Evidence map›Paper›PMID 29168496›Full record

ArticleNature chemistry2017

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.

Nicholas F Polizzi, Yibing Wu, Thomas Lemmin, Alison M Maxwell, Shao-Qing Zhang, Jeff Rawson, David N Beratan, Michael J Therien, William F DeGrado

Open access · greenAbstract read
In one paragraph

Article in Nature chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.

0numbers the graph read from it
0cells of the map it votes in
70citing papers in PubMed
5.1field-weighted citation impact, top 4% of its field
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

70 citing papers in PubMed, 125 citations in OpenAlex.

  1. Review
  2. Article
  3. AbioRxiv : the preprint server for biology · 2026
    Article
  4. Article
  5. De Novo Design of Near-Infrared Fluorescence-Activating Proteins.Journal of the American Chemical Society · 2026
    Article
  6. Review
  7. Article
  8. From single step hops to emergent biological phenomena.Journal of inorganic biochemistry · 2026
    Review
  9. Article
  10. Article
  11. bioRxiv : the preprint server for biology · 2025
    Article
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Review
  18. Design of a light and CaProceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  19. Confinement and Catalysis withinJournal of the American Chemical Society · 2025
    Article
  20. Article

10 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

9 authors at 2 institutions in 1 country.

Nicholas F PolizziDepartment of Biochemistry, Duke University, Durham, North Carolina 27710, USA.ORCID 0000-0001-8333-6789
Yibing WuDepartment of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.
Thomas LemminDepartment of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.
Alison M MaxwellDepartment of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.
Shao-Qing ZhangDepartment of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.
Jeff RawsonDepartment of Chemistry, Duke University, Durham, North Carolina 27708, USA.
David N BeratanDepartment of Biochemistry, Duke University, Durham, North Carolina 27710, USA.ORCID 0000-0003-4758-8676
Michael J TherienDepartment of Chemistry, Duke University, Durham, North Carolina 27708, USA.ORCID 0000-0003-4876-0036
William F DeGradoDepartment of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.ORCID 0000-0003-4745-263X
University of California, San Francisco · USDuke University · US

Funding

MOLECULAR AND CELLULAR BASIS OF CARDIOVASCULAR DISEASET32HL007731 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Brian L Black · 1992 to 2026
$12.4M
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
MAPPING OF ELECTRON TUNNELING PATHWAYS IN PROTEINSR01GM048043 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI DAVID BERATAN · 1993 to 2026
$6.0M
De novo design of alpha-helical bundlesR37GM054616 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI DEGRADO, WILLIAM · 2004 to 2013
$3.6M
DE NOVO DESIGN OF ALPHA HELICAL BUNDLESR01GM054616 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI DEGRADO, WILLIAM · 1996 to 2016
$2.4M
Charge-Transfer Dynamics Relevant to Protein-Mediated Energy TransductionR01GM071628 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI THERIEN, MICHAEL J · 2004 to 2014
$2.3M
High Performance Computer for Computational BiosciencesS10OD021596 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2016 to 2016
$443k
NHLBI NIH HHS T32 HL007731NIGMS NIH HHS R01 GM048043NIGMS NIH HHS R01 GM054616NIGMS NIH HHS R01 GM071628NIGMS NIH HHS R35 GM122603NIGMS NIH HHS R37 GM054616NIH HHS S10 OD021596
6 · The paper itself

Abstract

Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.

Indexed as

LigandsModels, MolecularPorphyrinsProteinsTemperatureLigandsPorphyrinsProteins

Identifiers

PMID29168496
PMCPMC5859929
OpenAlexW2748293325

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.