Evidence map›Paper›PMID 39975170›Full record

ArticlebioRxiv : the preprint server for biology2025

AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications.

Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R Burlingham, Gretchen Fixen, Tatsuya Morisaki, Hallie P Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh and 7 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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Gabriel GalindoDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
Daiki MaejimaSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan.
Jacob DeRooSchool of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
Scott R BurlinghamDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
Gretchen FixenDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
Tatsuya MorisakiDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.ORCID 0000-0001-7401-4673
Hallie P FebvreDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
Ryan HasbrookDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
Ning ZhaoDepartment of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA.ORCID 0000-0001-7092-6229
Soham GhoshSchool of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
E Handly MaytonDepartment of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins, CO, USA.
Christopher D SnowDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.ORCID 0000-0002-7690-3519
Brian J GeissSchool of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
Yasuyuki OhkawaMedical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.ORCID 0000-0001-6440-9954
Yuko SatoMedical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Hiroshi KimuraSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan.ORCID 0000-0003-0854-083X
Timothy J StasevichDepartment of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.ORCID 0000-0002-0151-6274

Funding

Quantifying the coordinated dynamics of single-gene transcription and translation in living cellsR35GM119728 · NIGMS · COLORADO STATE UNIVERSITY · PI Timothy Stasevich · 2016 to 2026
$4.2M
Multiplexed imaging of viral protein processing and assembly in live cellsR01AI168459 · NIAID · COLORADO STATE UNIVERSITY · PI Christopher Davis Snow · 2022 to 2026
$2.3M
Imaging cotranslational protein folding with high spatiotemporal resolution in living cellsR00GM141453 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI ZHAO, NING · 2023 to 2025
$747k
NIAID NIH HHS R01 AI168459NIGMS NIH HHS R00 GM141453NIGMS NIH HHS R35 GM119728
6 · The paper itself

Abstract

Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.

Identifiers

PMID39975170
PMCPMC11839053

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.