The DOI matches its Crossref record; 306 of the 306 references it cites were found in a registry or an index.
Understanding a protein fold: The physics, chemistry, and biology of α-helical coiled coils
Open accessAbstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures.This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods?This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils.At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp) n , direct the folding and assembly of amphipathic α helices into bundles.However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel, or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers).Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states.I discuss the current understanding of this problem at three levels: first, physics gives a parametric framework to generate the many possible coiled-coil backbone structures.Second, chemistry provides a means to explore and deliver sequence-to-structure relationships.Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology.I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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“The free energy landscape of coiled coils is complex, consisting of multiple local, energetically close minima.32,33”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [32]
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“For these reasons, achieving quantitative predictions of coiled-coil stability by calculating the free energy of oligomerization has been deemed one of the outstanding challenges in coiled coil research.32”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [32]
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“However, the computational design of multistate coiled-coil protein assemblies is challenging, as it requires accurate estimates of the free energy differences between multiple alternative coiled-coil conformations.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [32]
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Items 201–306 of 306
Maintaining and breaking symmetry in homomeric coiled-coil assemblies
Rhys, G. G., Wood, C. W., Lang, E. J. M., Mulholland, A., Brady, R. L., Thomson, A. R., & Woolfson, D. (2018) · Nature Communications · doi:10.1038/s41467-018-06391-y · Cited by 49 · cited 4×
“While this creates a productive playground for coiled-coil discovery, it also highlights a complex free-energy landscape with multiple states close in energy that must be navigated carefully (109, 144, 145).”
InfluentialSelf-citationCoiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states
Dawson, W., Martin, F. J. O., Rhys, G. G., Shelley, K. L., Brady, R. L., & Woolfson, D. N. (2021) · Chemical Science · doi:10.1039/d1sc00460c · Cited by 49
Self-citationNavigating the Structural Landscape of De Novo α-Helical Bundles
Rhys, G. G., Wood, C. W., Beesley, J. L., Zaccai, N. R., Burton, A. J., Brady, R. L., Thomson, A. R., & Woolfson, D. N. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b13354 · Cited by 48
Self-citationA Modular Vaccine Platform Combining Self‐Assembled Peptide Cages and Immunogenic Peptides
Morris, C., Glennie, S. J., Lam, H. S., Baum, H. E., Kandage, D., Williams, N., Morgan, D. J., Woolfson, D. N., & Davidson, A. D. (2019) · Advanced Functional Materials · doi:10.1002/adfm.201807357 · Cited by 47 · cited 1×
“…(166); the design of Self-Assembled peptide caGEs, SAGEs (167) and the applications of these in cell delivery and vaccine development (168, 169); the construction of arti fi cial transcription factors (119, 170) and cytoscaffolds (171) that assemble and function in bacterial cells; the…”
Self-citationPhysical tuning of galectin-3 signaling
Farhadi, S. A., Liu, R., Becker, M. W., Phelps, E. A., & Hudalla, G. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024117118 · Cited by 47 · cited 1×
“…with these water-soluble peptides (215); to explore valency effects in natural protein – protein interactions, e.g. , galectin-glycan binding (216); to develop Spy&Go, augmenting the widely used SpyCatcher system through multi-merization (217); and to facilitate the engineering and de novo…”
helixCAM: A platform for programmable cellular assembly in bacteria and human cells
Chao, G., Wannier, T. M., Gutierrez, C. S., Borders, N. C., Appleton, E., Chadha, A., Lebar, T., & Church, G. M. (2022) · Cell · doi:10.1016/j.cell.2022.08.012 · 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 · cited 2×
“While de novo protein design has been active for ≈ 40 years, the fi eld is now advancing rapidly and booming (51, 70, 110 – 112).”
Valsecchi, I., Crilat, E., Maldiney, R., Habricot, Y., Lignon, S., Lebrun, R., Miginiac, É., Ruelland, É., Jeannette, E., & Lebreton, S. (2013) · Molecular BioSystems · doi:10.1039/c3mb70128j · Cited by 46 · cited 1×
“[ Although there are examples of coiled-coil predictions within IDRs and vice versa (20, 256, 257).]”
Noone, D. P., Dijkstra, D. J., van der Klugt, T. T., van Veelen, P. A., de Ru, A. H., Hensbergen, P. J., Trouw, L. A., & Sharp, T. H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2208144119 · Cited by 46
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 · cited 2×
“PDB, Protein Data Bank. as “ peptide-PAINT ” or “ live-PAINT ” for high-resolution light microscopy (131, 132); and targeting natural coiled coils in vitro and in cells (133 – 137).”
