Evidence map›Paper›PMID 27239796›Full record

ArticleNature structural & molecular biology2016

Visualizing chaperone-assisted protein folding.

Scott Horowitz, Loïc Salmon, Philipp Koldewey, Logan S Ahlstrom, Raoul Martin, Shu Quan, Pavel V Afonine, Henry van den Bedem, Lili Wang, Qingping Xu and 3 more

Abstract read
In one paragraph

Article in Nature structural & molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.

0numbers the graph read from it
0cells of the map it votes in
34citing 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

34 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Review
  12. Article
  13. Article
  14. Stress-Responsive Periplasmic Chaperones in Bacteria.Frontiers in molecular biosciences · 2021
    Review
  15. Redefining Molecular Chaperones as Chaotropes.Frontiers in molecular biosciences · 2021
    Review
  16. How do Chaperones Bind (Partly) Unfolded Client Proteins?Frontiers in molecular biosciences · 2021
    Review
  17. Article
  18. Article
  19. Identifying dynamic, partially occupied residues using anomalous scattering.Acta crystallographica. Section D, Structural biology · 2019
    Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Scott HorowitzDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Loïc SalmonDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Philipp KoldeweyDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Logan S AhlstromDepartment of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA.
Raoul MartinDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Shu QuanState Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China.
Pavel V AfonineLawrence Berkeley National Laboratory, Berkeley, California, USA.
Henry van den BedemDivision of Biosciences, SLAC National Accelerator Laboratory, Stanford University, Stanford, California, USA.ORCID 0000-0003-2358-841X
Lili WangDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
Qingping XuJoint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Laboratory, Menlo Park, California, USA.
Raymond C TrievelDepartment of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
Charles L BrooksDepartment of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA.
James C A BardwellDepartment of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.

Funding

PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
Mechanism of an Acid Activated ChaperoneR01GM102829 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BARDWELL, JAMES, JAKOB, URSULA H. · 2013 to 2016
$1.8M
Acid-mediated processes in nucleic acids and proteinsR01GM107233 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BROOKS, CHARLES L · 2014 to 2017
$1.1M
The Role of Conditional Disorder in the Acid Stress-Sensing Chaperone HdeAF32GM108298 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI AHLSTROM, LOGAN S · 2014 to 2015
$71k
Howard Hughes Medical InstituteNIGMS NIH HHS F32 GM108298NIGMS NIH HHS P01 GM063210NIGMS NIH HHS R01 GM102829NIGMS NIH HHS R01 GM107233
6 · The paper itself

Abstract

Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.

Indexed as

Protein FoldingAmino Acid SequenceBinding SitesCarrier ProteinsCrystallography, X-RayEscherichia coliEscherichia coli ProteinsGene ExpressionKineticsMolecular Dynamics SimulationPeriplasmic ProteinsProtein BindingProtein Interaction Domains and MotifsProtein Structure, SecondaryRecombinant ProteinsThermodynamicsCarrier ProteinsE colicin-binding immunity protein Im7, E coliEscherichia coli ProteinsPeriplasmic ProteinsRecombinant ProteinsSpy protein, E coli

Identifiers

PMID27239796
PMCPMC4937829

What OpenQuestion holds

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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.