Evidence map›Paper›PMID 35811759›Full record

ArticleNature reviews. Chemistry2022

De novo metalloprotein design.

Matthew J Chalkley, Samuel I Mann, William F DeGrado

Abstract read
In one paragraph

Article in Nature reviews. Chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.

0numbers the graph read from it
0cells of the map it votes in
61citing 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

61 citing papers in PubMed.

  1. PrOMet: Accurate and Robust Metal-Binding Site and Type Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  2. Thermodynamic and Structural Determinants of Ni(II), Co(II), and Zn(II) Binding to an XHXXHXH Peptide Motif.Journal of peptide science : an official publication of the European Peptide Society · 2026
    Article
  3. Article
  4. Article
  5. Review
  6. Zero-shot design of abioRxiv : the preprint server for biology · 2026
    Article
  7. Article
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  9. Article
  10. Review
  11. Review
  12. Article
  13. Article
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  16. Article
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  18. bioRxiv : the preprint server for biology · 2025
    Article
  19. On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025
    Review
  20. Article

1 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

3 authors.

Matthew J ChalkleyDepartment of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA.
Samuel I MannDepartment of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA.
William F DeGradoDepartment of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA.

Funding

Deciphering the relationship between structure, dynamics and function in helical bundle proteinsR35GM122603 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WILLIAM DEGRADO · 2017 to 2026
$7.1M
A 600 MHz NMR console and cryoprobe for studies of macromolecules, drug discovery and cancer biomarkersS10OD023455 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, JOHN D · 2018 to 2018
$820k
O2-Reactivity in De Novo Designed Mononuclear, Non-Heme Fe ProteinsF32GM139379 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHALKLEY, MATTHEW · 2020 to 2022
$193k
De Novo Design of Functional Metalloporphyrin-Containing ProteinsF32GM130029 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MANN, SAMUEL I · 2018 to 2021
$178k
NIGMS NIH HHS F32 GM130029NIGMS NIH HHS F32 GM139379NIGMS NIH HHS R35 GM122603NIH HHS S10 OD023455
6 · The paper itself

Abstract

Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O

Identifiers

PMID35811759
PMCPMC9264687

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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.