Evidence map›Paper›PMID 30057025›Full record

ArticleStructure (London, England : 1993)2018

Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold.

Meghan Whitney Franklin, Sergey Nepomnyachiy, Ryan Feehan, Nir Ben-Tal, Rachel Kolodny, Joanna S G Slusky

Abstract read
In one paragraph

Article in Structure (London, England : 1993), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing 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

16 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. The Name Is Barrel, β-Barrel.Methods in molecular biology (Clifton, N.J.) · 2024
    Article
  5. The Art of War withAntibiotics (Basel, Switzerland) · 2023
    Review
  6. General features of transmembrane beta barrels from a large database.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  7. Article
  8. Article
  9. Review
  10. Article
  11. Outer membrane protein evolution.Current opinion in structural biology · 2021
    Review
  12. Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels.The journal of physical chemistry. B · 2021
    Article
  13. Article
  14. Article
  15. Article
  16. 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.

Meghan Whitney FranklinCenter for Computational Biology, University of Kansas, Lawrence, KS 66045, USA.
Sergey NepomnyachiyDepartment of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; Department of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel.
Ryan FeehanCenter for Computational Biology, University of Kansas, Lawrence, KS 66045, USA.
Nir Ben-TalDepartment of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
Rachel KolodnyDepartment of Computer Science, University of Haifa, Mount Carmel, Haifa 3498838, Israel.
Joanna S G SluskyCenter for Computational Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA. Electronic address: slusky@ku.edu.

Funding

Mentoring CoreP20GM103418 · NIGMS · UNIVERSITY OF KANSAS MEDICAL CENTER · PI Douglas E Wright · 2012 to 2026
$63.0M
Synthetic Chemical Biology CoreP20GM113117 · NIGMS · UNIVERSITY OF KANSAS LAWRENCE · PI OROZCO, ROBIN C. · 2016 to 2025
$23.9M
PHARMACEUTICAL ASPECTS OF BIOTECHNOLOGY TRAININGT32GM008359 · NIGMS · UNIVERSITY OF KANSAS LAWRENCE · PI SIAHAAN, TERUNA J., VOLKIN, DAVID · 1989 to 2018
$5.0M
DESIGNED BETA-STRANDS FOR INHIBITING EFFLUX PUMPS AND DISABLING ANTIBIOTIC RESISTANCEDP2GM128201 · NIGMS · UNIVERSITY OF KANSAS LAWRENCE · PI SLUSKY, JOANNA SG · 2017 to 2017
$2.3M
NIGMS NIH HHS DP2 GM128201NIGMS NIH HHS P20 GM103418NIGMS NIH HHS P20 GM113117NIGMS NIH HHS T32 GM008359
6 · The paper itself

Abstract

There are around 100 varieties of outer membrane proteins in each Gram-negative bacteria. All of these proteins have the same fold-an up-down β-barrel. It has been suggested that all membrane β-barrels excluding lysins are homologous. Here we suggest that β-barrels of efflux pumps have converged on this fold as well. By grouping structurally solved outer membrane β-barrels (OMBBs) by sequence we find that the membrane environment may have led to convergent evolution of the barrel fold. Specifically, the lack of sequence linkage to other barrels coupled with distinctive structural differences, such as differences in strand tilt and barrel radius, suggest that the outer membrane factor of efflux pumps evolutionarily converged on the barrel. Rather than being related to other OMBBs, sequence and structural similarity in the periplasmic region of the outer membrane factor of efflux pumps suggests an evolutionary link to the periplasmic subunit of the same pump complex.

Indexed as

Bacterial Outer Membrane ProteinsEvolution, MolecularGram-Negative BacteriaModels, MolecularProtein Conformation, beta-StrandProtein FoldingBacterial Outer Membrane Proteinsbeta barrelsconvergent evolutionCytoscapeCyToStructefflux pumpsmolecular evolutionouter membrane proteinsprimordial beta barrelsequence analysisstructure analysis

Identifiers

PMID30057025
PMCPMC6125174

What OpenQuestion holds

Textmetadata
LicenceTDM
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.