Cited by 149Protein Structure and DynamicsBiochemical and Structural CharacterizationChemical Synthesis and Analysis

The DOI matches its Crossref record; 158 of the 158 references it cites were found in a registry or an index.

Coiled-Coil Design: Updated and Upgraded

Woolfson, Derek N.·2017·Subcellular Biochemistry

Open this paper in CoChat — free account

Abstract

α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.

Integrity signals

Registry

Crossref · 10.1007/978-3-319-49674-0_2

Cites

158 of 158 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Predicting coiled coils from protein sequences.
Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953
The packing of α-helices: simple coiled-coils
Crick, F. H. C. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53001964 · Cited by 1,578
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
X-Ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil
O’Shea, E. K., Klemm, J. D., Kim, P. S., & Alber, T. (1991) · Science · doi:10.1126/science.1948029 · Cited by 1,444
Coiled coils: new structures and new functions
Lupas, A. N. (1996) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(96)10052-9 · Cited by 1,321
Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export
Koronakis, V. E., Sharff, A., Koronakis, E., Luisi, B. F., & Hughes, C. (2000) · Nature · doi:10.1038/35016007 · Cited by 1,086
The α-helix dipole and the properties of proteins
Hol, W. G. J., van Duijnen, P. T., & Berendsen, H. J. C. (1978) · Nature · doi:10.1038/273443a0 · Cited by 1,007
The Structure of α-Helical Coiled Coils
Lupas, A. N., & Gruber, M. (2005) · Advances in protein chemistry · doi:10.1016/s0065-3233(05)70003-6 · Cited by 681
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
King, N. P., Sheffler, W., Sawaya, M. R., Vollmar, B. S., Sumida, J. P., André, I., Gonen, T., Yeates, T. O., & Baker, D. A. (2012) · Science · doi:10.1126/science.1219364 · Cited by 655
The Design of Coiled-Coil Structures and Assemblies
Woolfson, D. N. (2005) · Advances in Protein Chemistry · doi:10.1016/s0065-3233(05)70004-8 · Cited by 585
Self-citation
[30] Prediction and analysis of coiled-coil structures
Lupas, A. N. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66032-7 · Cited by 575
Accurate design of co-assembling multi-component protein nanomaterials
King, N. P., Bale, J. B., Sheffler, W., McNamara, D. E., Gonen, S., Gonen, T., Yeates, T. O., & Baker, D. A. (2014) · Nature · doi:10.1038/nature13404 · Cited by 560
Helix to helix packing in proteins.
Chothia, C., Levitt, M., & Richardson, D. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90341-7 · Cited by 537
Antiparallel Leucine Zipper-Directed Protein Reassembly: Application to the Green Fluorescent Protein
Ghosh, I., Hamilton, A. D., & Regan, L. (2000) · Journal of the American Chemical Society · doi:10.1021/ja994421w · Cited by 535
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
Rose, P. W., Prlić, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J., Woo, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1214 · Cited by 519
Self-Assembling Cages from Coiled-Coil Peptide Modules
Fletcher, J. M., Harniman, R. L., Barnes, F. R. H., Boyle, A. L., Collins, A., Mantell, J., Sharp, T. H., Antognozzi, M., Booth, P. J., Linden, N., et al. (2013) · Science · doi:10.1126/science.1233936 · Cited by 491
Self-citation
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions
Delorenzi, M., & Speed, T. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.4.617 · Cited by 479
Rational design and application of responsive α-helical peptide hydrogels
Banwell, E. F., Abelardo, E., Adams, D. J., Birchall, M., Corrigan, A. M., Donald, A. M., Kirkland, M., Serpell, L. C., Butler, M. F., & Woolfson, D. N. (2009) · Nature Materials · doi:10.1038/nmat2479 · Cited by 478
Self-citation
Crystal structure of an isoleucine-zipper trimer
Harbury, P. B., Kim, P. S., & Alber, T. (1994) · Nature · doi:10.1038/371080a0 · Cited by 472
High-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
Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments
Padilla, J. E., Colovos, C., & Yeates, T. O. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.041614998 · Cited by 442
Peptide ‘Velcro’: Design of a heterodimeric coiled coil
O’Shea, E. K., Lumb, K. J., & Kim, P. S. (1993) · Current Biology · doi:10.1016/0960-9822(93)90063-t · Cited by 439
Paircoil2: improved prediction of coiled coils from sequence.
McDonnell, A. V., Jiang, T., Keating, A. E., & Berger, B. (2006) · Bioinformatics · doi:10.1093/bioinformatics/bti797 · Cited by 424
Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein
Dong, C., Beis, K., Nesper, J., Brunkan-LaMontagne, A. L., Clarke, B. R., Whitfield, C., & Naismith, J. H. (2006) · Nature · doi:10.1038/nature05267 · Cited by 374
SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures11Edited by J. Thornton
Walshaw, J., & Woolfson, D. N. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4545 · Cited by 357
Self-citation
Computational design of water-soluble α-helical barrels
Thomson, A. R., Wood, C. W., Burton, A. J., Bartlett, G. J., Sessions, R. B., Brady, R. L., & Woolfson, D. N. (2014) · Science · doi:10.1126/science.1257452 · Cited by 330
Self-citation
Peptide hydrogels
Dasgupta, A., Mondal, J. H., & Das, D. (2013) · RSC Advances · doi:10.1039/c3ra40234g · Cited by 316
The Fourier transform of a coiled-coil
Crick, F. H. C. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53001952 · Cited by 313
Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments
Gradišar, H., Abram, S. B., Doles, T., Vengust, D., Hafner‐Bratkovič, I., Mertelj, A., Webb, B., Šali, A., Klavžar, S., & Jerala, R. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1248 · Cited by 312
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
Boyken, S. E., Chen, Z., Groves, B., Langan, R. A., Oberdorfer, G., Ford, A., Gilmore, J. M., Xu, C., DiMaio, F., Pereira, J. H., et al. (2016) · Science · doi:10.1126/science.aad8865 · Cited by 303
De novo design of a transmembrane Zn 2+ -transporting four-helix bundle
Joh, N. H., Wang, T., Bhate, M., Acharya, R., Wu, Y., Grabe, M., Hong, M., Grigoryan, G., & DeGrado, W. F. (2014) · Science · doi:10.1126/science.1261172 · Cited by 301
The Crystal Structure of a Five-Stranded Coiled Coil in COMP: A Prototype Ion Channel?
Malashkevich, V. N., Kammerer, R. A., Efimov, V. P., Schulthess, T., & Engel, J. (1996) · Science · doi:10.1126/science.274.5288.761 · Cited by 301
Designing Heterodimeric Two-stranded α-Helical Coiled-coils
Litowski, J. R., & Hodges, R. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204257200 · Cited by 301
Crystal Structure of a Synthetic Triple-Stranded α-Helical Bundle
Lovejoy, B., Choe, S., Cascio, D., McRorie, D. K., DeGrado, W. F., & Eisenberg, D. S. (1993) · Science · doi:10.1126/science.8446897 · Cited by 288
High thermodynamic stability of parametrically designed helical bundles
Huang, P.-S., Oberdorfer, G., Xu, C., Pei, X. Y., Nannenga, B. L., Rogers, J. M., DiMaio, F., Gonen, T., Luisi, B., & Baker, D. (2014) · Science · doi:10.1126/science.1257481 · Cited by 277
A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology
Fletcher, J. M., Boyle, A. L., Bruning, M., Bartlett, G. J., Vincent, T. L., Zaccai, N. R., Armstrong, C. T., Bromley, E. H. C., Booth, P. J., Brady, R. L., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb300028q · Cited by 262
Self-citation
A Buried Polar Interaction Imparts Structural Uniqueness in a Designed Heterodimeric Coiled Coil
Lumb, K. J., & Kim, P. S. (1998) · Biochemistry · doi:10.1021/bi9850468 · Cited by 248
Analysis of α-Helical Coiled Coils with the Program TWISTER Reveals a Structural Mechanism for Stutter Compensation
Strelkov, S. V., & Burkhard, P. (2002) · Journal of Structural Biology · doi:10.1006/jsbi.2002.4454 · Cited by 246
More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials
Woolfson, D. N., & Mahmoud, Z. N. (2010) · Chemical Society Reviews · doi:10.1039/c0cs00032a · Cited by 236
Self-citation
Probing 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
A seven-helix coiled coil
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
Generation of protein lattices by fusing proteins with matching rotational symmetry
Sinclair, J. C., Davies, K. M., Vénien‐Bryan, C., & Noble, M. E. M. (2011) · Nature Nanotechnology · doi:10.1038/nnano.2011.122 · Cited by 227
Peptide and Protein Building Blocks for Synthetic Biology: From Programming Biomolecules to Self-Organized Biomolecular Systems
Bromley, E. H. C., Channon, K., Moutevelis, E., & Woolfson, D. N. (2008) · ACS Chemical Biology · doi:10.1021/cb700249v · Cited by 220
Self-citation
SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains
Thompson, K. E., Bashor, C. J., Lim, W. A., & Keating, A. E. (2012) · ACS Synthetic Biology · doi:10.1021/sb200015u · Cited by 218
Buried polar residues and structural specificity in the GCN4 leucine zipper
Gonzalez, L. C., Woolfson, D. N., & Alber, T. (1996) · Nature Structural Biology · doi:10.1038/nsb1296-1011 · Cited by 216
Self-citation
Predicting oligomerization states of coiled coils
Woolfson, D. N., & Alber, T. (1995) · Protein Science · doi:10.1002/pro.5560040818 · Cited by 214
Self-citation
Crystal Structure of a Divalent Metal Ion Transporter CorA at 2.9 Angstrom Resolution
Eshaghi, S., Niegowski, D., Kohl, A., Molina, D. M., Lesley, S. A., & Nordlund, P. (2006) · Science · doi:10.1126/science.1127121 · Cited by 210
A Periodic Table of Coiled-Coil Protein Structures
