- None of the tested models reproduces the PS headgroup order parameters within experimental accuracy but the best models suggest that the carboxyl group in serine headgroup does not rotate freely.
- Cation binding to bilayers containing PS lipids is overestimated in all the tested simulations, except in MacRog with potassium and CHARMM36 with the NBfix for the calcium. However, the latter underestimates the binding affinity.
- The qualitative response of PS lipid headgroups to the bound calcium and dilution with PC lipids do not agree with experiments in any of the tested models, indicating that the force field development is necessary for MD simulation studies of PS lipids and their interactions with other biomolecules.
There is a todo list in the manuscript, mainly containing missing details. Current contributors, please check the list (also in the supplementary information). One question regarding many points in the todo list is that how much simulation details we should put in the supplementary information when the data is shared in Zenodo? When the details are well described in Zenodo (for example here), it may not be necessary to repeat all the information in the SI. However, cases where the data is not much described in Zenodo but the repository contains all the files having all the information about simulations (for example this) are more complicated. Are there any opinions about this?
In addition, all kind of comments are welcomed, also from the people who have not contributed to the manuscript. At this point, I hope to have comments from as many people as possible, including also critical comments.
If you have major concerns about scientific content, I hope to hear about that before the end of January 2019. If there are no major concerns, I hope that we could submit the manuscript by the end of February 2019.
Hi,
ReplyDeleteplease find below my thoughts after reading the MS carefully. I think it's thorough and well-written and in general very close to submittable.
Intro:
-mention that PS only in the cytosolic leaflet
Fig.2:
-Mention in the legend which points are from this work.
-Do the points overlap or why are not all points shown? Would different markers help?
-Enlarge label, tick, and ticklabel fonts (holds for most figures)
Fig.5:
-Slipids, not Slipid
Fig.6:
-g_density could be rerun with a higher -sl value for smoother profiles, holds for other density profiles as well
-MacRog pure POPS is simulated with Verlet cutoff scheme, Piggot is rerunning with group cutoff scheme. Check if affects results & update figures when ready
Page 7:
-Something is wrong with the sentence
“Also, the sampled conformations of glycerol backbone significantly vary between different simulation models (Figs. S8, S9, S11 and S12), but further analysis is beyond the scope of this work which the PS headgroup.“
Fig.9:
-Change yellow to orange or sth else more visible
-Unify the spelling of MacRog (vs. MACROG) across the MS
-Caption could say that experiment uses K+ counterions (i.e. MacRog is the only data set that follows the experimental setup)
Fig.10:
-Why are some plots wider than others?
Acknowledgements: Add CSC and Emil Aaltonen foundation for Matti.
SI:
Figs.S10 & S11:
-Change line colors for more contrast
Fig.S17:
-Plots could again use a higher -sl value in g_density
-Insets not readable
Fig.S18:
-Replace light green and yellow by other colors
-Not all plots are of equal width
-Is the Ca2+ density peak really an order of magnitude larger in Lipid17?
Thanks for the comments, below are answers:
Delete>Intro:
>-mention that PS only in the cytosolic leaflet
This is now mentioned.
>Fig.2:
>-Mention in the legend which points are from this work.
>-Do the points overlap or why are not all points shown? Would different markers help?
>-Enlarge label, tick, and ticklabel fonts (holds for most figures)
There is now a version of this figure.
There is also some discussion in the GitHub issue:
https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/34
>Fig.5:
>-Slipids, not Slipid
I cannot change this myself, there is now a issue in GitHub:
https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/38
>Fig.6:
>-g_density could be rerun with a higher -sl value for smoother profiles, holds for other density profiles as well
>-MacRog pure POPS is simulated with Verlet cutoff scheme, Piggot is rerunning with group cutoff scheme.
>Check if affects results & update figures when ready
We have about 45 density profiles in the manuscript from simulations by different people and simulation programs. Even though we have done some progress in the automatization of the analysis, it would be quite a lot of work to recalculate all of these and update the figures. Because smoothing of profiles is not necessary, but would take some time, I did not do it now.
I have added a todo point about Verlet/group issue in MacRog after the figure.
>Page 7:
>-Something is wrong with the sentence
>“Also, the sampled conformations of glycerol backbone significantly vary between different simulation
>models (Figs. S8, S9, S11 and S12), but further analysis is beyond the scope of this work which the PS headgroup.“
This is now rewritten:
"Also, the sampled conformations of glycerol backbone significantly vary between different simulation models (Figs. S8, S9, S11 and S12), but further analysis is beyond the scope of this work which focuses on the PS headgroup."
