About

This in an open scientific collaboration project to understand the atomistic resolution structures of lipid bilayers. The projected 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 of these publications in based on the self-assesment of the contributors, as defined in the beginning of the project.

People mainly interested on the used 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: Attempt was resolve the atomistic resolution structure of phospholipid by interpreting the NMR data with molecular dynamics simulations. However, none of the available models was accurate enough for full structure but useful structural details were successfully resolved. The publication describing the results is published in the Journal of Physical Chemistry B. All the related files available from GitHub.

NMRLipids II: Comparison between NMR and molecular dynamics simulation results reveals that the interaction between zwitterionic phospholipid bilayer and cations (Na\(^+\) and Ca\(^{2+}\)) is too strong in most models. Due to overestimated ion binding several results in the literature may have to be reconsidered. The publication describing the results is published in the Physical Chemistry Chemical Physics. All the related files available from GitHub.

NMRLipids III: The goal is to quantitatively qualify the lipid cholesterol interactions in lipid bilayer models by using the NMR and x-ray data. With this approach also the quality of the intermolecular interactions in atomistic resolution molecular dynamics models could be assessed. The project is in good speed and is discussed in the Data Contributions page (discussion started December 1, 2014 by Peter Heftberger), on its dedicated blog post, and GitHub repository has been opened. The current version of the manuscript is available from GitHub.

NMRLipids IV: Primarily measured but also simulated NMR order parameters will be collected also for other than phophatidylcholine (these are discussed in NMRlipids I) headgroup. The information will be used to understand structural differences between different lipid molecules in bilayers.

NMRlipids V: Invited review about validation and interpretation of atomistic resolution structure of lipid bilayers. The project was discussed in a blog post and in GitHub. The manuscript is published on BBA Biomembranes.

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!

      Delete

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