Chung, C.-I., Zhang, Q., & Shu, X. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b03476 · Cited by 44 · cited 1×
“…with aromatic cores that might be suitable for electron transfer (82, 83); to direct the assembly of reversible protein condensates in living cells (213, 214); to encapsulate carbon nanotubes with these water-soluble peptides (215); to explore valency effects in natural protein – protein…”
Badieyan, S., Sciore, A., Eschweiler, J. D., Koldewey, P., Cristie‐David, A. S., Ruotolo, B. T., Bardwell, J. C. A., Su, M., & Marsh, E. N. G. (2017) · ChemBioChem · doi:10.1002/cbic.201700406 · Cited by 44
De novo designed peptides for cellular delivery and subcellular localisation
Rhys, G. G., Cross, J. A., Dawson, W. M., Thompson, H. F., Shanmugaratnam, S., Savery, N. J., Dodding, M. P., Höcker, B., & Woolfson, D. N. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01076-6 · Cited by 44 · cited 5×
“Interestingly, we fi nd that the basic peptide of the antiparallel heterodimer, apCC-Di-B, is a highly ef fi cient cell-penetrating peptide, which, once inside mammalian cells, localizes to proteins of interest fused to its partner apCC-Di-A (162).”
InfluentialSelf-citationCannon, K. A., Nguyen, V. N., Morgan, C., & Yeates, T. O. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00392 · Cited by 43 · cited 1×
“…here too (see below); to construct arti fi cial cages by appending CC-Tri, CC-Tet, or CC-Pent to natural proteins with complementary symmetries (199 – 202); to form de fi ned oligomers of photosynthetic reaction centers in membranes (203); to display multiple sugar moieties (204),…”
Cryo-EM structure of the autoinhibited state of myosin-2
Heissler, S. M., Arora, A. S., Billington, N., Sellers, J. R., & Chinthalapudi, K. (2021) · Science Advances · doi:10.1126/sciadv.abk3273 · Cited by 41
Tuning coiled coil stability with histidine-metal coordination
Tunn, I., León, A. D. S. D., Blank, K. G., et al. (2018) · Nanoscale · doi:10.1039/c8nr07259k · Cited by 40 · cited 1×
“…strand displacement in peptide – peptide interactions (189); exploring the mechanics of biomaterials using biomolecular simulations and experiments (190 – 192); engineering hybrid (natural plus designed) arti fi cial transcription factors in Escherichia coli (193); designing molecular switches…”
Measuring the conformational space of square four-helical bundles with the program samCC
Dunin-Horkawicz, S., & Lupas, A. N. (2010) · Journal of Structural Biology · doi:10.1016/j.jsb.2010.01.023 · Cited by 39 · cited 1×
“Panels B and C are adapted from Walshaw and Woolfson (2003) (96) with permission. structures parametrically and energetically (32, 37 – 39).”
Functional and Structural Roles of Coiled Coils
Hartmann, M. D. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-49674-0_3 · Cited by 39 · cited 1×
“This area is not without its controversy, however, and Hartmann provides a more detailed review of the different proteins, alternative mechanisms, and the overall biology (241).”
Molecular Interactions Driving Intermediate Filament Assembly
Vermeire, P., Stalmans, G., Lilina, A. V., et al. (2021) · Cells · doi:10.3390/cells10092457 · Cited by 39 · cited 1×
“Instead, Strelkov et al. have applied a divide-and-conquer plus modeling approach to build a structural picture of this abundant and complex class of molecules (224, 251).”
Programmable T7-based synthetic transcription factors
Hussey, B. J., & McMillen, D. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky785 · Cited by 38 · cited 1×
“…simulations and experiments (190 – 192); engineering hybrid (natural plus designed) arti fi cial transcription factors in Escherichia coli (193); designing molecular switches (beacons) for detecting natural proteins (194); masking therapeutic antibodies that can be activated by…”
Plaper, T., Aupič, J., Dekleva, P., Lapenta, F., Keber, M. M., Jerala, R., & Benčina, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-88315-3 · Cited by 38 · cited 3×
“…de novo coiled-coil modules have been CC-Di-AB (92) and related heterodimeric systems, such as Hodges ’ E/K peptides (117, 118), Keating ’ s SYNZIP systems (124), and others from Jerala (91, 94), Mason (93, 182), O ’ Shea JBC REVIEWS: Understanding α -helical coiled coils (116), and Vinson (183).”
EFhd2 Affects Tau Liquid–Liquid Phase Separation
Vega, I. E., Umstead, A., & Kanaan, N. M. (2019) · Frontiers in Neuroscience · doi:10.3389/fnins.2019.00845 · Cited by 37
Crystallographic Studies of Intermediate Filament Proteins
Guzenko, D., Chernyatina, A. A., & Strelkov, S. V. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-49674-0_6 · