A multiplexed bacterial two-hybrid for rapid characterization of protein–protein interactions and iterative protein design

W. Clifford Boldridge, Ajasja Ljubetič (), Hwangbeom Kim, Nathan Lubock, Dániel Szilágyi, Jonathan Lee, Andrej Brodnik, Roman Jerala () and Sriram Kosuri ()
Additional contact information
W. Clifford Boldridge: University of California
Ajasja Ljubetič: National Institute of Chemistry
Hwangbeom Kim: University of California
Nathan Lubock: University of California
Dániel Szilágyi: University of Primorska
Jonathan Lee: University of California
Andrej Brodnik: University of Primorska
Roman Jerala: National Institute of Chemistry
Sriram Kosuri: University of California

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-023-38697-x Abstract (text/html)

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:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38697-x

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

DOI: 10.1038/s41467-023-38697-x

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

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