Evidence map›Paper›PMID 40745093›Full record

ArticleNature materials2025

Bond-centric modular design of protein assemblies.

Shunzhi Wang, Andrew Favor, Ryan D Kibler, Joshua M Lubner, Andrew J Borst, Nicolas Coudray, Rachel L Redler, Huat Thart Chiang, William Sheffler, Yang Hsia and 6 more

Abstract read
In one paragraph

Article in Nature materials, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Chemical reviews · 2026
    Review
  5. Reverse-engineering amyloid strains with generative protein design.bioRxiv : the preprint server for biology · 2026
    Article
  6. Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026
    Review
  7. Review
  8. Review
  9. Article
  10. Review
  11. Article
  12. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Shunzhi WangDepartment of Biochemistry, University of Washington, Seattle, WA, USA. swang523@uw.edu.ORCID 0000-0001-5033-7478
Andrew FavorInstitute for Protein Design, University of Washington, Seattle, WA, USA.ORCID 0000-0002-9977-2785
Ryan D KiblerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-6984-9887
Joshua M LubnerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-1506-0949
Andrew J BorstDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-4297-7824
Nicolas CoudrayDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0002-6050-2219
Rachel L RedlerDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-0621-1303
Huat Thart ChiangDepartment of Chemical Engineering, University of Washington, Seattle, WA, USA.ORCID 0000-0002-0042-7958
William ShefflerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Yang HsiaDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7467-8373
Neville P BethelDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Zhe LiDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Damian C EkiertDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.
Gira BhabhaDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.ORCID 0000-0003-0624-6178
Lilo D PozzoDepartment of Chemical Engineering, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7104-9061
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.ORCID 0000-0001-7896-6217

Funding

NCCAT: National Center for CryoEM Access and Training- Supplement for Windows 10 and FFIU24GM129539 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2018 to 2023
$53.9M
Unravelling lipid trafficking for the bacterial outer membraneR35GM128777 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Damian Ekiert · 2018 to 2026
$4.1M
Designed Vehicles for Blood Brain Barrier TraversalR01AG063845 · NIA · UNIVERSITY OF WASHINGTON · PI BAKER, DAVID · 2019 to 2023
$2.5M
Burroughs Wellcome Fund (BWF) 1199630NIA NIH HHS R01 AG063845NIGMS NIH HHS R35 GM128777NIGMS NIH HHS U24 GM129539U.S. Department of Energy (DOE) DE-SC0019288
6 · The paper itself

Abstract

Directional interactions that generate regular coordination geometries are a powerful means of guiding molecular and colloidal self-assembly, but implementing such high-level interactions with proteins remains challenging due to their complex shapes and intricate interface properties. Here we describe a modular approach to protein nanomaterial design inspired by the rich chemical diversity that can be generated from the small number of atomic valencies. We design protein building blocks using deep learning-based generative tools, incorporating regular coordination geometries and tailorable bonding interactions that enable the assembly of diverse closed and open architectures guided by simple geometric principles. Experimental characterization confirms the successful formation of more than 20 multicomponent polyhedral protein cages, two-dimensional arrays and three-dimensional protein lattices, with a high (10%-50%) success rate and electron microscopy data closely matching the corresponding design models. Due to modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable networks for designer nanomaterials.

Indexed as

NanostructuresProteinsDeep LearningModels, MolecularProteins

Identifiers

PMID40745093
PMCPMC12484077

What OpenQuestion holds

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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.