De novo design of transmembrane fluorescence-activating proteins

Jingyi Zhu, Mingfu Liang, Ke Sun, Yu Wei, Ruiying Guo, Lijing Zhang, Junhui Shi, Dan Ma, Qi Hu, Gaoxingyu Huang and Peilong Lu ()
Additional contact information
Jingyi Zhu: Zhejiang University
Mingfu Liang: Zhejiang University
Ke Sun: Westlake Laboratory of Life Sciences and Biomedicine
Yu Wei: Westlake Laboratory of Life Sciences and Biomedicine
Ruiying Guo: Westlake Laboratory of Life Sciences and Biomedicine
Lijing Zhang: Westlake Laboratory of Life Sciences and Biomedicine
Junhui Shi: Westlake Laboratory of Life Sciences and Biomedicine
Dan Ma: Westlake Laboratory of Life Sciences and Biomedicine
Qi Hu: Westlake Laboratory of Life Sciences and Biomedicine
Gaoxingyu Huang: Westlake Laboratory of Life Sciences and Biomedicine
Peilong Lu: Westlake Laboratory of Life Sciences and Biomedicine

Nature, 2025, vol. 640, issue 8057, 249-257

Abstract: Abstract The recognition of ligands by transmembrane proteins is essential for the exchange of materials, energy and information across biological membranes. Progress has been made in the de novo design of transmembrane proteins1–6, as well as in designing water-soluble proteins to bind small molecules7–12, but de novo design of transmembrane proteins that tightly and specifically bind to small molecules remains an outstanding challenge13. Here we present the accurate design of ligand-binding transmembrane proteins by integrating deep learning and energy-based methods. We designed pre-organized ligand-binding pockets in high-quality four-helix backbones for a fluorogenic ligand, and generated a transmembrane span using gradient-guided hallucination. The designer transmembrane proteins specifically activated fluorescence of the target fluorophore with mid-nanomolar affinity, exhibiting higher brightness and quantum yield compared to those of enhanced green fluorescent protein. These proteins were highly active in the membrane fraction of live bacterial and eukaryotic cells following expression. The crystal and cryogenic electron microscopy structures of the designer protein–ligand complexes were very close to the structures of the design models. We showed that the interactions between ligands and transmembrane proteins within the membrane can be accurately designed. Our work paves the way for the creation of new functional transmembrane proteins, with a wide range of applications including imaging, ligand sensing and membrane transport.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41586-025-08598-8 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:640:y:2025:i:8057:d:10.1038_s41586-025-08598-8

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-025-08598-8

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().