6M6Z

A de novo designed transmembrane nanopore, TMH4C4

Summary for 6M6Z

• Entry DOI: 10.2210/pdb6m6z/pdb
• EMDB information: 30126
• Descriptor: TMH4C4 (1 entity in total)
• Functional Keywords: nanopore, de novo design, membrane protein, de novo protein
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 93822.29

Authors

Lu, P.,Xu, C.,Reggiano, G.,Xu, Q.,DiMaio, F.,Baker, D. (deposition date: 2020-03-16, release date: 2020-06-24, Last modification date: 2024-03-27)

Primary citation

Xu, C.,Lu, P.,Gamal El-Din, T.M.,Pei, X.Y.,Johnson, M.C.,Uyeda, A.,Bick, M.J.,Xu, Q.,Jiang, D.,Bai, H.,Reggiano, G.,Hsia, Y.,Brunette, T.J.,Dou, J.,Ma, D.,Lynch, E.M.,Boyken, S.E.,Huang, P.S.,Stewart, L.,DiMaio, F.,Kollman, J.M.,Luisi, B.F.,Matsuura, T.,Catterall, W.A.,Baker, D.
Computational design of transmembrane pores.
Nature, 585:129-134, 2020

PubMed Abstract: Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore-but not the 12-helix pore-enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.

PubMed: 32848250
DOI: 10.1038/s41586-020-2646-5

Experimental method

ELECTRON MICROSCOPY (5.9 Å)