De novo design of transmembrane β barrels
- 19 February 2021
- journal article
- research article
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 371 (6531), 801-+
- https://doi.org/10.1126/science.abc8182
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a “hypothesis, design, and test” approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.Keywords
Funding Information
- National Institutes of Health (R01 GM051329)
- National Institutes of Health (P01 GM072694)
- National Institutes of Health (R01 GM079440)
- National Institutes of Health (T32 GM008403)
- National Institutes of Health (P41 GM128577)
- National Institutes of Health (P30 GM124165)
- U.S. Department of Energy (DE-AC02-06CH11357)
- National Institutes of Health (S10OD021527)
- Nordstrom Barrier Institute for Protein Design Directors Fund
- Eric and Wendy Schmidt by recommendation of the the Schmidt Futures program
- Howard Hughes Medical Institute
- Air Force Office of Scientific Research (FA9550-18-1-0297)
- Open Philanthropy Project
- Wellcome Trust Centre for Mitochondrial Research (094232/Z/10/Z)
- Fulbright Belgium
- Medical Research Council (MR/P018491/1)
- Biotechnology and Biological Sciences Research Council (BB/M011151/1)
This publication has 100 references indexed in Scilit:
- Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networksJournal of Biomolecular NMR, 2013
- Improvements to Robotics-Inspired Conformational Sampling in RosettaPLOS ONE, 2013
- Real-Time Sensing and Discrimination of Single Chemicals Using the Channel of Phi29 DNA Packaging NanomotorACS Nano, 2012
- The soluble, periplasmic domain of OmpA folds as an independent unit and displays chaperone activity by reducing the self-association propensity of the unfolded OmpA transmembrane β-barrelBiophysical Chemistry, 2011
- Overcoming Hysteresis to Attain Reversible Equilibrium Folding for Outer Membrane Phospholipase A in Phospholipid BilayersJournal of Molecular Biology, 2011
- Self‐Association of Unfolded Outer Membrane ProteinsMacromolecular Bioscience, 2010
- TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shiftsJournal of Biomolecular NMR, 2009
- Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteinsNature Biotechnology, 2004
- An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein ComplexesJournal of Molecular Biology, 2003
- NMRPipe: A multidimensional spectral processing system based on UNIX pipesJournal of Biomolecular NMR, 1995