Evidence map›Paper›PMID 42082787›Full record

ArticleNature chemistry2026

Emergence of specific binding and catalysis from a designed generalist binding protein.

Yuda Chen, Sagar Bhattacharya, Lena Bergmann, Galen J Correy, Sophia K Tan, Kaipeng Hou, Justin T Biel, Lei Lu, Ian Bakanas, Jason E Gestwicki and 5 more

Abstract read
In one paragraph

Article in Nature chemistry, 2026. 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.

  1. Review
  2. Article
  3. AbioRxiv : the preprint server for biology · 2026
    Article
  4. Article
  5. Article
  6. Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026
    Review
  7. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Yuda Chen *Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Sagar Bhattacharya *Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Lena Bergmann *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Galen J Correy *Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.ORCID 0000-0001-5155-7325
Sophia K TanDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.ORCID 0000-0002-6181-7810
Kaipeng HouDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Justin T BielDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Lei LuDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.ORCID 0000-0001-7097-1505
Ian BakanasDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Jason E GestwickiDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.ORCID 0000-0002-6125-3154
Alexander N VolkovVIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.ORCID 0000-0002-0103-059X
Ivan V KorendovychDepartment of Chemistry and Biochemistry, Baylor University, Waco, TX, USA.ORCID 0000-0001-8144-783X
Nicholas F PolizziDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID 0000-0001-8333-6789
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. jfraser@fraserlab.com.ORCID 0000-0002-5080-2859
William F DeGradoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA. bill.degrado@ucsf.edu.ORCID 0000-0003-4745-263X

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Aina E. Cohen, KEITH O HODGSON · 2020 to 2026
$43.3M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
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
Understanding Evolution of Protein Function Through Design.R35GM119634 · NIGMS · SYRACUSE UNIVERSITY · PI KORENDOVYCH, IVAN V · 2016 to 2025
$4.3M
Equipment for Discovering and Manipulating Macromolecular Conformational EnsemblesR35GM145238 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$3.1M
Differential Scanning Fluorimetry (DSF) Methods for Studying Protein StabilityR01GM141299 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GESTWICKI, JASON E · 2021 to 2024
$1.5M
De novo design of small-molecule-binding proteinsR00GM135519 · NIGMS · DANA-FARBER CANCER INST · PI POLIZZI, NICHOLAS · 2022 to 2024
$747k
Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation) DRG-2522-24National Science Foundation (NSF) MCB- 2306190NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P30 GM133894NIGMS NIH HHS R00 GM135519NIGMS NIH HHS R01 GM141299NIGMS NIH HHS R35 GM119634NIGMS NIH HHS R35 GM122603NIGMS NIH HHS R35 GM145238Sandler Foundation 7032759U.S. Department of Health & Human Services | National Institutes of Health (NIH) GM145238U.S. Department of Health & Human Services | National Institutes of Health (NIH) R00GM135519U.S. Department of Health & Human Services | National Institutes of Health (NIH) R35GM122603
6 · The paper itself

Abstract

Binding and catalysis play central roles in living systems. While natural proteins have finely tuned affinities for their primary ligands, they also bind weakly and promiscuously to other molecules, which serve as starting points for the incremental evolution of different specificities. Thus, modern proteins have emerged from the joint exploration of sequence and structural space. Interactions between natural proteins and small molecules can be systematically profiled by crystallographic fragment screening in defined geometries, yet this approach has not been applied to highly designable de novo proteins. Here we apply this method to explore the binding specificity of a de novo small-molecule-binding protein, apixaban-binding helical bundle. As in nature, we found that it formed weak complexes, which were excellent starting points for the design of entirely distinct functions, including a turn-on fluorophore binder and a highly efficient Kemp eliminase with a catalytic efficiency of 3,200,000 M

Indexed as

CatalysisProtein BindingBinding SitesModels, Molecular

Identifiers

PMID42082787
PMCPMC13245809

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.