De novo design of semisynthetic protein nanopores

Lee Schnaider; A. Katherine Hatstat; Alistair J. Scott; Sophia K. Tan; Richard G. Hambley; William Dawson; Rhys C. Griffiths; Rian C. Kormos; Arthur Alves de Melo; Eric Tse; Nicholas F. Polizzi; Elizabeth Jayne Wallace; Gregory E. Merz; William F. DeGrado

doi:10.1101/2025.09.08.674823

BiochemistrybioRxivSep 8, 2025

Preprint

De novo design of semisynthetic protein nanopores

Lee Schnaider iD, A. Katherine Hatstat iD, Alistair J. Scott, Sophia K. Tan iD, Richard G. Hambley, William Dawson iD, Rhys C. Griffiths, Rian C. Kormos iD, Arthur Alves de Melo iD, Eric Tse iD, Nicholas F. Polizzi iD, Elizabeth Jayne Wallace iD, Gregory E. Merz iD, William F. DeGrado iD

Abstract

Protein nanopores are essential components of single-molecule oligonucleotide sequencing and sensing devices. Here, we demonstrate that installing additional de novo subunits enables large-scale architectural changes of nanopore complexes. We design de novo proteins that integrate seamlessly with the CsgG pore to form 18-subunit, 315-kilodalton complexes with precisely sculpted pore architectures and tailored ion conduction, opening new possibilities for engineering enhanced nanopores with customized structural and functional properties.

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