Evidence map›Paper›PMID 41279593›Full record

ArticlebioRxiv : the preprint server for biology2025

De novo design of metal-oxide templating proteins.

Amijai Saragovi, Harley Pyles, Timothy F Huddy, Wenzhao Dai, Xinqi Li, Andrew J Borst, Nikita Hanikel, Alexis Courbet, Paul Kwon, Fátima A Dávila-Hernández and 13 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

23 authors.

Amijai SaragoviInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0002-4376-1390
Harley PylesInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0003-2695-4075
Timothy F HuddyInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Wenzhao DaiInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Xinqi LiPhysical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Andrew J BorstInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Nikita HanikelInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0002-3292-5070
Alexis CourbetInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Paul KwonInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0001-7928-1009
Fátima A Dávila-HernándezInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0002-7699-2750
Ryan KiblerInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Dionne K VafeadosInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0002-2560-8907
Aza AllenInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0001-8053-9070
Kenneth D CarrInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
Asim K BeraInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0001-9473-2912
Alex KangInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0001-5487-0499
Evans BrackenbroughInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0009-0004-1476-0219
Sakshi SchmidPhysical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Yuna BaePhysical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
Lance StewartInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0003-4264-5125
Shuai ZhangPhysical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
James De YoreoPhysical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
David BakerInstitute for Protein Design, University of Washington, Seattle, WA, 98105, USA.ORCID 0000-0001-7896-6217

Funding

X-ray Scattering Technology CoreP30GM133893 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI Lin Yang · 2019 to 2026
$38.6M
Structure-based design of broadly protective coronavirus vaccinesP01AI167966 · NIAID · UNIVERSITY OF WASHINGTON · PI Neil King, David Veesler · 2022 to 2026
$15.3M
De Novo Design of Minibinder Antagonists for COVID-19 and Future PandemicsR01AI160052 · NIAID · UNIVERSITY OF WASHINGTON · PI BAKER, DAVID, FULLER, DEBORAH H. · 2021 to 2025
$3.5M
Designed Vehicles for Blood Brain Barrier TraversalR01AG063845 · NIA · UNIVERSITY OF WASHINGTON · PI BAKER, DAVID · 2019 to 2023
$2.5M
NIAID NIH HHS P01 AI167966NIAID NIH HHS R01 AI160052NIA NIH HHS R01 AG063845NIGMS NIH HHS P30 GM133893
6 · The paper itself

Abstract

Protein design now enables the precise arrangement of atoms on the nanometer length scales of inorganic crystal nuclei, opening up the possibility of templating the growth of metal oxides including semiconductors. We designed proteins presenting regularly repeating interfaces containing functional groups that organize ions and water molecules, and characterized their ability to bind to and template metal oxides. Two interfaces promoted the growth of hematite under conditions that otherwise resulted in the formation of magnetite. Three interfaces promoted ZnO nucleation under conditions where traditional ZnO-binding peptides and control proteins were ineffective. Designed cyclic assemblies with these ZnO nucleating interfaces lining interior cavities promoted ZnO growth within the cavity. CryoEM analysis of a designed octahedral nanocage revealed atomic density likely corresponding to the growing ZnO directly adjacent to the designed nucleation promoting interfaces. These findings demonstrate that designed proteins can direct the formation of metal oxides not observed in biological systems, opening the door to protein-semiconductor hybrid materials.

Identifiers

PMID41279593
PMCPMC12636617

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.