De novo design of transmembrane β barrels
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.
- Authors:
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[1];
[2];
[3];
[2];
[4];
[5];
[6];
[4];
[7];
[8];
[2];
[8];
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[9]
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA., Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA.
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA.
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA., Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA.
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA., Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA., Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1766354
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- Science
- Additional Journal Information:
- Journal Name: Science Journal Volume: 371 Journal Issue: 6531; Journal ID: ISSN 0036-8075
- Publisher:
- American Association for the Advancement of Science (AAAS)
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Vorobieva, Anastassia A., White, Paul, Liang, Binyong, Horne, Jim E., Bera, Asim K., Chow, Cameron M., Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q., Harvey, Sophie R., Marx, Dagan C., Khan, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., and Baker, David. De novo design of transmembrane β barrels. United States: N. p., 2021.
Web. doi:10.1126/science.abc8182.
Vorobieva, Anastassia A., White, Paul, Liang, Binyong, Horne, Jim E., Bera, Asim K., Chow, Cameron M., Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q., Harvey, Sophie R., Marx, Dagan C., Khan, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., & Baker, David. De novo design of transmembrane β barrels. United States. https://doi.org/10.1126/science.abc8182
Vorobieva, Anastassia A., White, Paul, Liang, Binyong, Horne, Jim E., Bera, Asim K., Chow, Cameron M., Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q., Harvey, Sophie R., Marx, Dagan C., Khan, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., and Baker, David. Thu .
"De novo design of transmembrane β barrels". United States. https://doi.org/10.1126/science.abc8182.
@article{osti_1766354,
title = {De novo design of transmembrane β barrels},
author = {Vorobieva, Anastassia A. and White, Paul and Liang, Binyong and Horne, Jim E. and Bera, Asim K. and Chow, Cameron M. and Gerben, Stacey and Marx, Sinduja and Kang, Alex and Stiving, Alyssa Q. and Harvey, Sophie R. and Marx, Dagan C. and Khan, G. Nasir and Fleming, Karen G. and Wysocki, Vicki H. and Brockwell, David J. and Tamm, Lukas K. and Radford, Sheena E. and Baker, David},
abstractNote = {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.},
doi = {10.1126/science.abc8182},
journal = {Science},
number = 6531,
volume = 371,
place = {United States},
year = {Thu Feb 18 00:00:00 EST 2021},
month = {Thu Feb 18 00:00:00 EST 2021}
}
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Works referenced in this record:
Principles determining the structure of β-sheet barrels in proteins I. A theoretical analysis
journal, March 1994
- Murzin, Alexey G.; Lesk, Arthur M.; Chothia, Cyrus
- Journal of Molecular Biology, Vol. 236, Issue 5
Turn stability in β-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns
journal, February 2003
- Blandl, Tamas; Cochran, Andrea G.; Skelton, Nicholas J.
- Protein Science, Vol. 12, Issue 2
Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding
journal, September 2018
- Franklin, Meghan Whitney; Slusky, Joanna S. G.
- Journal of Molecular Biology, Vol. 430, Issue 18
De novo design of potent and selective mimics of IL-2 and IL-15
journal, January 2019
- Silva, Daniel-Adriano; Yu, Shawn; Ulge, Umut Y.
- Nature, Vol. 565, Issue 7738
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria
journal, July 2020
- Horne, Jim E.; Brockwell, David J.; Radford, Sheena E.
- Journal of Biological Chemistry, Vol. 295, Issue 30
An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins
journal, August 2017
- Michalik, Marcin; Orwick-Rydmark, Marcella; Habeck, Michael
- PLOS ONE, Vol. 12, Issue 8
Secondary and Tertiary Structure Formation of the β-Barrel Membrane Protein OmpA is Synchronized and Depends on Membrane Thickness
journal, November 2002
- Kleinschmidt, Jörg H.; Tamm, Lukas K.
- Journal of Molecular Biology, Vol. 324, Issue 2
Accurate computational design of multipass transmembrane proteins
journal, March 2018
- Lu, Peilong; Min, Duyoung; DiMaio, Frank
- Science, Vol. 359, Issue 6379
ß-barrel Channel Proteins as Tools in Nanotechnology
book, January 2014
- Fioroni, Marco; Dworeck, Tamara; Rodriguez-Ropero, Francisco
- Advances in Experimental Medicine and Biology, p. 794
MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG
journal, November 2017
- Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W.
- Protein Science, Vol. 27, Issue 1
Design of Monomeric Water-Soluble β-Hairpin and β-Sheet Peptides
book, August 2014
- Jiménez, M. Angeles; Köhler, Valentin
- Protein Design, p. 15-52
Folding and assembly of β-barrel membrane proteins
journal, November 2004
- Tamm, Lukas K.; Hong, Heedeok; Liang, Binyong
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1666, Issue 1-2
Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily
journal, November 2001
- Greene, Lesley H.; Chrysina, Evangelia D.; Irons, Laurence I.
- Protein Science, Vol. 10, Issue 11
OmpA can form folded and unfolded oligomers
journal, January 2013
- Wang, H.; Andersen, K. K.; Vad, B. S.
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 1
β-Bulges: Extensive structural analyses of β-sheets irregularities: β-Bulges Conservation
journal, September 2013
- Craveur, Pierrick; Joseph, Agnel Praveen; Rebehmed, Joseph
- Protein Science, Vol. 22, Issue 10
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
journal, September 2013
- Kamisetty, H.; Ovchinnikov, S.; Baker, D.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 39
The transition state for folding of an outer membrane protein
journal, February 2010
- Huysmans, G. H. M.; Baldwin, S. A.; Brockwell, D. J.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 9
Stochastic Sensing of TNT with a Genetically Engineered Pore
journal, August 2005
- Guan, Xiyun; Gu, Li-Qun; Cheley, Stephen
- ChemBioChem, Vol. 6, Issue 10
Interstrand Pairing Patterns in β-Barrel Membrane Proteins: The Positive-outside Rule, Aromatic Rescue, and Strand Registration Prediction
journal, December 2005
- Jackups, Ronald; Liang, Jie
- Journal of Molecular Biology, Vol. 354, Issue 4
Refolding and oriented insertion of a membrane protein into a lipid bilayer.
journal, August 1992
- Surrey, T.; Jahnig, F.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 16
OPM database and PPM web server: resources for positioning of proteins in membranes
journal, September 2011
- Lomize, Mikhail A.; Pogozheva, Irina D.; Joo, Hyeon
- Nucleic Acids Research, Vol. 40, Issue D1
Folding Intermediates of a β-Barrel Membrane Protein. Kinetic Evidence for a Multi-Step Membrane Insertion Mechanism † , ‡
journal, January 1996
- Kleinschmidt, Jörg H.; Tamm, Lukas K.
- Biochemistry, Vol. 35, Issue 40
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
journal, April 2012
- Fleishman, Sarel J.; Baker, David
- Cell, Vol. 149, Issue 2
Amino acid distributions in integral membrane protein structures
journal, May 2001
- Ulmschneider, Martin B.; Sansom, Mark S. P.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1512, Issue 1
Effects of turn residues in directing the formation of the β-sheet and in the stability of the β-sheet
journal, September 2001
- Chen, Pei-Yeh; Lin, Chih-Kai; Lee, Chung-Tien
- Protein Science, Vol. 10, Issue 9
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
journal, January 2007
- Conchillo-Solé, Oscar; de Groot, Natalia S.; Avilés, Francesc X.
- BMC Bioinformatics, Vol. 8, Issue 1
Structural and Functional Roles of the Surface-Exposed Loops of the β-Barrel Membrane Protein OmpA fromEscherichia coli
journal, June 1999
- Koebnik, Ralf
- Journal of Bacteriology, Vol. 181, Issue 12
Transmembrane β-barrels: Evolution, folding and energetics
journal, December 2017
- Chaturvedi, Deepti; Mahalakshmi, Radhakrishnan
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1859, Issue 12
Elastic coupling of integral membrane protein stability to lipid bilayer forces
journal, February 2004
- Hong, H.; Tamm, L. K.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 12
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Generalized Fragment Picking in Rosetta: Design, Protocols and Applications
journal, August 2011
- Gront, Dominik; Kulp, Daniel W.; Vernon, Robert M.
