Wednesday, October 2, 2019

Current status of the project

2.10.2019 the NMRlipids IV manuscript about PS lipids is now accepted to be published in the Journal of Physical Chemistry B

12.9.2019 Revised version of the NMRlipids IV manuscript about PS lipids is now submitted to the Journal of Physical Chemistry B

26.6.2019 The NMRlipids IV manuscript about PS lipids is now submitted to the Journal of Physical Chemistry B

31.5.2019 The first annual NMRlipids workshop post was published



23.4.2019 NMRlipids IVb: Assembling the PE & PG results post was published



22.11.2018 The first annual NMRlipids workshop is coming!

NMRlipids workshop 2019 May 15th to 17th

20.9.2018 Homepages of my group are now published. Check and share also the announcement of open Ph.D. student position.

20.9.2018 NMRlipids III: Quantitative measure for the force field quality needed post was published


18.9.2018 NMRlipids IV: Challenges in evaluating counterion binding affinity to PS bilayers post was published


15.9.2018 Google has launched a new Dataset search engine. It seems to find the data from NMRlipids project very well.

13.9.2018 Poster presented about NMRlipids IV project in Tiny Lip­ids With Grand Func­tions workshop in Helsinki, Fin­land, 19 - 22 Au­gust 2018:


4.7.2018 A lot of data has been contributed to the NMRlipids III and IV projects. Especially the NMRlipids III project is delayed because the main focus has recently been in the ion-membrane interactions. Currently the first priority is to finish the manuscript about PS lipids from NMRlipids IV, the second to finish the manuscript about lipid-cholesterol interaction from NMRlipids III, and the third to progress the manuscript about PE and PG lipids.


4.7.2018 NMRlipids IV: First draft of the manuscript about PS lipids post was published.

3.5.2018 Samuli Ollila received a academy research fellow position from the academy of Finland for five years. The research plan includes the development of the NMRlipids project.


13.4.2018 PS-headgroup order parameter comparison now also shows results for Amber Lipid 17:



12.4.2018 New NMRlipids-related publication: Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization post was published


30.1.2018 Database of the NMRlipids simulations and experiments post was published.

22.12.2017 NMRlipids IV: Current status and reorganization of the manuscript post was published

8.12.2017 Results from CHARMM36 simulation with cationic surfactants was added to Quantifying the effect of bound charge on headgroup order parameters post.

27.7.2017 Quantifying the effect of bound charge on headgroup order parameters post was published.

31.3.2017 NMRlipids III: Preliminary version of the manuscript post is published.

9.3.2017 NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PE, PG and PS lipids post is published. Almost any kind of simulations of these lipids in bilayers would be useful at this stage.

15.2.2017 My activity in NMRlipids project has been low during the last months due to other commitments. However, I have now again possibility to advance NMRlipids III and IV projects (updates will follow soon). We have also published a blog post about the future of NMRlipids project.

29.11.2016 NMRlipids project will be presented in PHOS16 Conference (Philosophy and History of Open Science) held in Helsinki on 31.11.-1.12.2016. There should be also live stream available.

12.11.2016 NMRlipids II manuscript Molecular electrometer and binding of cations to phospholipid bilayers accepted for publication in Physical Chemistry Chemical Physics, and the preprint is available on the journal web page.

16.10.2016 Zenodo has been updated as described in their news page. There are a lot of improvements but this one is probably the most important for us: "The current 2GB per file limit is removed, in favour of a 50GB per dataset limit". This means that we do not have to split the trajectories in 2GB pieces anymore.

7.10.2016 The final version of NMRlipids II manuscript (lipid-ion interactions) submitted to Physical Chemistry Chemical Physics.

9.9.2016 NMRlipids II manuscript (lipid-ion interactions) "accepted for publication after revisions" to Physical Chemistry Chemical Physics.

13.7.2016 NMRlipids II manuscript (lipid-ion interactions) has been now submitted to Physical Chemistry Chemical Physics.

1.7.2016 NMRlipids III: Preliminary observations post was published.

30.5.2016 Toward submission of NMRlipids II publication (lipid-ion interactions) (2) post was published.

20.5.2016 The new data delivered for NMRlipids II project raised a question about the order parameter responses on bound charges in CHARMM36 model. If you have CHARMM36 simulation data of PC bilayer with known amount of charged amphiphiles and you are willing to share it for the project, please let us know.

24.2.2016  Our goal from the beginning has been to immediately publish all the scientific content related to the project. One relevant part of the content are discussions between reviewers and authors during the peer review process. We have now published two peer reviewed articles: NMRlipids I and NMRlipids V. In both cases we have asked from the editor if we can publish also the reviewers' comments since everything else is public. As expected, in the NMRlipids I case the Journal of Physical Chemistry staff replied that this is not possible. However, editorial and publishing teams of BBA Membranes'  were positive about publishing the referees' comments in the case of NMRlipids V publication. Both referees were also sympathetic to the idea. However, one of them declined stating permission to make comments available should be asked a priori, at the same time referees are invited to review a paper. This is an important learning point from this experience.

25.1.2016 The review written in the NMRlipids V project has been now accepted to be published in BBA - Biomembranes and is available also from their webpage.

19.1.2016  Does the glycerol backbone structure depend on initial structure? post was published.

21.12.2015 Towards submission of NMRlipids II publication (lipid-ion interactions) post was published.
 
24.11.2015 The review written in the NMRlipids V project has been now submitted.

29.10.2015 The NMRlipids I publication is already available also through the journal website.

28.10.2015 The first manuscript (NMRlipids I) based on the data and discussions presented through this blog is now accepted to be published in the Journal of Physical Chemistry B. We thank all the contributors and followers for courage to participate this project.

13.10.2015 We have received a new revision request for the first manuscript (NMRLipids I project). The first version of the reply is already in GitHub. There were essentially no new comments compared to the first revision round so I will not make a new post for this. If you have comments, you can comment the Revision requested for the first manuscript post or GitHub. If there will not be objections I will submit the revision on Friday this week (16.10.2015).

28.9.2015 NMRLipids V project: Review about validations of membrane MD simulations was published. This is a project to write an invited review on a topic strongly related to the blog content.

28.9.2015 The title of the blog has been changed to "The NMRlipids project: Open Collaboration to understand lipid systems in atomistic resolution".

24.9.2015 The NMRLipids project will be discussed in Mindtreck 2015 conference in Tampere. At least one of the sessions may be live streamed, see the facebook event.

22.8.2015 The revised version of the first manuscript is now submitted.

20.7.2015 Revision requested for the first manuscript post was published.


6.7.2015 About page describing the different subprojects and Workflow page suggesting new workflow for these projects are now published.

26.5.2015 The first manuscript produced in this blog was considered to be
"primarily directed toward an audience of specialists doing closely related work and that lack a clear description of impact on the broader field of chemistry" by the editor of the Journal of American Chemical Society and it was rejected without peer review process. Thus, the manuscript has been now submitted to the Journal of Physical Chemistry (another journal ran by american chemical society).

15.5.2015 The first manuscript produced in this blog is now submitted to the Journal of American Chemical Society.

12.5.2015 The first manuscript produced in this blog will be submitted to the Journal of American Chemical Society by the end of this weeḱ.

25.3.2015 Mapping scheme for lipid atom names for universal analysis scripts post was published.

17.3.2015  Towards first submission to journal (2) post was published.

9.3.2015 Current and future activity post was published.

6.3.2015 Samuli will talk about this project in the event organized by the Open Knowledge Finland (OKFFI) on 10.3.2015 in University of Helsinki. There will also live stream from the event through this link http://vn-rec.it.helsinki.fi (user: video, pw: video)

6.2.2015  The first draft of the ion-lipid interaction manuscript was published.

16.1.2015 Towards first submission to journal post was published.

16.1.2015 The current version of the new manuscript is now updated to arXiv http://arxiv.org/abs/1309.2131v2. There will be soon a new post about the further proceeding.

