Sculpting conducting nanopore size and shape through de novo protein design

Affiliations
  • 1Department of Biochemistry, The University of Washington, Seattle, WA, USA.
  • 2Institute for Protein Design, University of Washington, Seattle, WA, USA.
  • 3Biozentrum, University of Basel, Basel, Switzerland.
  • 4Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT.
  • 5Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium.
  • 6VUB-VIB Center for Structural Biology, Brussels, Belgium.
  • 7Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA.
  • 8Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • 9Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
  • 10VIB Center for AI and Computational Biology, Belgium.

Published on:

Abstract

Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.