Evidence map›Paper›PMID 29695721›Full record

ArticleNature communications2018

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.

Tanguy Le Marchand, Matteo de Rosa, Nicola Salvi, Benedetta Maria Sala, Loren B Andreas, Emeline Barbet-Massin, Pietro Sormanni, Alberto Barbiroli, Riccardo Porcari, Cristiano Sousa Mota and 8 more

Abstract read
In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing 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

32 citing papers in PubMed.

  1. Article
  2. Article
  3. Interfacial Dynamics and Growth Modes of βJournal of chemical information and modeling · 2023
    Article
  4. Disease-relevant βNature communications · 2023
    Article
  5. Review
  6. Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  7. The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  8. Chemical reviews · 2022
    Review
  9. Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Investigation of D76N βJournal of the American Society for Mass Spectrometry · 2021
    Article
  16. Predicting stable binding modes from simulated dimers of the D76N mutant ofComputational and structural biotechnology journal · 2021
    Article
  17. Article
  18. Article
  19. The role of the IThe Journal of biological chemistry · 2020
    Article
  20. Collagen I Weakly Interacts with the β-Sheets of βJournal of the American Chemical Society · 2020
    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

18 authors.

Tanguy Le MarchandCentre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
Matteo de RosaDipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.ORCID http://orcid.org/0000-0002-8634-5426
Nicola SalviInstitut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France.ORCID http://orcid.org/0000-0003-1515-6908
Benedetta Maria SalaDipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
Loren B AndreasCentre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
Emeline Barbet-MassinCentre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
Pietro SormanniDepartment of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
Alberto BarbiroliDipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy.
Riccardo PorcariWolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK.
Cristiano Sousa MotaESRF - The European Synchrotron, 38043, Grenoble, France.
Daniele de SanctisESRF - The European Synchrotron, 38043, Grenoble, France.
Martino BolognesiDipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.ORCID http://orcid.org/0000-0002-9253-5170
Lyndon EmsleyCentre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
Vittorio BellottiWolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK.ORCID http://orcid.org/0000-0002-0467-864X
Martin BlackledgeInstitut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France.
Carlo CamilloniDipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. carlo.camilloni@unimi.it.
Guido PintacudaCentre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France. guido.pintacuda@ens-lyon.fr.
Stefano RicagnoDipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. stefano.ricagno@unimi.it.ORCID http://orcid.org/0000-0001-6678-5873

Funding

European Research Council 648974
6 · The paper itself

Abstract

Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins.

Indexed as

Amyloidogenic ProteinsAmyloidosisbeta 2-MicroglobulinCrystallography, X-RayHumansMolecular Dynamics SimulationMutagenesis, Site-DirectedNuclear Magnetic Resonance, BiomolecularPoint MutationProtein Aggregation, PathologicalProtein FoldingProtein StabilityAmyloidogenic Proteinsbeta 2-Microglobulin

Identifiers

PMID29695721
PMCPMC5916882

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Registered trials

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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.