23.12.2014  New version of the manuscript (2)  post was published.

21.11.2014 New manuscript written on the results reported in this blog is available for commenting: New version of the manuscript. The manuscript covers only the results for fully hydrated bilayers, effect of dehydration and effect of cholesterol. A separate manuscript will be written about ion-lipid interactions.

18.11.2014 New manuscript written about the results reported in this blog will be made available for commenting on Friday 21th of November.

12.11.2014 The post About glycerol conformations is now updated. The incorrect stereospecifity in GAFFlipid for g\(_1\) segment was due to the intial structure downloaded from lipidbook, not due to the GAFFlipid force field. The updated figure with the results:


10.10.2014 Together with Hubert Santuz we have started a GitHub organization https://github.com/NMRlipids. It contains a repository: https://github.com/NMRLipids/nmrlipids.blogspot.fi. The idea is to collect all the relevant files related to the project there. There are already some files and there will be more. If you are familiar with git you can add your files by making a pull request. If you are not familiar you can also make as previously (add a link to a comment) and ask us to add it into the GitHub. Downloading the data should be straightforward without any understanding about the git system. It took a couple of hours for me to get familiar with the git system. The time was well spent and I recommend it to everyone.

7.10.2014 We have added a new page called Data Contributions as an attempt to arrange the discussion. The idea is that all the new data would be sent by commenting the Data Contibutions page. Yet, let us keep the other comments under each separate post.

1.9.2014  The post About glycerol conformations was published.

20.8.2014 Presentations describing the nmrlipids project in the International Workshop on Biomembranes - From Fundamentals to Applications were posted.

19.5.2014 The post Towards a new version of the manuscript was published.

13.5.2014 To Do List has been added as a page in the top panel.

2.5.2014  The post Response of headgroup and glycerol order parameters to changing conditions: Results, reviewing the current results for the responses of the headgroup and glycerol order parameters to the changing conditions, was published.

29.4.2014 The R/S hydrogen labeling was wrong for MacRog in the previous plot. The correct one was reported by Matti Javanainen. Here is the new plot:
Now also the MacRog is in good agreement with experiments, in addition to CHARMM.
  

24.4.2014 Based on discussions with Antti Lamberg and Patrick Fuchs we have now plotted the results with the sign, and the R/S hydrogen labeling


It seems that the CHARMM36 results are in the best agreement with experiments. (However, the R/S hydrogen labeling in MacRog has to be still confirmed).

16.4.2014 Patrick wrote a comment on how to tell R and S and hydrogens apart.

11.4.2014 The lipid forcefield comparison at full hydration updated—now contains results for 12 force fields.

10.4.2014 The post On the signs of the order parameters was published.

10.4.2014 We have added a page containing information about the authors of the project (see the top panel).

31.3.2014 The new version of order parameter calculation script is now available at https://www.dropbox.com/sh/au7cglb7i4o0uvy/65dRNta_bM
It will now calculate also the sign. Also the *hdb file to protonate the Berger lipids with Gromacs g_protonate tool is now available. Note that there was a bug in the script shared in the original figshare package: It takes only the first 75 lipids in to account. Thus, if you have used it for the larger systems you have not taken all the available statistics into account. For my own Berger results, this makes a very small difference though. It would be very useful if someone would make a tool which would directly calculate the order parameters from the Gromacs *trr file.

14.3.2014 The lipid force field comparison at full hydration was published.

9.3.2014 Antti demonstrated that it is possible to get a very good agreement with the experimentally measured order parameters by simply sampling a large set of randomly modified dihedral potentials, choosing the most promising ones, and repeating this randomised refinement a few times.

25.2.2014 This is our new front page: A simple list the most relevant events, ordered by date. Its purpose is to help you keep up with what is happening on the blog—in posts as well as in comments.

25.2.2014 Blog post discussing the accuracy of order parameter measurements was published.

16.2.2014  Samuli gave a presentation related to the nmrlipids-project at the Biophysical Society meeting.

13.2.2014 The first attempt to modify the Berger dihedral parameters was reported with a preliminary conclusion that removing all dihedral potentials improved the choline- but impaired the g1 order parameters.

12.2.2014  Our current knowledge of the behaviour as a function of dehydration gathered into a single plot.


23.1.2014  Our current knowledge of the behaviour as a function of ion concentration gathered into a single plot.


23.1.2014  Our current knowledge of the behaviour as a function of cholesterol content gathered into a single plot.


21.1.2014 Our current knowledge of the full hydration behaviour gathered into a single plot.


10.12.2013 Patrick filed a Redmine Bug about reaction field simulations with Gromacs 4.0.7 not being reproducible with 4.5.3., which he commented first here on Oct 25th.

29.10.2013 Samuli wrote a guest post to the MARTINI group blog: PN vector orientation not a good measure for evaluating phospholipid force field performance, use head group order parameters instead.

2.10.2013 The first results were shortly reviewed and some short term goals were set in a new blog post.

13.9.2013 The first comment and the first contribution.

10.9.2013 A post discussing the motivation for the project:
and the first three scientific posts were published:


9.9.2013 The first version of the manuscript was published.

11.7.2013 The policy for publication credits was published.

3.7.2013 The nmrlipid.blogspot.fi was opened with a post that stated our aim.

28.6.2013 The project was first time publicly discussed in a presentation at the Biological membranes: challenges in simulations and experiments -meeting in Paris.

Friday, May 31, 2019

The first annual NMRlipids workshop

Twelve contributors participated in the first annual NMRlipids workshop in Berlin from 15th to 17th of May 2019. The flexible schedule included six presentations and a significant fraction of time was devoted to discussions and working towards the goals of the workshop.

The workshop was opened by Samuli Ollila presenting the current status and open issues in the NMRlipids project (slides available here). The presentation was followed by a discussion to determine the main goals of the workshop:
  1. Define a quantitative quality measure for the structural quality of a lipid bilayer simulation.
  2. Create instructions on how to contribute data into the NMRlipids databank.
  3. Create a universal code to visualize lipid structures in simulations (for example, see this figure).
The second day of the workshop was opened by Ivan Gushchin presenting a principal component analysis of lipid structures (slides available from here). This was followed by Patrick Fuchs presenting the status of analysis code to calculate order parameters from united atom simulations, and Tiago Ferreira presenting order parameter experiments using natural abundance 13C NMR. At the end of the second day,  Stephanie Dawson presented publishing possibilities offered by www.scienceopen.com. The third day of the workshop was opened by Ivan Gushchin presenting the relation between lipid bilayer densities and scattering form factors (slides available from here).

The main outcomes of the workshop are listed here (topics 1-3 correspond to the goals listed above and 4-7 are additional outcomes):
  1. A quantitative measure for the structural quality of lipid bilayer simulations. The aim was to define a simple machine and human readable measure for the structural quality of lipid bilayer in simulations using scattering form factors and order parameters. The main applications would be the NMRlipids III project (see post and post and issue) and the lipid databank. For order parameters, the proposal was to measure the distance from experimental values using the size of the error bar as a unit (see the first page in the document). For the form factor, the task turned out to be more complicated and universal quality measure was not yet defined (see the pages 1-2 in the document).
  2. Instructions to contribute data into the NMRlipids databank. The aim was to generate straightforward instructions on how to contribute data into the NMRlipids project in the way to enable automatic analysis and indexing. The suggestion was to update the current indexing system and read the metadata directly from hashtags given in Zenodo descriptions. Preliminary script to pull data from Zenodo was created, but it is not publicly available yet. I have opened an issue for further discussion.
  3. Visualize structural differences between force fields and lipids. The aim was to create a code which automatically visualizes lipid structure by generating figures like this, and analyze the differences between PC, PS, PG and PE headgroup structures as suggested in the NMRlipids IVb project. The code for this was generated, but it is not yet publicly available.
  4. The analysis code to calculate order parameters from united atom models by Patrick Fuchs is progressing, but it is not yet publicly available. The merging with the current order parameters calculation code was superficially discussed. See also the discussion in the blog after the workshop.
  5. In the discussion following the presentation by Tiago Ferreira, we concluded that the sn-1 chain order parameters from natural abundance 13C NMR may be less accurate than 0.02 (the previously used quantitative accuracy of order parameters) due to the spectral overlap. The order parameters from specifically deuterated samples are probably more accurate for this region. This is relevant for the quantitative quality measure and for the NMRlipids III project. Further discussion is in the issue.  
  6. In the discussion following the presentation by Ivan Gushchin about lipid bilayer density profiles and scattering form factors, we concluded that some of the complications in the NMRlipids III project could be potentially resolved by separately analyzing the effect of POPC and cholesterol densities to the form factors from POPC/cholesterol mixture. 
  7. The possibilities of using Markov state modeling presented by Ivan Gushchin (slide 5) to understand lipid structures and transition rates were discussed. 
The workshop was overall successful and the second NMRlipids workshop will be most likely organized at least partially with the same concept.

Explanation how to measure order parameters with 13C NMR

Thursday, May 9, 2019

NMRlipids III: Quantifying intermolecular interactions in binary lipid mixtures

After trying to rationalize the data in the NMRlipids III manuscript, I think that we should emphasize more the evaluation of lipid-cholesterol interactions in binary lipid bilayer against experiments. As far as I know, the quantitative comparison of intermolecular interactions between simulations and experiments has not been done much. Therefore, the procedures in this manuscript could be useful also for other than POPC/cholesterol mixtures.

To facilitate this, I plotted the absolute values of POPC sn-1 acyl chain order parameters as a function of cholesterol concentration from experiments (Fig. 1) and different simulations (slopes*pdf, see also the SI).
Fig 1: Absolute values of sn-1 acyl chain order parameters from experiments (points). The lines are fitted to the values with 0-50 mol % of cholesterol.
The increase is approximately linear below equimolar concentration in both simulations and experiments. To compare the ordering effect of cholesterol between different simulations and experiments, I made a linear fit to the data as a function of cholesterol and plotted the slopes for each carbon segment (Fig. 2).
Fig 2: Slopes of order parameters as a function of cholesterol. Determined by fitting equation SCH(Cchol) =kOPCchol + SCH(0) to the data in Fig 1 (experiment) and slopes*pdf (currently S2-S7 in the SI).
Such a plot enables the comparison of cholesterol ordering effect between different simulations and experiments, even though the data would not be measured exactly at the same concentrations. We could also add some literature data with fewer cholesterol concentrations or other lipid media in this figure for comparison.

In addition, the quantitative quality measure for the force field quality, recently contributed by Hanne Antila, could help to evaluate the intermolecular interactions. Some preliminary results are already in the manuscript, but some details in the analysis may need refinement, see issues 65 and 64 in the MATCH repository.

The most important ToDos to progress the manuscript are listed here:
  1. We need to define a appropriate quantitative quality measure to be used in this manuscript, for discussion see issues 65 and 64 in the MATCH repository.
  2. The changes in cholesterol order parameters upon dilution with POPC could be also analyzed from experiments and different simulations.
  3. Results from Lipid14 simulations with cholesterol model would be useful, see issue 7.
  4. Additional data from the literature could be added in the figure showing acyl chain order parameters slopes (Fig. 2).
  5. Figure showing form factors should be updated after all the form factors are calculated properly and the scaling method for experimental form factors is decided, see issue 18.
  6. Section S1 in the supplementary information about reproducibility of CHARMM36 simulations should be written based on the discussion in issue 4. 
  7. Section S3 in the supplementary information about the effect of undulations on the order parameters should be written based on the discussion in issue 16.
  8. The used accuracy for the experimental acyl chain order should be decided, see issue 15.
 

Wednesday, April 24, 2019

NMRlipids IV: Toward submission of the manuscript about PS lipids (2)

The manuscript describing results about PS lipids from the NMRlipids IV project has progressed substantially since the previous blog post, and I believe that it is almost ready for submission now. However, we cannot proceed with the submission before we have simulation details from the data delivered by Tom Piggot, Jesper Madsen and Josef Melcr, see ToDo points in the supplementary information.

