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High thermodynamic stability of parametrically designed helical bundles
Open accessAbstract
We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.
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“However, the majority of de novo designed coiled coils are hyperstable, with melting points exceeding 100 °C.11,12”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [11]
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Cites
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
REFMAC 5 for the refinement of macromolecular crystal structures
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M., Long, F., & Vagin, A. A. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911001314 · Cited by 8,415
[14]Determination and analysis of urea and guanidine hydrochloride denaturation curves
Pace, C. N. (1986) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(86)31045-0 · Cited by 2,267
A Switch Between Two-, Three-, and Four-stranded Coiled Coils in GCN4 Leucine Zipper Mutants
Harbury, P. B., Zhang, T., Kim, P. S., & Alber, T. (1993) · Science · doi:10.1126/science.8248779 · Cited by 1,490
A New Generation of the IMAGIC Image Processing System
van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R., & Schatz, M. X. (1996) · Journal of Structural Biology · doi:10.1006/jsbi.1996.0004 · Cited by 1,229
Macromolecular Modeling with Rosetta
Das, R., & Baker, D. A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062906.171838 · Cited by 995
Self-citationToward High-Resolution de Novo Structure Prediction for Small Proteins
Bradley, P. H., Misura, K. M. S., & Baker, D. A. (2005) · Science · doi:10.1126/science.1113801 · Cited by 865
Self-citationRosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Fleishman, S. J., Leaver‐Fay, A., Corn, J. E., Strauch, E., Khare, S. D., Koga, N., Ashworth, J. R., Murphy, P. M., Richter, F. M., Lemmon, G., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020161 · Cited by 659
Self-citationHigh-Resolution Protein Design with Backbone Freedom
Harbury, P. B., Plecs, J. J., Tidor, B., Alber, T., & Kim, P. S. (1998) · Science · doi:10.1126/science.282.5393.1462 · Cited by 458
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions
Kumar, M. D. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj103 · Cited by 416
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design
Huang, P., Ban, Y. A., Richter, F. M., André, I., Vernon, R. M., Schief, W. R., & Baker, D. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024109 · Cited by 371
Self-citationThe Fourier transform of a coiled-coil
Crick, F. H. C. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53001952 · Cited by 313
De NovoDesign of Helical Bundles as Models for Understanding Protein Folding and Function
Hill, R. B., Raleigh, D. P., Lombardi, A., & DeGrado, W. F. (2000) · Accounts of Chemical Research · doi:10.1021/ar970004h · Cited by 299
Improved molecular replacement by density- and energy-guided protein structure optimization
DiMaio, F., Terwilliger, T. C., Read, R. J., Wlodawer, A., Oberdorfer, G., Wagner, U. G., Valkov, E., Alon, A., Fass, D., Axelrod, H. L., et al. (2011) · Nature · doi:10.1038/nature09964 · Cited by 246
Self-citationProbing Designability via a Generalized Model of Helical Bundle Geometry
Grigoryan, G., & DeGrado, W. F. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.058 · Cited by 232
Liu, J., Zheng, Q., Deng, Y., Cheng, C.-S., Kallenbach, N. R., & Lu, M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604871103 · Cited by 227
Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces
Grigoryan, G., Kim, Y. H., Acharya, R., Axelrod, K., Jain, R. M., Willis, L. J., Drndić, M., Kikkawa, J. M., & DeGrado, W. F. (2011) · Science · doi:10.1126/science.1198841 · Cited by 204
De novo designed peptides for biological applications
Boyle, A. L., & Woolfson, D. N. (2011) · Chemical Society Reviews · doi:10.1039/c0cs00152j · Cited by 194
A de novo peptide hexamer with a mutable channel
