Membrane protein solubilization and structure determination using de novo–designed proteins
Abstract
Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a general deep learning–based design approach for solubilizing native membrane proteins while preserving their sequence, fold, active-site, and ligand-binding properties. Genetically encoded de novo protein WRAPs [water-soluble RFdiffused amphipathic proteins] surround the lipid-interacting hydrophobic surfaces, rendering them thermostable and water-soluble without the need for detergents. We design WRAPs for both monomeric and oligomeric beta-barrel outer membrane proteins and helical multipass transmembrane proteins. A 2.95-angstrom-resolution cryo–electron microscopy structure of WRAPed mycobacterial porin demonstrates that WRAPs can be used for the structural determination of membrane proteins in solution. As a step toward syphilis vaccine development, we generated soluble versions of Treponema pallidum antigens.
Article Details
Journal Info
Science
American Association for the Advancement of Science
Authors (33)
Ljubica Mihaljević
David E. Kim
Pooja D. Bandawane
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Helen E. Eisenach
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Andrew J. Borst
Alexis Courbet
Connor Weidle
Kenneth D. Carr
Everton Bettin
Department of Pediatrics, UConn Health, Farmington, CT, USA.
Qiushi Liu
Kymab, a Sanofi Company, Babraham Research Campus, Cambridge, UK.
Aldo T. Trejos
Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
Sagardip Majumder
Surabhi Kokane
Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Alexander Stevens
Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Edin Muratspahić
Thomas Schlichthaerle
Marc Expòsit
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Xinting Li
Mila Lamb
Analisa Nicole Azcárraga Murray
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Rashmi Ravichandran
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Elizabeth C. Williams
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Shuyuan Hu
Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA.
Lynda Stuart
Linda Grillová
Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
Nicholas R. Thomson
Michael Landreh
Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Pengxiang Chang
Kymab, a Sanofi Company, Babraham Research Campus, Cambridge, UK.
Lorenzo Giacani
Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
Melissa J. Caimano
Department of Pediatrics, UConn Health, Farmington, CT, USA.
Kelly L. Hawley
Department of Pediatrics, UConn Health, Farmington, CT, USA.
Neil P. King
David Baker