Evidence map›Paper›PMID 29877794›Full record

ArticleeLife2018

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T Justin Rettenmaier, José Brandão-Neto, Nicholas M Pearce, Frank von Delft, James A Wells, James S Fraser

Abstract read
In one paragraph

Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.

0numbers the graph read from it
0cells of the map it votes in
122citing 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

122 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Phosphatase Signaling as a Therapeutic Strategy in Schizophrenia.International journal of molecular sciences · 2026
    Review
  6. Article
  7. Review
  8. Review
  9. Article
  10. Review
  11. Article
  12. Article
  13. Other Techniques.Advances in biochemical engineering/biotechnology · 2026
    Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

62 more citing papers are in PubMed but not listed here.

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.

Daniel A Keedy *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID http://orcid.org/0000-0002-9184-7586
Zachary B Hill *Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.
Justin T BielDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID http://orcid.org/0000-0002-0935-8362
Emily KangDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.
T Justin RettenmaierCellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.
José Brandão-NetoDiamond Light Source, Didcot, United Kingdom.ORCID https://orcid.org/0000-0001-6015-320X
Nicholas M PearceCrystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.ORCID http://orcid.org/0000-0002-6693-8603
Frank von DelftDiamond Light Source, Didcot, United Kingdom.ORCID http://orcid.org/0000-0003-0378-0017
James A WellsDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.ORCID http://orcid.org/0000-0001-8267-5519
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID http://orcid.org/0000-0002-5080-2859

Funding

User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI CORIE Y RALSTON · 2017 to 2026
$28.6M
RESEARCH TRAINING IN CHEMISTRY AND CHEMICAL BIOLOGYT32GM064337 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CRAIK, CHARLES SCOTT · 2002 to 2021
$7.8M
Eliminating Critical Systematic Errors In Structural Biology With Next-Generation SimulationR01GM124149 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HOLTON, JAMES M · 2017 to 2024
$2.5M
Supplement to Resolving ensemble averaged conformations by multi-temperature x-ray crystallography - Equipment 2020R01GM123159 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRASER, JAMES SOLOMON · 2018 to 2021
$2.3M
Affinity-directed tagging of protein binding partners in signalingR01CA191018 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WELLS, JAMES A · 2014 to 2018
$1.6M
Model Comparison in Structural BiologyR21GM110580 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FRASER, JAMES SOLOMON · 2014 to 2015
$419k
Mapping the conformation-specific interactome of signaling proteinsK99CA203002 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HILL, ZACHARY BENJAMIN · 2016 to 2017
$203k
Studying how a general allosteric site regulates protein kinase functionF31CA180378 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RETTENMAIER, TERRY JUSTIN · 2013 to 2015
$87k
NCI NIH HHS CA191018NCI NIH HHS (F31 CA180378NCI NIH HHS F31 CA180378NCI NIH HHS K99 CA203002NCI NIH HHS K99CA203002NIGMS NIH HHS GM110580NIGMS NIH HHS GM123159NIGMS NIH HHS GM124149NIGMS NIH HHS GM124169NIGMS NIH HHS P30 GM124169NIGMS NIH HHS R01 GM123159NIGMS NIH HHS T32 GM064337Wellcome Trust
6 · The paper itself

Abstract

Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.

Indexed as

Allosteric RegulationProtein ConformationAllosteric SiteBinding SitesCrystallography, X-RayHumansKineticsModels, MolecularMutationProtein BindingProtein Tyrosine Phosphatase, Non-Receptor Type 1TemperatureProtein Tyrosine Phosphatase, Non-Receptor Type 1allosteryE. colihumanmolecular biophysicsphosphataseprotein dynamicsstructural biology

Identifiers

PMID29877794
PMCPMC6039181

What OpenQuestion holds

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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.