Wednesday, July 4, 2018

NMRlipids IV: First draft of the manuscript about PS lipids

Thank you again for the 168 comments in the two previous blog posts about NMRlipids IV project (NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PE, PG and PS lipids and NMRlipids IV: Current status and reorganization of the manuscript) and numerous contributions to the GitHub repository.

First draft of the manuscript summarizing the results related to PS lipids is now compiled. As discussed previously, the goal is to first finish the manuscript about PS headgroup and then progress with PG and PE results separately. In addition to the up-to-date manuscript (pdf, tex) and supplementary information (pdf, tex), also the figures and data are available in the GitHub repository.

I believe that the manuscript already contains most of our conclusions, but several issues need to be addressed before we can start to prepare the submission. Most important current issues are listed here, accompanied with the names of persons who can hopefully help me to resolve the issues.
  1. We need slightly more detailed description of the NMR experiments by Tiago Ferreira. Also the results and discussion about the experiments, including Figure 1, needs to be polished.
  2. Atom names and dihedral notations should be made consistent between the chemical structures in figure 2, and dihedral angles distributions in  figures S6 and S7 by Pavel Buslaev. I am not sure if we could just the atom names currently used in figure 2, or if we need more labels. Slight polishing of figures S6 and S7 is also needed.
  3. The subjective ranking criteria in figure 4 by Markus Miettinen should be probably improved, see issue #4 in the GitHub repository.
  4. CHARMM36 data from POPC:POPS (5:1) mixtures with added NaCl would be highly useful for figure 6. CHARMM36 gives two maxima in the counterion density profiles in figure 5, while for example Lipid17 gives only one. From the right column of figure 6 we could see if this difference is reflected to the order parameter response of PS headgroup to the excess counterion concentration. Data from Gromos-CKP would also be useful for this. If someone has such data or is willing to generate it, let us know. 
  5. CHARMM36 simulations with the added CaCl2, but without the new NBfix, mentioned by Jesper Madsen would be useful for figure 9
  6. Lipid17 simulations ran with the Amber package, mentioned by Batuhan Kav, would be useful for figure 9
  7. Details of simulations by Thomas Piggot, Jesper Madsen, Fernando Favela, Batuhan Kav, Markus Miettinen, Josef Melcr and Matti Javanainen should be added in section S1 in the supplementary information (tex file here).
In addition, all comments regarding the current manuscript are welcomed. I will continue working with the manuscript and keep the the list updated.  

1 comment:

  1. Regarding the issue number 4 in the above list, I realized that the mentioned data for Gromos-CKP has already been contributed by Tom Piggot: http://nmrlipids.blogspot.com/2017/03/nmrlipids-iv-headgroup-glycerol.html?showComment=1528213129976#c8319083196182661431

    I will proceed in adding this into the manuscript.

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