- PLoS ONE, Vol. 6, Issue 8
Folding of β-sheets in membranes: specificity and promiscuity in peptide model systems
journal, June 2001
- Bishop, Christopher M.; Walkenhorst, William F.; Wimley, William C.
- Journal of Molecular Biology, Vol. 309, Issue 4
Role of Aromatic Side Chains in the Folding and Thermodynamic Stability of Integral Membrane Proteins
journal, July 2007
- Hong, Heedeok; Park, Sangho; Flores Jiménez, Ricardo H.
- Journal of the American Chemical Society, Vol. 129, Issue 26
Modular and tunable biological feedback control using a de novo protein switch
journal, July 2019
- Ng, Andrew H.; Nguyen, Taylor H.; Gómez-Schiavon, Mariana
- Nature, Vol. 572, Issue 7768
Folding of β -barrel membrane proteins in lipid bilayers — Unassisted and assisted folding and insertion
journal, September 2015
- Kleinschmidt, Jörg H.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1848, Issue 9
Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport
journal, June 2017
- Joh, Nathan H.; Grigoryan, Gevorg; Wu, Yibing
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 372, Issue 1726
Toward genomic identification of β-barrel membrane proteins: Composition and architecture of known structures
journal, February 2002
- Wimley, William C.
- Protein Science, Vol. 11, Issue 2
WebLogo: A Sequence Logo Generator
journal, May 2004
- Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
- Genome Research, Vol. 14, Issue 6, p. 1188-1190
β-Barrel Proteins That Reside in the Escherichia coli Outer Membrane in Vivo Demonstrate Varied Folding Behavior in Vitro
journal, September 2008
- Burgess, Nancy K.; Dao, Thuy P.; Stanley, Ann Marie
- Journal of Biological Chemistry, Vol. 283, Issue 39
Conformational investigation of designed short linear peptides able to fold into β-hairpin structures in aqueous solution
journal, April 1996
- Alba, Eva de; Jiménez, M. Angeles; Rico, Manuel
- Folding and Design, Vol. 1, Issue 2
Escherichia coli OmpA retains a folded structure in the presence of sodium dodecyl sulfate due to a high kinetic barrier to unfolding
journal, December 2001
- Ohnishi, Satoshi; Kameyama, Keiichi
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1515, Issue 2
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
journal, September 2004
- Fernandez-Escamilla, Ana-Maria; Rousseau, Frederic; Schymkowitz, Joost
- Nature Biotechnology, Vol. 22, Issue 10
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks
journal, June 2013
- Shen, Yang; Bax, Ad
- Journal of Biomolecular NMR, Vol. 56, Issue 3
Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers
journal, May 2011
- Moon, C. P.; Fleming, K. G.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 25
Real-Time Sensing and Discrimination of Single Chemicals Using the Channel of Phi29 DNA Packaging Nanomotor
journal, March 2012
- Haque, Farzin; Lunn, Jennifer; Fang, Huaming
- ACS Nano, Vol. 6, Issue 4
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
journal, November 2016
- Park, Hahnbeom; Bradley, Philip; Greisen, Per
- Journal of Chemical Theory and Computation, Vol. 12, Issue 12
Natural -sheet proteins use negative design to avoid edge-to-edge aggregation
journal, March 2002
- Richardson, J. S.; Richardson, D. C.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 5
Control over overall shape and size in de novo designed proteins
journal, September 2015
- Lin, Yu-Ru; Koga, Nobuyasu; Tatsumi-Koga, Rie
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 40
Principles determining the structure of β-sheet barrels in proteins II. The observed structures
journal, March 1994
- Murzin, Alexey G.; Lesk, Arthur M.; Chothia, Cyrus
- Journal of Molecular Biology, Vol. 236, Issue 5
Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling
journal, February 2012
- Hyberts, Sven G.; Milbradt, Alexander G.; Wagner, Andreas B.