Moutevelis, E., & Woolfson, D. N. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.11.028 · Cited by 204
Self-citation
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
Installing hydrolytic activity into a completely de novo protein framework
Burton, A. J., Thomson, A. R., Dawson, W., Brady, R. L., & Woolfson, D. N. (2016) · Nature Chemistry · doi:10.1038/nchem.2555 · Cited by 202
Self-citation
A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering
Reinke, A. W., Grant, R. A., & Keating, A. E. (2010) · Journal of the American Chemical Society · doi:10.1021/ja907617a · Cited by 197
De novo designed peptides for biological applications
Boyle, A. L., & Woolfson, D. N. (2011) · Chemical Society Reviews · doi:10.1039/c0cs00152j · Cited by 194
Self-citation
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
Self-citation
Comparison of antiparallel and parallel two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization.
Monera, O. D., Zhou, N., Kay, C. M., & Hodges, R. S. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)36502-0 · Cited by 183
Self-Assembly of α-Helical Coiled Coil Nanofibers
Dong, H., Paramonov, S. E., & Hartgerink, J. D. (2008) · Journal of the American Chemical Society · doi:10.1021/ja8037323 · Cited by 178
Model systems for membrane fusion
Marsden, H. R., Tomatsu, I., & Kros, A. (2010) · Chemical Society Reviews · doi:10.1039/c0cs00115e · Cited by 177
Electrostatic Interactions Control the Parallel and Antiparallel Orientation of .alpha.-Helical Chains in Two-Stranded .alpha.-Helical Coiled-Coils
Monera, O. D., Kay, C. M., & Hodges, R. S. (1994) · Biochemistry · doi:10.1021/bi00179a010 · Cited by 170
A Set of de Novo Designed Parallel Heterodimeric Coiled Coils with Quantified Dissociation Constants in the Micromolar to Sub-nanomolar Regime
Thomas, F., Boyle, A. L., Burton, A. J., & Woolfson, D. N. (2013) · Journal of the American Chemical Society · doi:10.1021/ja312310g · Cited by 162
Self-citation
De novo protein design: how do we expand into the universe of possible protein structures?
Woolfson, D. N., Bartlett, G. J., Burton, A. J., Heal, J. W., Niitsu, A., Thomson, A. R., & Wood, C. W. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.05.009 · Cited by 160
Self-citation
CC+: a relational database of coiled-coil structures
Testa, O. D., Moutevelis, E., & Woolfson, D. N. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn675 · Cited by 158
Self-citation
Modular Design of Self-Assembling Peptide-Based Nanotubes
Burgess, N. C., Sharp, T. H., Thomas, F., Wood, C. W., Thomson, A. R., Zaccai, N. R., Brady, R. L., Serpell, L. C., & Woolfson, D. N. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b03973 · Cited by 156
Self-citation
Protein stability: computation, sequence statistics, and new experimental methods
Magliery, T. J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.09.002 · Cited by 156
Designed heterodimerizing leucine zippers with a ranger of pIs and stabilities up to 10−15 M
Moll, J. R., Ruvinov, S., Pastan, I., & Vinson, C. (2001) · Protein Science · doi:10.1110/ps.39401 · Cited by 153
A Reduced SNARE Model for Membrane Fusion
Marsden, H. R., Elbers, N. A., Bomans, P. H. H., Sommerdijk, N. A. J. M., & Kros, A. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200804493 · Cited by 152
Repacking protein cores with backbone freedom: structure prediction for coiled coils.
Harbury, P. B., Tidor, B., & Kim, P. S. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.18.8408 · Cited by 149
The crystal structure of the designed trimeric coiled coil coil‐VaLd: Implications for engineering crystals and supramolecular assemblies
Ogihara, N. L., Weiss, M. S., Eisenberg, D. S., & DeGrado, W. F. (1997) · Protein Science · doi:10.1002/pro.5560060109 · Cited by 145
New currency for old rope: from coiled-coil assemblies to α-helical barrels
Woolfson, D. N., Bartlett, G. J., Bruning, M., & Thomson, A. R. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.03.002 · Cited by 141
Self-citation
Historical 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
A Designed Heterotrimeric Coiled Coil
Nautiyal, S., Woolfson, D. N., King, D., & Alber, T. (1995) · Biochemistry · doi:10.1021/bi00037a001 · Cited by 141
Self-citation
A structural basis for Mg2+ homeostasis and the CorA translocation cycle
Payandeh, J., & PAI, E. F. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601269 · Cited by 134
The design of antiparallel coiled coils
Oakley, M. G. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00232-3 · Cited by 133
Principles of Helix-Helix Packing in Proteins: The Helical Lattice Superposition Model
Walther, D. M., Eisenhaber, F., & Argos, P. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0044 · Cited by 127
