Wednesday, December 12, 2018

NMRlipids IV: Toward submission of the manuscript about PS lipids

I believe that the manuscript about PS lipids contains now all the essential content (see also the supplementary information). The main results are:
  • 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. 

Wednesday, December 5, 2018

Correlation times of C–H bond direction in different force fields

We are starting a small project to see how well the correlation times of C–H bond vectors are reproduced in different force fields. We aim to simply follow the analysis of the R1 and τeff times as was done earlier by Tiago, Samuli, et al. for the Berger force field, but for all the different force fields available at the Zenodo repository of NMRlipids.

The plan is to not make this an official NMRlipids project, but still to do it fully openly; to this end, we warmly welcome anyone interested to follow the progress and to participate on GitHub!

Leftin and Brown have published experimental Rtimes for many different lipids in various temperatures and at various field strengths. Concerning the experimental τeff times, in Tiago's paper they are reported for POPC at full hydration and 298 K, and they have also been published for DMPC at low hydration and 300 K. However, as many of the trajectories at the Zenodo repository have DPPC, the experimental τeff times for DPPC at full hydration would be warmly welcomed.

Beyond force field comparison, possibly interesting physical questions to look from the data would be the effects of hydration, salts, and cholesterol on C-H bond dynamics. A possible extension could also be to look at the temperature dependence.

Hanne Antila and Markus Miettinen