Evidence map›Paper›PMID 36633947›Full record

ArticleSTAR protocols2023

Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells.

Beatriz Calle, Edgar Gonzalez-Rodriguez, Keira E Mahoney, Anna Cioce, Ganka Bineva-Todd, Omur Y Tastan, Chloe Roustan, Helen Flynn, Stacy A Malaker, Benjamin Schumann

Open access · goldAbstract read
In one paragraph

Article in STAR protocols, 2023. 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 35% 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, 3 citations in OpenAlex.

  1. Article
  2. 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

10 authors at 2 institutions in 2 countries.

Beatriz CalleDepartment of Chemistry, Imperial College London, London W12 0BZ, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Tumour-Host Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Edgar Gonzalez-RodriguezDepartment of Chemistry, Imperial College London, London W12 0BZ, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Keira E MahoneyDepartment of Chemistry, Yale University, New Haven, CT 06511, USA.
Anna CioceDepartment of Chemistry, Imperial College London, London W12 0BZ, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Ganka Bineva-ToddChemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Omur Y TastanChemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Chloe RoustanStructural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK.
Helen FlynnProteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK.
Stacy A MalakerDepartment of Chemistry, Yale University, New Haven, CT 06511, USA.
Benjamin SchumannDepartment of Chemistry, Imperial College London, London W12 0BZ, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London NW1 1AT, UK. Electronic address: b.schumann@imperial.ac.uk.
The Francis Crick Institute · GBYale University · US

Funding

X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Gregory L Hura · 2017 to 2026
$28.6M
ZINC DEFICIENCY &PROTEIN EXPRESSION IN RAT OLFACTORY BULBSP41RR005351 · NCRR · UNIVERSITY OF GEORGIA (UGA) · PI VENOT, ANDRE · 1989 to 2011
$18.4M
Investigating the Surface GlycoproteomeR01CA200423 · NCI · STANFORD UNIVERSITY · PI Carolyn Bertozzi · 2015 to 2026
$3.8M
Toward understanding the role of altered glycosylation in cancerR35GM147039 · NIGMS · YALE UNIVERSITY · PI Stacy Alyse Malaker · 2022 to 2026
$2.0M
Photocrosslinking probes to discover glycan-dependent interactionsR21DK112733 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI KOHLER, JENNIFER J · 2016 to 2018
$664k
An enzymatic approach to study cancer-associated cell-surface glycoproteins: exploration of mucin-degrading bacterial metalloproteasesF32GM126663 · NIGMS · STANFORD UNIVERSITY · PI MALAKER, STACY ALYSE · 2017 to 2019
$125k
Antibody-fucosidase conjugates as therapy for hepatocellular carcinomaF32CA224985 · NCI · STANFORD UNIVERSITY · PI PEH, JESSIE · 2018 to 2019
$70k
Biotechnology and Biological Sciences Research Council BB/V008439/1Biotechnology and Biological Sciences Research Council BB/V014862/1Cancer Research UK FC001060Cancer Research UK FC001112Cancer Research UK L FC001749Medical Research Council CC2127Medical Research Council FC001060Medical Research Council FC001112Medical Research Council L FC001749NCI NIH HHS F32 CA224985NCI NIH HHS R01 CA200423NCRR NIH HHS P41 RR005351NIDDK NIH HHS R21 DK112733NIGMS NIH HHS F32 GM126663NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P41 GM103393NIGMS NIH HHS R35 GM147039Wellcome Trust 218304/Z/19/ZWellcome Trust CC2127Wellcome Trust FC001060Wellcome Trust FC001112Wellcome Trust FC001749
6 · The paper itself

Abstract

Despite the known disease relevance of glycans, the biological function and substrate specificities of individual glycosyltransferases are often ill-defined. Here, we describe a protocol to develop chemical, bioorthogonal reporters for the activity of the GalNAc-T family of glycosyltransferases using a tactic termed bump-and-hole engineering. This allows identification of the protein substrates and glycosylation sites of single GalNAc-Ts. Despite requiring transfection of cells with the engineered transferases and enzymes for biosynthesis of bioorthogonal substrates, the tactic complements methods in molecular biology. For complete details on the use and execution of this protocol, please refer to Schumann et al. (2020)

Indexed as

N-AcetylgalactosaminyltransferasesProteinsGlycosylationHumansPeptidesPolysaccharidesN-AcetylgalactosaminyltransferasesPeptidesPolysaccharidesProteinsCell-based AssaysMass SpectrometryMolecular/Chemical ProbesProtein BiochemistryProteomics

Identifiers

PMID36633947
PMCPMC9843269
OpenAlexW4315498048

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.