Evidence map›Paper›PMID 39394803›Full record

ArticleAngewandte Chemie (International ed. in English)2025

Computational Stabilization of a Non-Heme Iron Enzyme Enables Efficient Evolution of New Function.

Brianne R King, Kiera H Sumida, Jessica L Caruso, David Baker, Jesse G Zalatan

Abstract read
In one paragraph

Article in Angewandte Chemie (International ed. in English), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Brianne R KingDepartment of Chemistry, University of Washington, Seattle, Washington, 98195, USA.ORCID https://orcid.org/0000-0003-3592-5882
Kiera H SumidaDepartment of Chemistry, University of Washington, Seattle, Washington, 98195, USA.ORCID https://orcid.org/0000-0003-2773-9676
Jessica L CarusoDepartment of Chemistry, University of Washington, Seattle, Washington, 98195, USA.ORCID https://orcid.org/0009-0009-1692-3233
David BakerInstitute of Protein Design, University of Washington, Seattle, Washington, 98195, USA.ORCID https://orcid.org/0000-0001-7896-6217
Jesse G ZalatanDepartment of Chemistry, University of Washington, Seattle, Washington, 98195, USA.ORCID https://orcid.org/0000-0002-1458-0654

Funding

TRAINING IN MOLECULAR BIOPHYSICST32GM008268 · NIGMS · UNIVERSITY OF WASHINGTON · PI KOLLMAN, JUSTIN M, ZHENG, NING · 1988 to 2023
$8.6M
Spatial Organization in Biochemical Reaction NetworksR35GM124773 · NIGMS · UNIVERSITY OF WASHINGTON · PI Jesse George Zalatan · 2017 to 2026
$3.9M
NIGMS NIH HHS R35 GM124773NIGMS NIH HHS T32 GM008268
6 · The paper itself

Abstract

Deep learning tools for enzyme design are rapidly emerging, and there is a critical need to evaluate their effectiveness in engineering workflows. Here we show that the deep learning-based tool ProteinMPNN can be used to redesign Fe(II)/αKG superfamily enzymes for greater stability, solubility, and expression while retaining both native activity and industrially relevant non-native functions. This superfamily has diverse catalytic functions and could provide a rich new source of biocatalysts for synthesis and industrial processes. Through systematic comparisons of directed evolution trajectories for a non-native, remote C(sp

Indexed as

Directed Molecular EvolutionBiocatalysisDeep LearningEnzyme StabilityNonheme Iron ProteinsProtein EngineeringNonheme Iron ProteinsBiocatalysisDirected evolutionHydroxylationnon-heme iron(II) α-ketoglutarate-dependent oxygenaseProtein design

Identifiers

PMID39394803
PMCPMC11723803

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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.