De novo design of orthogonal peptide pairs forming parallel coiled‐coil heterodimers
Gradišar, H., & Jerala, R. (2010) · Journal of Peptide Science · doi:10.1002/psc.1331 · Cited by 125
Rational Design of Helical Nanotubes from Self-Assembly of Coiled-Coil Lock Washers
Xu, C., Liu, R., Mehta, A. K., Guerrero-Ferreira, R., Wright, E. R., Dunin-Horkawicz, S., Morris, K. L., Serpell, L. C., Zuo, X., Wall, J. S., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4074529 · Cited by 123
Design of protein conformational switches
Ambroggio, X. I., & Kuhlman, B. A. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.05.014 · Cited by 122
Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies
Egelman, E. H., Xu, C., DiMaio, F., Magnotti, E. L., Modlin, C., Yu, X., Wright, E., Baker, D. A., & Conticello, V. P. (2015) · Structure · doi:10.1016/j.str.2014.12.008 · Cited by 120
In Situ Modification of Plain Liposomes with Lipidated Coiled Coil Forming Peptides Induces Membrane Fusion
Versluis, F., Voskuhl, J., van Kolck, B., Zope, H. R., Bremmer, G. M., Albregtse, T., & Kros, A. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4031227 · Cited by 117
Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection
Sun, L., Young, L. N., Zhang, X., Boudko, S. P., Fokine, A., Zbornik, E. A., Roznowski, A. P., Molineux, I. J., Rossmann, M. G., & Fane, B. A. (2013) · Nature · doi:10.1038/nature12816 · Cited by 116
CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
Wood, C. W., Bruning, M., Ibarra, A. Á., Bartlett, G. J., Thomson, A. R., Sessions, R. B., Brady, R. L., & Woolfson, D. N. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu502 · Cited by 116
Self-citation
Predicting specificity in bZIP coiled-coil protein interactions
Fong, J. H., Keating, A. E., & Singh, M. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r11 · Cited by 114
Systems Chemistry: Logic Gates, Arithmetic Units, and Network Motifs in Small Networks
Wagner, N., & Ashkenasy, G. (2008) · Chemistry - A European Journal · doi:10.1002/chem.200801850 · Cited by 109
Extended knobs-into-holes packing in classical and complex coiled-coil assemblies☆
Walshaw, J., & Woolfson, D. N. (2003) · Journal of Structural Biology · doi:10.1016/j.jsb.2003.10.014 · Cited by 104
Self-citation
Squaring the Circle in Peptide Assembly: From Fibers to Discrete Nanostructures by de Novo Design
Boyle, A. L., Bromley, E. H. C., Bartlett, G. J., Sessions, R. B., Sharp, T. H., Williams, C. L., Curmi, P. M. G., Forde, N. R., Linke, H., & Woolfson, D. N. (2012) · Journal of the American Chemical Society · doi:10.1021/ja3053943 · Cited by 104
Self-citation
LOGICOIL—multi-state prediction of coiled-coil oligomeric state
Vincent, T. L., Green, P. J., & Woolfson, D. N. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts648 · Cited by 103
Self-citation
The evolution and structure prediction of coiled coils across all genomes.
Rackham, O. J. L., Madera, M., Armstrong, C. T., Vincent, T. L., Woolfson, D. N., & Gough, J. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.032 · Cited by 97
Self-citation
Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone
Trigg, J., Gutwin, K., Keating, A. E., & Berger, B. (2011) · PLoS One · doi:10.1371/journal.pone.0023519 · Cited by 91
Synthetic biology through biomolecular design and engineering
Channon, K. M., Bromley, E. H. C., & Woolfson, D. N. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.06.006 · Cited by 91
Self-citation
Local and macroscopic electrostatic interactions in single α-helices
Baker, E. G., Bartlett, G. J., Crump, M. P., Sessions, R. B., Linden, N., Faul, C. F. J., & Woolfson, D. N. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1739 · Cited by 91
Self-citation
Design of Heterotetrameric Coiled Coils: Evidence for Increased Stabilization by Glu-−Lys+Ion Pair Interactions
Fairman, R., Chao, H.-G., Lavoie, T., Villafranca, J. J., Matsueda, G. R., & Novotný, J. (1996) · Biochemistry · doi:10.1021/bi952784c · Cited by 88
Probing the “Dark Matter” of Protein Fold Space
Taylor, W. R., Chelliah, V., Hollup, S. M., MacDonald, J. T., & Jonassen, I. (2009) · Structure · doi:10.1016/j.str.2009.07.012 · Cited by 87
Designed α-Helical Tectons for Constructing Multicomponent Synthetic Biological Systems
Bromley, E. H. C., Sessions, R. B., Thomson, A. R., & Woolfson, D. N. (2008) · Journal of the American Chemical Society · doi:10.1021/ja804231a · Cited by 84
Self-citation
Sequence and Structural Duality: Designing Peptides to Adopt Two Stable Conformations
Pandya, M. J., Cerasoli, E., Joseph, A., Stoneman, R. G., Waite, E., & Woolfson, D. N. (2004) · Journal of the American Chemical Society · doi:10.1021/ja045568c · Cited by 84
Self-citation