Zaccai, N. R., Chi, B., Thomson, A. R., Boyle, A. L., Bartlett, G. J., Bruning, M., Linden, N., Sessions, R. B., Booth, P. J., Brady, R. L., et al. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.692 · Cited by 189
Improved low-resolution crystallographic refinement with Phenix and Rosetta
DiMaio, F., Echols, N., Headd, J. J., Terwilliger, T. C., Adams, P. D., & Baker, D. A. (2013) · Nature Methods · doi:10.1038/nmeth.2648 · Cited by 183
Self-citationphenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
Terwilliger, T. C., DiMaio, F., Read, R. J., Baker, D. A., Bunkòczi, G., Adams, P. D., Grosse‐Kunstleve, R. W., Afonine, P. V., & Echols, N. (2012) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-012-9129-3 · Cited by 145
Self-citationHistorical review: Another 50th anniversary – new periodicities in coiled coils
Gruber, M. (2003) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2003.10.008 · Cited by 141
Peters, J., Baumeister, W. P., & Lupas, A. N. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0221 · Cited by 115
Sampling Bottlenecks in De novo Protein Structure Prediction
Kim, D. E., Blum, B., Bradley, P. H., & Baker, D. A. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.07.063 · Cited by 101
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Geierhaas, C. D., Nickson, A. A., Lindorff‐Larsen, K., Clarke, J., & Vendruscolo, M. (2006) · Protein Science · doi:10.1110/ps.062383807 · Cited by 56
Conformational and geometrical properties of idealized β-barrels in proteins
Chou, K., Carlacci, L., & Maggiora, G. M. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80193-7 · Cited by 47
Tyka, M. D., Jung, K., & Baker, D. A. (2012) · Journal of Computational Chemistry · doi:10.1002/jcc.23069 · Cited by 44
Self-citationA modifiedACORNto solve protein structures at resolutions of 1.7 Å or better
Jia-Xing, Y., Woolfson, M. M., Wilson, K. S., & Dodson, E. J. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490502576x · Cited by 37
Nannenga, B. L., Iadanza, M. G., Vollmar, B. S., & Gonen, T. (2013) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps1715s72 · Cited by 30
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Hsia, Y., Bale, J. B., Gonen, S., Shi, D., Sheffler, W., Fong, K. K., Nattermann, U., Xu, C., Huang, P., Ravichandran, R., et al. (2016) · Nature · doi:10.1038/nature18010 · Cited by 443
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Bhardwaj, G., Mulligan, V. K., Bahl, C. D., Gilmore, J. M., Harvey, P. J., Cheneval, O., Buchko, G. W., Pulavarti, S. V. S. R. K., Kaas, Q., Eletsky, A., et al. (2016) · Nature · doi:10.1038/nature19791 · Cited by 445
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Metadata
- Authors
- Huang, P.-S., Oberdorfer, G., Xu, C., Pei, X. Y., Nannenga, B. L., Rogers, J. M., DiMaio, F., Gonen, T., Luisi, B., & Baker, D.
- Affiliations
- University of Washington (US)
- University of Graz (AT)
- University of Cambridge (GB)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Huang, Po-Ssu
- Oberdorfer, Gustav
- Xu, Chunfu
- Baker, David
- ORCID
- Venue
- Science
- Published
- 2014-10-24
- Volume
- 346
- Issue
- 6208
- Pages
- 481-485
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4612401
- OpenAlex
- W1976603396
- Cited by
- 277
- References
- 32
- Citations by year
- 2026: 17 · 2025: 17 · 2024: 16 · 2023: 22 · 2022: 24 · 2021: 28 · 2020: 23 · 2019: 29 · 2018: 15 · 2017: 30 · 2016: 37 · 2015: 17 · 2014: 2
- FWCI
- 11.76
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- Wellcome Trust (076846)
- Diamond Light Source
- European Commission (332094)
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- protein design, helical bundle, coiled coil, thermodynamic stability, protein folding free energy, combinatorial designs
- MeSH terms
- Protein Denaturation, Thermodynamics, Protein Engineering, Protein Structure, Secondary, Crystallography, X-Ray, Combinatorial Chemistry Techniques
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