- Journal of Biomolecular NMR, Vol. 52, Issue 4
Sequence Motifs and Antimotifs in β-Barrel Membrane Proteins from a Genome-Wide Analysis: The Ala-Tyr Dichotomy and Chaperone Binding Motifs
journal, October 2006
- Jackups, Ronald; Cheng, Sarah; Liang, Jie
- Journal of Molecular Biology, Vol. 363, Issue 2
Principles for designing ideal protein structures
journal, November 2012
- Koga, Nobuyasu; Tatsumi-Koga, Rie; Liu, Gaohua
- Nature, Vol. 491, Issue 7423
Curvature Elasticity and Refolding of OmpA in Large Unilamellar Vesicles
journal, October 2006
- Pocanschi, Cosmin L.; Patel, Geetika J.; Marsh, Derek
- Biophysical Journal, Vol. 91, Issue 8
PASTA 2.0: an improved server for protein aggregation prediction
journal, May 2014
- Walsh, Ian; Seno, Flavio; Tosatto, Silvio C. E.
- Nucleic Acids Research, Vol. 42, Issue W1
Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane β-Barrel OmpA
journal, December 2016
- Danoff, Emily J.; Fleming, Karen G.
- Biochemistry, Vol. 56, Issue 1
RaptorX server: A Resource for Template-Based Protein Structure Modeling
book, January 2014
- Källberg, Morten; Margaryan, Gohar; Wang, Sheng
- Protein Structure Prediction. Methods in Molecular Biology
Principles for designing proteins with cavities formed by curved β sheets
journal, January 2017
- Marcos, Enrique; Basanta, Benjamin; Chidyausiku, Tamuka M.
- Science, Vol. 355, Issue 6321
Assembly of the β -Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts
journal, November 2012
- Misra, Rajeev
- ISRN Molecular Biology, Vol. 2012
A simple method for displaying the hydropathic character of a protein
journal, May 1982
- Kyte, Jack; Doolittle, Russell F.
- Journal of Molecular Biology, Vol. 157, Issue 1, p. 105-132
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
The beta bulge: a common small unit of nonrepetitive protein structure.
journal, June 1978
- Richardson, J. S.; Getzoff, E. D.; Richardson, D. C.
- Proceedings of the National Academy of Sciences, Vol. 75, Issue 6
Local sequence of protein β-strands influences twist and bend angles: Side Chain Influences β-Strand Twisting
journal, February 2014
- Fujiwara, Kazuo; Ebisawa, Shinichi; Watanabe, Yuka
- Proteins: Structure, Function, and Bioinformatics, Vol. 82, Issue 7
Overcoming Hysteresis to Attain Reversible Equilibrium Folding for Outer Membrane Phospholipase A in Phospholipid Bilayers
journal, October 2011
- Moon, C. Preston; Kwon, Sarah; Fleming, Karen G.
- Journal of Molecular Biology, Vol. 413, Issue 2
A mortise–tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes
journal, June 2014
- Leyton, Denisse L.; Johnson, Matthew D.; Thapa, Rajiv
- Nature Communications, Vol. 5, Issue 1
De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
journal, May 2016
- Boyken, S. E.; Chen, Z.; Groves, B.
- Science, Vol. 352, Issue 6286
Single-molecule DNA detection with an engineered MspA protein nanopore
journal, December 2008
- Butler, T. Z.; Pavlenok, M.; Derrington, I. M.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 52
Rapid fabrication of precise high-throughput filters from membrane protein nanosheets
journal, January 2020
- Tu, Yu-Ming; Song, Woochul; Ren, Tingwei
- Nature Materials, Vol. 19, Issue 3
Gene duplications in the structural evolution of chymotrypsin
journal, February 1979
- McLachlan, A. D.