A coiled-coil motif that sequesters ions to the hydrophobic core
Hartmann, M. D., Ridderbusch, O., Zeth, K., Albrecht, R., Testa, O. D., Woolfson, D. N., Sauer, G., Dunin-Horkawicz, S., Lupas, A. N., & Alvarez, B. H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907256106 · Cited by 82
Self-citation
Engineered Coiled-Coil Protein Microfibers
Hume, J., Sun, J., Jacquet, R., Renfrew, P. D., Martin, J. A., Bonneau, R., Gilchrist, M. L., & Montclare, J. K. (2014) · Biomacromolecules · doi:10.1021/bm5004948 · Cited by 82
Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design
Sharp, T. H., Bruning, M., Mantell, J., Sessions, R. B., Thomson, A. R., Zaccai, N. R., Brady, R. L., Verkade, P., & Woolfson, D. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1118622109 · Cited by 80
Self-citation
Preferred side-chain constellations at antiparallel coiled-coil interfaces
Hadley, E. B., Testa, O. D., Woolfson, D. N., & Gellman, S. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709068105 · Cited by 79
Self-citation
Temporal Control of Membrane Fusion through Photolabile PEGylation of Liposome Membranes
Kong, L., Askes, S. H. C., Bonnet, S. A., Kros, A., & Campbell, F. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201509673 · Cited by 78
Multistate approaches in computational protein design
Davey, J. A., & Chica, R. A. (2012) · Protein Science · doi:10.1002/pro.2128 · Cited by 76
Design and Characterization of a Homodimeric Antiparallel Coiled Coil
Gurnon, D. G., Whitaker, J. A., & Oakley, M. G. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0357590 · Cited by 75
Evaluation of threading specificity and accuracy
Bryant, S. H. (1996) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199610)26:2 · Cited by 73
Controlling the Assembly of Coiled–Coil Peptide Nanotubes
Thomas, F., Burgess, N. C., Thomson, A. R., & Woolfson, D. N. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201509304 · Cited by 72
Self-citation
Design and Characterization of an Intramolecular Antiparallel Coiled Coil Peptide
Myszka, D. G., & CHAIKEN, I. M. (1994) · Biochemistry · doi:10.1021/bi00175a003 · Cited by 71
Design and Characterization of a Heterodimeric Coiled Coil that Forms Exclusively with an Antiparallel Relative Helix Orientation
McClain, D. L., Woods, H. L., & Oakley, M. G. (2001) · Journal of the American Chemical Society · doi:10.1021/ja004099l · Cited by 70
Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties
Aronsson, C., Dånmark, S., Zhou, F., Öberg, P. Å., Enander, K., Su, H., & Aili, D. (2015) · Scientific Reports · doi:10.1038/srep14063 · Cited by 66
Coiled-coil assembly by peptides with non-heptad sequence motifs
Hicks, M. R., Holberton, D. V., Kowalczyk, C., & Woolfson, D. N. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00021-7 · Cited by 64
Self-citation
A Set of Computationally Designed Orthogonal Antiparallel Homodimers that Expands the Synthetic Coiled-Coil Toolkit
Negron, C., & Keating, A. E. (2014) · Journal of the American Chemical Society · doi:10.1021/ja507847t · Cited by 61
Crystal structure of a designed, thermostable, heterotrimeric coiled coil
Nautiyal, S., & Alber, T. (1999) · Protein Science · doi:10.1110/ps.8.1.84 · Cited by 60
Computational design of protein self-assembly
Norn, C., & André, I. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.04.002 · Cited by 59
Following polypeptide folding and assembly with conformational switches
Pagel, K., & Koksch, B. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.09.005 · Cited by 57
Generalized Crick Equations for Modeling Noncanonical Coiled Coils
Offer, G., Hicks, M. R., & Woolfson, D. N. (2002) · Journal of Structural Biology · doi:10.1006/jsbi.2002.4448 · Cited by 57
Self-citation
An Antiparallel α-Helical Coiled-Coil Model System for Rapid Assessment of Side-Chain Recognition at the Hydrophobic Interface
Hadley, E. B., & Gellman, S. H. (2006) · Journal of the American Chemical Society · doi:10.1021/ja067178r · Cited by 56
Computer Modelling of the α-Helical Coiled Coil: Packing of Side-chains in the Inner Core
Offer, G., & Sessions, R. B. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0352 · Cited by 56
The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State
Oshaben, K. M., Salari, R., McCaslin, D. R., Chong, L. T., & Horne, W. S. (2012) · Biochemistry · doi:10.1021/bi301132k · Cited by 56
Resolving single membrane fusion events on planar pore-spanning membranes
Schwenen, L. L. G., Hubrich, R., Milovanović, D., Geil, B., Yang, J., Kros, A., Jahn, R., & Steinem, C. (2015) · Scientific Reports · doi:10.1038/srep12006 · Cited by 55
De Novo Protein Design as a Methodology for Synthetic Bioinorganic Chemistry
Mocny, C. S., & Pecoraro, V. L. (2015) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5b00175 · Cited by 53
