Evidence map›Paper›PMID 27151862›Full record

ArticleScience (New York, N.Y.)2016

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.

Scott E Boyken, Zibo Chen, Benjamin Groves, Robert A Langan, Gustav Oberdorfer, Alex Ford, Jason M Gilmore, Chunfu Xu, Frank DiMaio, Jose Henrique Pereira and 4 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Science (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 162 papers.

0numbers the graph read from it
0cells of the map it votes in
162citing 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

162 citing papers in PubMed.

  1. Article
  2. Review
  3. De Novo Design of Near-Infrared Fluorescence-Activating Proteins.Journal of the American Chemical Society · 2026
    Article
  4. Chemical reviews · 2026
    Review
  5. Article
  6. Article
  7. Article
  8. Review
  9. Review
  10. Article
  11. Review
  12. Article
  13. Chemical science · 2025
    Article
  14. Article
  15. Article
  16. Computational design of pH-sensitive binders.bioRxiv : the preprint server for biology · 2025
    Article
  17. Review
  18. Article
  19. Beyond Dimerization: Harnessing Tetrameric Coiled-Coils for Nanostructure Assembly.Angewandte Chemie (International ed. in English) · 2025
    Article
  20. Article

102 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Scott E BoykenDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Zibo ChenDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA.
Benjamin GrovesDepartment of Electrical Engineering, University of Washington, Seattle, WA 98195, USA.
Robert A LanganDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Gustav OberdorferDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA.
Alex FordDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Jason M GilmoreDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Chunfu XuDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Frank DiMaioDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Jose Henrique PereiraInstitute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria. Joint BioEnergy Institute, Emeryville, CA 94608, USA.
Banumathi SankaranPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Georg SeeligDepartment of Electrical Engineering, University of Washington, Seattle, WA 98195, USA. Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Peter H ZwartPhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. The Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories, 1 Cyclotron Road, Berkeley, CA 94720, USA.
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. dabaker@u.washington.edu.

Funding

Howard Hughes Medical Institute
6 · The paper itself

Abstract

In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

Indexed as

Protein MultimerizationCrystallography, X-RayHydrogen BondingHydrophobic and Hydrophilic InteractionsModels, ChemicalProtein EngineeringProtein Interaction MappingProtein Interaction MapsProteinsProtein StabilityProtein Structure, SecondaryProteins

Identifiers

PMID27151862
PMCPMC5497568

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.