- Journal of Molecular Biology, Vol. 128, Issue 1
Protein charge distribution in proteomes and its impact on translation
journal, May 2017
- Requião, Rodrigo D.; Fernandes, Luiza; de Souza, Henrique José Araujo
- PLOS Computational Biology, Vol. 13, Issue 5
Outer Membrane Protein A of Escherichia coli Inserts and Folds into Lipid Bilayers by a Concerted Mechanism †
journal, April 1999
- Kleinschmidt, Jörg H.; den Blaauwen, Tanneke; Driessen, Arnold J. M.
- Biochemistry, Vol. 38, Issue 16
De novo design of bioactive protein switches
journal, July 2019
- Langan, Robert A.; Boyken, Scott E.; Ng, Andrew H.
- Nature, Vol. 572, Issue 7768
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
journal, June 2009
- Shen, Yang; Delaglio, Frank; Cornilescu, Gabriel
- Journal of Biomolecular NMR, Vol. 44, Issue 4
The lipocalin protein family: structure and function
journal, August 1996
- Flower, Darren R.
- Biochemical Journal, Vol. 318, Issue 1
De novo design of a non-local β-sheet protein with high stability and accuracy
journal, October 2018
- Marcos, Enrique; Chidyausiku, Tamuka M.; McShan, Andrew C.
- Nature Structural & Molecular Biology, Vol. 25, Issue 11
Using Xplor-NIH for NMR Molecular Structure Determination
journal, October 2006
- Schwieters, Charles D.; Kuszewski, John J.; Clore, G. Marius
- ChemInform, Vol. 37, Issue 44
Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm
journal, February 2013
- Moon, C. Preston; Zaccai, Nathan R.; Fleming, Patrick J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995
- Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
- Journal of Biomolecular NMR, Vol. 6, Issue 3
Self-Association of Unfolded Outer Membrane Proteins
journal, June 2010
- Tan, Alexandra Ebie; Burgess, Nancy K.; DeAndrade, Diana S.
- Macromolecular Bioscience, Vol. 10, Issue 7
Measurement of the β-sheet-forming propensities of amino acids
journal, February 1994
- Minor, Daniel L.; Kim, Peter S.
- Nature, Vol. 367, Issue 6464
Kinetics of Insertion and Folding of Outer Membrane Proteins by Gel Electrophoresis
book, June 2019
- Schüßler, Andre; Herwig, Sascha; Kleinschmidt, Jörg H.
- Lipid-Protein Interactions: Methods and Protocols, p. 145-162
Improvements to Robotics-Inspired Conformational Sampling in Rosetta
journal, May 2013
- Stein, Amelie; Kortemme, Tanja
- PLoS ONE, Vol. 8, Issue 5
Folding membrane proteins in vitro: A table and some comments
journal, December 2014
- Popot, Jean-Luc
- Archives of Biochemistry and Biophysics, Vol. 564
The tyrosine corner: A feature of most greek key β-barrel proteins
journal, November 1994
- Hemmingsen, Jens M.; Gernert, Kim M.; Richardson, Jane S.
- Protein Science, Vol. 3, Issue 11
Computational redesign of the lipid-facing surface of the outer membrane protein OmpA
journal, July 2015
- Stapleton, James A.; Whitehead, Timothy A.; Nanda, Vikas
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 31
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-barrel
journal, November 2011
- Danoff, Emily J.; Fleming, Karen G.
- Biophysical Chemistry, Vol. 159, Issue 1
Outer membrane protein folding from an energy landscape perspective
journal, December 2017
- Schiffrin, Bob; Brockwell, David J.; Radford, Sheena E.
- BMC Biology, Vol. 15, Issue 1
PDBsum: Structural summaries of PDB entries
journal, October 2017
- Laskowski, Roman A.; Jabłońska, Jagoda; Pravda, Lukáš
- Protein Science, Vol. 27, Issue 1
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
De novo design of a fluorescence-activating β-barrel
journal, September 2018
- Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William
- Nature, Vol. 561, Issue 7724
Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles
journal, April 2015
- Marty, Michael T.; Baldwin, Andrew J.; Marklund, Erik G.
- Analytical Chemistry, Vol. 87, Issue 8