Controlling the rate of coiled coil driven membrane fusion
Zheng, T., Voskuhl, J., Versluis, F., Zope, H. R., Tomatsu, I., Marsden, H. R., & Kros, A. (2013) · Chemical Communications · doi:10.1039/c3cc38926j · Cited by 53
Targeted anion transporter delivery by coiled-coil driven membrane fusion
Mora, N. L., Bahreman, A., Valkenier, H., Li, H., Sharp, T. H., Sheppard, D. N., Davis, A. P., & Kros, A. (2016) · Chemical Science · doi:10.1039/c5sc04282h · Cited by 52
Open‐and‐shut cases in coiled‐coil assembly: α‐sheets and α‐cylinders
Walshaw, J., & Woolfson, D. N. (2001) · Protein Science · doi:10.1110/ps.36901 · Cited by 50
Self-citation
Artificial metalloenzymes derived from three-helix bundles
Tebo, A. G., & Pecoraro, V. L. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2014.12.034 · Cited by 50
SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
Armstrong, C. T., Vincent, T. L., Green, P. J., & Woolfson, D. N. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr299 · Cited by 49
Self-citation
A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch
Lizatović, R., Aurelius, O., Stenström, O., Drakenberg, T., Akke, M., Logan, D. T., & André, I. (2016) · Structure · doi:10.1016/j.str.2016.03.027 · Cited by 48
Computational protein design of ligand binding and catalysis
Feldmeier, K., & Höcker, B. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2013.10.002 · Cited by 48
Peptide Tic-Tac-Toe: Heterotrimeric Coiled-Coil Specificity from Steric Matching of Multiple Hydrophobic Side Chains
Schnarr, N. A., & Kennan, A. J. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0174940 · Cited by 47
Protein design: Past, present, and future
Regan, L., Caballero, D., Hinrichsen, M. R., Virrueta, A., Williams, D. M., & O’Hern, C. S. (2015) · Biopolymers · doi:10.1002/bip.22639 · Cited by 46
Conformational Transition between Four and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction
Liu, J., Zheng, Q., Deng, Y., Kallenbach, N. R., & Lu, M. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.05.063 · Cited by 45
Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
Potapov, V., Kaplan, J. B., & Keating, A. E. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004046 · Cited by 45
Structural Dynamics and Topology of Phosphorylated Phospholamban Homopentamer Reveal Its Role in the Regulation of Calcium Transport
Vostrikov, V. V., Mote, K. R., Verardi, R., & Veglia, G. (2013) · Structure · doi:10.1016/j.str.2013.09.008 · Cited by 44
Design of a Heterotrimeric α-Helical Bundle by Hydrophobic Core Engineering
Kashiwada, A., Hiroaki, H., Kohda, D., Nango, M., & Tanaka, T. (1999) · Journal of the American Chemical Society · doi:10.1021/ja993190q · Cited by 43
Predicting helix orientation for coiled‐coil dimers
Apgar, J. R., Gutwin, K. N., & Keating, A. E. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22118 · Cited by 36
Designed Coiled Coils Promote Folding of a Recombinant Bacterial Collagen
Yoshizumi, A., Fletcher, J. M., Yu, Z., Persikov, A. V., Bartlett, G. J., Boyle, A. L., Vincent, T. L., Woolfson, D. N., & Brodsky, B. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.217364 · Cited by 35
Self-citation
Deriving Heterospecific Self-Assembling Protein–Protein Interactions Using a Computational Interactome Screen
Crooks, R. O., Baxter, D., Panek, A. S., Lubben, A., & Mason, J. M. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.11.022 · Cited by 35
A Hierarchic Approach to the Design of Hexameric Helical Barrels
Ghirlanda, G., Lear, J. D., Ogihara, N. L., Eisenberg, D. S., & DeGrado, W. F. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00233-4 · Cited by 33
Investigating the Tolerance of Coiled-Coil Peptides to Nonheptad Sequence Inserts
Hicks, M. R., Walshaw, J., & Woolfson, D. N. (2002) · Journal of Structural Biology · doi:10.1006/jsbi.2002.4462 · Cited by 33
Self-citation
Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression
Bale, J. B., Park, R. U., Liu, Y., Gonen, S., Gonen, T., Cascio, D., King, N. P., Yeates, T. O., & Baker, D. A. (2015) · Protein Science · doi:10.1002/pro.2748 · Cited by 32
Accessibility, Reactivity, and Selectivity of Side Chains within a Channel of de Novo Peptide Assembly
Burton, A. J., Thomas, F., Agnew, C., Hudson, K. L., Halford, S. E., Brady, R. L., & Woolfson, D. N. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4053027 · Cited by 30
Self-citation
Characterization of a highly flexible self‐assembling protein system designed to form nanocages
Patterson, D. P., Su, M., Franzmann, T. M., Sciore, A., Skiniotis, G., & Marsh, E. N. G. (2013) · Protein Science · doi:10.1002/pro.2405 · Cited by 30
Increasing the affinity of selective bZIP‐binding peptides through surface residue redesign
