Evidence map›Paper›PMID 39975260›Full record

ArticlebioRxiv : the preprint server for biology2025

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 Biel, Lei Lu, Ian Bakanas, Alexander N Volkov and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
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

5 · Who and what money

Authors and funding

14 authors.

Yuda ChenDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Sagar BhattacharyaDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Lena BergmannDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.ORCID 0000-0003-1336-0323
Galen J CorreyDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.ORCID 0000-0001-5155-7325
Sophia K TanDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Kaipeng HouDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Justin BielDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.ORCID 0000-0002-0935-8362
Lei LuDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Ian BakanasDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
Alexander N VolkovVIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
Ivan V KorendovychDepartment of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA.
Nicholas F PolizziDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.ORCID 0000-0002-5080-2859
William F DeGradoDepartment of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.

Funding

A Synchrotron Radiation Structural Biology ResourcesP30GM133894 · NIGMS · STANFORD UNIVERSITY · PI Thomas Michael Weiss · 2020 to 2026
$43.3M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI 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
Equipment for Discovering and Manipulating Macromolecular Conformational EnsemblesR35GM145238 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$3.1M
De novo design of small-molecule-binding proteinsR00GM135519 · NIGMS · DANA-FARBER CANCER INST · PI POLIZZI, NICHOLAS · 2022 to 2024
$747k
NIGMS NIH HHS P30 GM124169NIGMS NIH HHS P30 GM133894NIGMS NIH HHS R00 GM135519NIGMS NIH HHS R35 GM122603NIGMS NIH HHS R35 GM145238
6 · The paper itself

Abstract

The evolution of binding and catalysis played a central role in the emergence of life. 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 stepwise, incremental evolution of entirely new specificities. Thus, modern proteins emerged from the joint exploration of sequence and structural space. The ability of natural proteins to bind small molecule fragments in well-defined geometries has been widely evaluated using methods including crystallographic fragment screening. However, this approach had not been applied to

Identifiers

PMID39975260
PMCPMC11838529

What OpenQuestion holds

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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.