PS lipids. The manuscript is almost ready for submission. The related files are available from the GitHub repository.

NMRLipids IVb (manuscript in preparation)Headgroup and glycerol backbone structures of zwitterionic phosphatidylethanolamine (PE) and negatively charged phosphatidylglycerol (PG) lipids are studied with and without salt. The  manuscript status is discussed in a recent blog post and the related files are available at the GitHub repository.

NMRlipids V (journal article published): Validation of the structure and dynamics of lipid bilayer MD simulations against NMR and scattering data is reviewed. Simulations give generally a good description for the hydrophobic membrane core, but not for the hydrophilic interface. The related files are available from the GitHub repository.

3 comments:

  1. Hi,
    finally here comes our (Peter Heftberger & mine) contribution to POPC/ cholesterol. All SAXS data analyzed for form factor changes upon increasing cholesterol content (0 - 50 mol%). All information and data can be accessed from https://drive.google.com/folderview?id=0BypC9VEx1ib_flRzLTlsVFE1VG9PTjhCMVdROWFrVXpQb2Z3eXlsZXhsaUJSR2RucmNkenc&usp=sharing.

    If there are questions, please do let us know.
    Cheers, Georg

    ReplyDelete
    Replies
    1. Thanks for the major contribution. I have added the data also into the GitHub folder of this project (NMRLipids III, https://github.com/NMRLipids/NmrLipidsCholXray/tree/master/DATA/POPC-Cholesterol). The form factors from simulations are still tentative and are located in the scratch folder of the repository. We should make a script to plot these into the same figure.

      I have been planning that in this project (and also in other projects from now on) the manuscript would be written and updated in the GitHub from the very beginning. I hope that this would be more efficient and would ease the following of the projects. Thus, the next steps here would to write the very tentative manuscript and make figures, in addition to checking several technical details.

      I have almost finished of writing a new blog page discussing the new workflow in this and other projects. This should clarify the above mentioned usage of the GitHub repositories.

      However, I am on parental leave now which means that I am not able to do much before late September. After I am back on full time work I will sketch the manuscript and figures as soon as possible (unless someone else does it before that).

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    2. Congratulations to starting a family! This is a great thing to happen!! Anyway no haste on this part of project. We will also have to find a way to plot experimental uncertainties. We will do this as the project evolves. Cheers!

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