>Fig.9:
>-Change yellow to orange or sth else more visible
>-Unify the spelling of MacRog (vs. MACROG) across the MS
>-Caption could say that experiment uses K+ counterions (i.e. MacRog is the only data set that follows the experimental setup)
I have opened a GitHub issue about the yellow color: https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/40
MacRog spelling is changed in Fig. 9
POPS is purchased from Avanti in the experimental reference and they come with Na+ counterions. I did not find any notion that the counterions would be exchanged to K+ in there. Unless I have missed something, the Lipid14/17 simulation would be the only data set that follows the experimental setup. I guess that K+ was used with MacRog because sodium had a very strong binding affinity in this model.
>Fig.10:
>-Why are some plots wider than others?
This was due to some missing data, it is fixed now.
>Acknowledgements: Add CSC and Emil Aaltonen foundation for Matti.
These are added.
>SI:
>Figs.S10 & S11:
>-Change line colors for more contrast
I have added a todo note about this.
>Fig.S17:
>-Plots could again use a higher -sl value in g_density
>-Insets not readable
For density profiles, see answer above.
I increased the size of the figure, I can read the insets now.
>Fig.S18:
>-Replace light green and yellow by other colors
>-Not all plots are of equal width
>-Is the Ca2+ density peak really an order of magnitude larger in Lipid17?
I have replaced the colors.
The plot widths and density peaks were due to some missing data, those are fixed now.
Hi -
ReplyDeletecertain places still require improvements, but I find the manuscript at a good state!
In some paragraphs, I would change the narration from "what is wrong" to more "how it likely is" (if possible). I wouldn't like this nice work to be understood only as a force-field comparison paper.
It is impossible to write the changes in a comment, so I will try to express myself rather through a commit to GitHub in the nearest future.
BR,
Josef
Hi,
ReplyDeleteIn general I think the manuscript could benefit from adding introductionary sentences when referring to figures aka. "holding the reader's hand". For example, "to investigate XXX, we present XXX in figure XXX". Also, I personally prefer a caption structure where 1st sentence summarizes the theme of the figure (example: experimental and simulated order parameters for PS lipids), then middlle part explains the details, and the last gives a brief conclusion (Example: Force fields do not reproduce the experimental data)
I have not worked through about half the manuscript editing the language as I go, I'll expect to start uploading my suggested edits in my github tomorrow.
Cheers,
Hanne
Thanks for the comments and edits.
DeleteI have now updated based on some of your todo points in the commit: https://github.com/NMRLipids/NMRlipidsIVotherHGs/commit/01531a261fe09f4fef1b6ab4cac68c98e9c975f9
I have now included also comments by Tiago Ferreira sent by email, see this commit: https://github.com/NMRLipids/NMRlipidsIVotherHGs/commit/dc592db2f84b38e91eeda1f87353ed12019c7686
ReplyDeleteIn addition to these comments Tiago asked a questions, which I answer here:
"just a question: the order parameters of the alpha and beta will probably always be dependent on the glycerol backbone - except if the phosphorus orientation is independent on the glycerol backbone (which is unlikely I guess). Did you try calculating already the orientations of the phosphor group for the different force-fields (I think you did but I don’t remember)? "
I think that this has not been done systemically. Especially, I think that the relation to the glycerol backbone structure is not clear.
I think that the manuscript is already pretty close to be ready for the submission.
ReplyDeleteI am listing here the current todo list before the submission.
1) There are still simulation details to be filled in the SI by Tom Piggot, Jesper Madsen and Joseph Melcr. We also need a confirmation that Amber simulations were ran with Amber18 (or then the correct version), and a possible citation for the package. See todo points in https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Manuscript/manuscriptPSsuppl.pdf
2) There are still couple of questions in todo points related to the experimental details in the manuscript. Some updates are also asked for figures 1 and S6.
3) Colours with better constrast and rescaling of the y-axis has been suggested for figures S10 and S11 made by Pavel Buslaev.
4) Updates on figures 3, 5, 6 and 10 have been suggested:
https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/38
https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/44
Thanks to the contributions by Pavel Buslaev and Tiago Ferreira, the points 2) and 3) are now done.
Delete1) and 4) are yet to be done before we can proceed with the manuscript.
Dear Samuli, I have changed the colors and rescaled figures S10 and S11. Please find them via link
ReplyDeletehttps://drive.google.com/drive/folders/1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2?usp=sharing