Evidence map›Paper›PMID 39651780›Full record

ArticleThe journal of physical chemistry. B2024

Solid-State NMR Validation of OPLS4: Structure of PC-Lipid Bilayers and Its Modulation by Dehydration.

Milla Kurki, Alexey M Nesterenko, Nicolai E Alsaker, Tiago M Ferreira, Sami Kyllönen, Antti Poso, Piia Bartos, Markus S Miettinen

Abstract read
In one paragraph

Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Article
  2. Frontiers in cellular and infection microbiology · 2026
    Article
  3. 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

8 authors.

Milla KurkiSchool of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.ORCID 0000-0001-8311-6057
Alexey M NesterenkoComputational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.ORCID 0000-0003-1592-257X
Nicolai E AlsakerDepartment of Chemistry, University of Bergen, 5007 Bergen, Norway.ORCID 0009-0000-5544-4715
Tiago M FerreiraInstitut für Physik─NMR, Martin-Luther-Universität Halle-Wittenberg, 06099 Halle, Germany.ORCID 0000-0002-0312-1479
Sami KyllönenSchool of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.ORCID 0009-0009-3136-6869
Antti PosoSchool of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.ORCID 0000-0003-4196-4204
Piia BartosSchool of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland.ORCID 0000-0001-6002-1856
Markus S MiettinenComputational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway.ORCID 0000-0002-3999-4722

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the structure and dynamics of biomembranes with atomic resolution. The validity of the representations obtained is determined by the accuracy and realism of the MD model (force field). Here, we evaluated the proprietary OPLS4 force field of Schrödinger, Inc. against atomic-resolution experimental data, and compared its performance to CHARMM36, one of the best-performing openly available force fields. As a benchmark, we used high-resolution nuclear magnetic resonance (NMR) order parameters for C-H bonds─directly and reliably calculable from MD simulations─measured in phosphatidylcholine (PC) lipid bilayers under varying hydration conditions. Comparisons were made with two dehydration data sets: for saturated (1,2-dimyristoylphosphatidylcholine, DMPC) lipid bilayers from the literature and for unsaturated (1-palmitoyl-2-oleoylphosphatidylcholine, POPC) lipid bilayers measured here. Our findings indicate that OPLS4 reproduces the structure and dehydration response of PC-lipid bilayers fairly well, even slightly outperforming CHARMM36. Both models' main inaccuracies appear in (1) the order parameter magnitudes in the glycerol backbone and unsaturated carbon segments and (2) the qualitatively differing structural response of the PC headgroup to dehydration compared to experiments. In summary, this work underscores the importance of independent validation for (proprietary) force fields and highlights the striking similarities and nuanced differences between OPLS4 and CHARMM36 in describing biomembranes.

Indexed as

Lipid BilayersMagnetic Resonance SpectroscopyMolecular Dynamics SimulationPhosphatidylcholinesDimyristoylphosphatidylcholineWater1-palmitoyl-2-oleoylphosphatidylcholineDimyristoylphosphatidylcholineLipid BilayersPhosphatidylcholinesWater

Identifiers

PMID39651780
PMCPMC11664586

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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.