Evidence map›Paper›PMID 34139165›Full record

ReviewCell systems2021

Fundamentals to function: Quantitative and scalable approaches for measuring protein stability.

Beatriz Atsavapranee, Catherine D Stark, Fanny Sunden, Samuel Thompson, Polly M Fordyce

Abstract readReview
In one paragraph

Review in Cell systems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing 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

21 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Towards routine accurate electron-density studies of biological macromolecules.Acta crystallographica. Section D, Structural biology · 2026
    Article
  5. Article
  6. Review
  7. Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026
    Review
  8. Article
  9. Article
  10. Article
  11. Article
  12. A combinatorially complete epistatic fitness landscape in an enzyme active site.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  13. Article
  14. Fluorescence-Based Protein Stability Monitoring-A Review.International journal of molecular sciences · 2024
    Review
  15. Article
  16. Article
  17. Article
  18. Folding stabilities of ribosome-bound nascent polypeptides probed by mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  19. Review
  20. Review
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

5 authors.

Beatriz AtsavapraneeDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Catherine D StarkDepartment of Biochemistry, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA.
Fanny SundenDepartment of Biochemistry, Stanford University, Stanford, CA 94305, USA.
Samuel ThompsonDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: samthom@stanford.edu.
Polly M FordyceDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA. Electronic address: pfordyce@stanford.edu.

Funding

Study of Nonenzymatic and Enzymatic Phosphoryl TransferR01GM064798 · NIGMS · STANFORD UNIVERSITY · PI Polly Morrell Fordyce, DANIEL HERSCHLAG · 2002 to 2026
$5.9M
NIGMS NIH HHS R01 GM064798
6 · The paper itself

Abstract

Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.

Indexed as

Protein FoldingProteinsKineticsProtein StabilityThermodynamicsProteinsbiophysical characterizationcalorimetrymass spectrometryprotein foldingprotein folding kineticsprotein folding thermodynamicsprotein stabilityproteolysisspectroscopy

Identifiers

PMID34139165
PMCPMC9337709

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.