Evidence map›Paper›PMID 30177739›Full record

ArticleScientific reports2018

YesU from Bacillus subtilis preferentially binds fucosylated glycans.

Joe Tiralongo, Oren Cooper, Tom Litfin, Yuedong Yang, Rebecca King, Jian Zhan, Huiying Zhao, Nicolai Bovin, Christopher J Day, Yaoqi Zhou

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2018. 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
0.5field-weighted citation impact, top 36% 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

3 citing papers in PubMed, 8 citations in OpenAlex.

  1. Review
  2. Review
  3. LectinOracle: A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022
    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

10 authors at 4 institutions in 3 countries.

Joe TiralongoInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia. j.tiralongo@griffith.edu.au.
Oren CooperInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
Tom LitfinInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
Yuedong YangSchool of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China.
Rebecca KingInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
Jian ZhanInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
Huiying ZhaoQueensland Institute of Medical Research, Brisbane, Queensland, Australia.
Nicolai BovinShemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Christopher J DayInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia.
Yaoqi ZhouInstitute for Glycomics, Griffith University, Gold Coast Campus, QLD 4222, Australia. yaoqi.zhou@griffith.edu.au.ORCID 0000-0002-9958-5699
Griffith University · AUInstitute of Bioorganic Chemistry · RUQIMR Berghofer Medical Research Institute · AUSun Yat-sen University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The interaction of carbohydrate-binding proteins (CBPs) with their corresponding glycan ligands is challenging to study both experimentally and computationally. This is in part due to their low binding affinity, high flexibility, and the lack of a linear sequence in carbohydrates, as exists in nucleic acids and proteins. We recently described a function-prediction technique called SPOT-Struc that identifies CBPs by global structural alignment and binding-affinity prediction. Here we experimentally determined the carbohydrate specificity and binding affinity of YesU (RCSB PDB ID: 1oq1), an uncharacterized protein from Bacillus subtilis that SPOT-Struc predicted would bind high mannose-type glycans. Glycan array analyses however revealed glycan binding patterns similar to those exhibited by fucose (Fuc)-binding lectins, with SPR analysis revealing high affinity binding to Lewis

Indexed as

Amino SugarsBacillus subtilisBacterial AdhesionBacterial ProteinsBinding SitesCaco-2 CellsCarbohydrate SequenceCloning, MolecularEscherichia coliFucoseGene ExpressionGlycosylationHumansKineticsLewis Blood Group AntigensMolecular Docking SimulationAmino SugarsBacterial ProteinsFucoselacto-N-fucopentaose IIILewis a oligosaccharideLewis Blood Group AntigensOligosaccharidesPolysaccharidesReceptors, Cell SurfaceRecombinant Proteinssaccharide-binding proteins

Identifiers

PMID30177739
PMCPMC6120924
OpenAlexW2889524412

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.