Kaplan, J. B., Reinke, A. W., & Keating, A. E. (2014) · Protein Science · doi:10.1002/pro.2477 · Cited by 27
Structural Plasticity of the Coiled-Coil Domain of Rotavirus NSP4
Sastri, N. P., Viskovska, M., Hyser, J. M., Tanner, M. R., Banks, L. D., Sankaran, B., Prasad, B. V. V., & Estes, M. K. (2014) · Journal of Virology · doi:10.1128/jvi.02227-14 · Cited by 27
Multistate Protein Design Using CLEVER and CLASSY
Negron, C., & Keating, A. E. (2013) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-394292-0.00008-4 · Cited by 25
Exploring alternate states and oligomerization preferences of coiled‐coils by de novo structure modeling
Rämisch, S., Lizatović, R., & André, I. (2015) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24729 · Cited by 24
Structural Test of the Parameterized-backbone Method for Protein Design
Plecs, J. J., Harbury, P. B., Kim, P. S., & Alber, T. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.051 · Cited by 23
Design of a heterotetrameric coiled coil
Root, B. C., Pellegrino, L. D., Crawford, E. D., Kokona, B., & Fairman, R. (2009) · Protein Science · doi:10.1002/pro.30 · Cited by 22
TOPOFOLD , the designed modular biomolecular folds: polypeptide‐based molecular origami nanostructures following the footsteps of DNA
Kočar, V., Abram, S. B., Doles, T., Bašić, N., Gradišar, H., Pisanski, T., & Jerala, R. (2014) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1289 · Cited by 21
A non-zipper-like tetrameric coiled coil promotes membrane fusion
Zheng, T., Bulacu, M., Daudey, G. A., Versluis, F., Voskuhl, J., Martelli, G., Raap, J., Sevink, G. J. A., Kros, A., & Boyle, A. L. (2016) · RSC Advances · doi:10.1039/c5ra26175a · Cited by 21
Alpha-Helical Peptide Assemblies
Bromley, E. H. C., & Channon, K. J. (2011) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-415906-8.00001-7 · Cited by 20
The d′--d--d′ Vertical Triad Is Less Discriminating Than the a′--a--a′ Vertical Triad in the Antiparallel Coiled-Coil Dimer Motif
Steinkruger, J. D., Bartlett, G. J., Hadley, E. B., Fay, L., Woolfson, D. N., & Gellman, S. H. (2012) · Journal of the American Chemical Society · doi:10.1021/ja208855x · Cited by 20
Self-citation
Constructing arrays of proteins
Sinclair, J. C. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2013.10.004 · Cited by 20
Coiled-coil driven membrane fusion: zipper-like vs. non-zipper-like peptide orientation
Versluis, F., Pardo, J. J. D., Voskuhl, J., & Kros, A. (2013) · Faraday Discussions · doi:10.1039/c3fd00061c · Cited by 20
Selective Formation of AAB‐ and ABC‐Type Heterotrimeric α‐Helical Coiled Coils
Kiyokawa, T., Kanaori, K., Tajima, K., Kawaguchi, M., Mizuno, T., Oku, J., & Tanaka, T. (2004) · Chemistry - A European Journal · doi:10.1002/chem.200305729 · Cited by 20
Coiled‐coil length: Size does matter
Surkont, J., Diekmann, Y., Ryder, P. V., & Pereira‐Leal, J. B. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24932 · Cited by 19
De Novo Design of Xeno‐Metallo Coiled Coils
Slope, L. N., & Peacock, A. F. A. (2015) · Chemistry - An Asian Journal · doi:10.1002/asia.201501173 · Cited by 19
Strong Contributions from Vertical Triads to Helix-Partner Preferences in Parallel Coiled Coils
Steinkruger, J. D., Bartlett, G. J., Woolfson, D. N., & Gellman, S. H. (2012) · Journal of the American Chemical Society · doi:10.1021/ja3063088 · Cited by 16
Self-citation
Crystal Structure of the Escherichia coli Peptide Deformylase
Chan, M. K., Gong, W., Rajagopalan, P. T. R., Hao, B., Tsai, C. M., & Pei, D. (1998) · Biochemistry · doi:10.1021/bi985044n · Cited by 10
Molecular properties of two proteins homologous to PduO‐type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii
Tanaka, Y., Sasaki, T., Kumagai, I., Yasutake, Y., Yao, M., Tanaka, I., & Tsumoto, K. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21303 · Cited by 10
A silk purse from a sow's ear — bioinspired materials based on α-helical coiled coils
Quinlan, R. A., Bromley, E. H. C., & Pohl, E. (2015) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2014.12.010 · Cited by 8
Heterotrimeric Coiled Coils with Core Residue Urea Side Chains
Diss, M. L., & Kennan, A. J. (2008) · The Journal of Organic Chemistry · doi:10.1021/jo802379p · Cited by 7
Manipulation of protein-complex function by using an engineered heterotrimeric coiled-coil switch
Mizuno, T., Suzuki, K., Imai, T., Kitade, Y., Furutani, Y., Kudou, M., Oda, M., Kandori, H., Tsumoto, K., & Tanaka, T. (2009) · Organic & Biomolecular Chemistry · doi:10.1039/b901118h · Cited by 3
A de novo designed hexameric coiled-coil peptide with iodotyrosine
Lizatović, R., Aurelius, O., Stenström, O., Drakenberg, T., Akke, M., Logan, D. T., & André, I. (2015) · Worldwide Protein Data Bank · doi:10.2210/pdb5ehb/pdb · Cited by 1

