Evidence map›Paper›PMID 37616238›Full record

ArticleJournal of chemical theory and computation2023

Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions.

Matti Javanainen, Peter Heftberger, Jesper J Madsen, Markus S Miettinen, Georg Pabst, O H Samuli Ollila

Open access · hybridAbstract read
In one paragraph

Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
4.2field-weighted citation impact, top 5% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed, 27 citations in OpenAlex.

  1. Article
  2. Review
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  4. Spatially regulated mRNA translation enables functional membrane protein integration in synthetic cells.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
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  6. Article
  7. Review
  8. Article
  9. Review
  10. Article
  11. Evaluating Polarizable Biomembrane Simulations against Experiments.Journal of chemical theory and computation · 2024
    Article
  12. Article
  13. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 4 institutions in 6 countries.

Matti JavanainenInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16000 Prague 6, Czech Republic.ORCID 0000-0003-4858-364X
Peter HeftbergerBiophysics, Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria.
Jesper J MadsenGlobal and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States.ORCID 0000-0003-1411-9080
Markus S MiettinenFachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.ORCID 0000-0002-3999-4722
Georg PabstBiophysics, Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria.ORCID 0000-0003-1967-1536
O H Samuli OllilaInstitute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.ORCID 0000-0002-8728-1006
University of Graz · ATUniversity of Helsinki · FIUniversity of Bergen · NOUniversity of South Florida · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.

Indexed as

Lipid BilayersPhosphatidylcholinesCholesterolMolecular Dynamics Simulation1-palmitoyl-2-oleoylphosphatidylcholineCholesterolLipid BilayersPhosphatidylcholines

Identifiers

PMID37616238
PMCPMC10536986
OpenAlexW4386127336

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.