I have now changed the title of the manuscript to "Headgroup structure and cation binding in phosphatidylserine lipid bilayers". Let me know if you think that we should add molecular dynamics and/or NMR experiments in the title, or if you have other suggestions.

If you have any comments regarding the manuscript, please let me know. I would like to proceed with the submission as soon as possible. I think that a suitable journal for the manuscript would be, e.g., The Journal of Physical Chemistry B or Physical Chemistry Chemical Physics. Let me know if there are opinions about this.


Tuesday, April 23, 2019

NMRlipids IVb: Assembling the PE & PG results

As discussed in the previous post, the NMRlipids IV project concerning PE, PG and PS lipids was divided into two parts. The first part about the results from PS lipids is approaching to the submission, while the second part about PE and PG lipids is in a more preliminary stage.

I have now started to assemble the contributed data for PE and PG lipids into a manuscript in a new GitHub repository. From now on, I will call this part of the project as NMRlipids IVb. Current status of the manuscript and most important things to todo are summarized in this post.

Headgroup and glycerol backbone order parameters from lipids with different headgroups in experiments

Experimental order parameters delivered by Tiago Ferreira with the information about the sign revealed that the 𝛽-carbon order parameter of PG lipids is positive, while other lipids have negative order parameter for this carbon (Fig. 1). Therefore, the structure of PG lipid seems to be distinct from PC and PE, in contrast to the conclusions from the order parameter data without sign information in the previous post.

Figure 1: Experimental order parameters of the headgroup and glycerol backbone region C-H bonds from experiments. For literature references, see the manuscript draft.

 

Headgroup and glycerol backbone order parameters of PE and PG lipids in simulations

The experimental information about order parameter signs enables a similar comparison between different simulation models and experiments for PE and PG lipids as done previously for PC and PS lipids in NMRlipids I and NMRlipids IV projects. This comparison (Fig. 2) and the results in NMRlipids I and NMRlipids IV projects suggest that the differences between PC, PE, PG, and PS headgroups are well captured in CHARMM36 simulations, although order parameters of all C-H bonds are not within the experimental error for any of the lipids. Therefore, the structural differences between lipid headgroups could be analyzed from the CHARMM36 simulations, perhaps in a similar way as done for the PS headgroup in the NMRlipids IV project. The contributed data for PE and PG lipids from united atom simulations is not yet analyzed, partly because of the lack of suitable programs for the automatic analysis of the data.

Figure 2: Headgroup and glycerol backbone order parameters from PE (left) and PG (right) lipid bilayers from experiments and different simulation models. For literature references, see the manuscript draft.

 

Cation binding to lipid bilayers containing PE and PG lipids

Sodium binding to PE lipid bilayers seems to be slightly weaker than in corresponding simulations for PC lipids, but experimental data is not available. For calcium binding to PE lipids, we do not have experimental nor simulation data yet.

As discussed in the NMRlipids IV project, the counterion binding to negatively charged lipid bilayer is complicated to assess against experimental data. However, the results from PC:PG mixtures from CHARMM36 and Slipids simulations indicate that sodium ions could be slightly overbinding to PG lipids, similarly to PS lipids in the NMRlipids IV project. For calcium binding to PG containing lipid bilayers, we have data only from CHARMM36 simulations and the conclusions are not yet fully clear.

 

ToDo:

  1. Analyze united atom simulations of PE lipids (GROMOS, CHARMM36ua, OPLS-UA, Berger, and GROMOS-CKP) listed in Table I in the manuscript with or without the new code for united atom data.
  2. Analyze structural differences between POPC, POPE, POPG and POPS headgroups from CHARMM36 simulations. The most reasonable first step would be probably to follow a similar analysis that was done for PS lipids in the NMRlipids IV project.
  3. Simulation data for PG lipids with different force fields would be useful. Currently, we have only CHARMM36 and Slipids.
  4. Simulation data from POPC:POPG (1:1) mixtures with sodium counterions and different CaCl2 concentrations (0-1M) from different force fields would be useful. Currently, we have results only from CHARMM36.