Sorted by citations

Multicomponent peptide assemblies
Raymond, D. M., & Nilsson, B. L. (2018) · Chemical Society Reviews · doi:10.1039/c8cs00115d · Cited by 348
Protein Design: From the Aspect of Water Solubility and Stability
Qing, R., Hao, S., Smorodina, E., Jin, D., Zalevsky, A. O., & Zhang, S. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00757 · Cited by 334
Recent advances in de novo protein design: Principles, methods, and applications
Pan, X., & Kortemme, T. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100558 · Cited by 228
Power to the protein: enhancing and combining activities using the Spy toolbox
Keeble, A. H., & Howarth, M. R. (2020) · Chemical Science · doi:10.1039/d0sc01878c · Cited by 189
DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences
Ludwiczak, J., Winski, A., Szczepaniak, K., Alva, V., & Dunin-Horkawicz, S. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty1062 · Cited by 189

See all 149

Authors: Woolfson, D. N.
Affiliations: University of Bristol (GB)
Corresponding author: Woolfson, Derek N.
ORCID: Woolfson, Derek N.
Venue: Subcellular Biochemistry
Publisher: Springer International Publishing
Published: 2017
Volume: 82
Pages: 35-61
ISSN: 0306-0225 (ISSN-L)
DOI: 10.1007/978-3-319-49674-0_2
OpenAlex: W2579233876
Cited by: 149
References: 158
Citations by year: 2026: 5 · 2025: 9 · 2024: 14 · 2023: 24 · 2022: 18 · 2021: 27 · 2020: 18 · 2019: 9 · 2018: 16 · 2017: 9
FWCI: 17.68
Type: book chapter
Language: en
Open access: closed
Licence: www.springer.com/tdm (unspecified)
Locations: Sub-cellular biochemistry/Subcellular biochemistry (publishedVersion)
PubMed (publishedVersion)
Explore Bristol Research (submittedVersion)
Bristol Research (University of Bristol) (submittedVersion)
Funders: Biotechnology and Biological Sciences Research Council (BB/L01386X/1)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
Keywords: alpha-helical coiled coil, protein folding, protein-protein interaction domains, rational protein design, de novo protein design, protein assembly, synthetic biology, protein-based materials
MeSH terms: Protein Conformation, alpha-Helical, Animals, Humans, Models, Molecular, Proteins, Protein Folding, Protein Interaction Domains and Motifs

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Coiled-Coil Design: Updated and Upgraded

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks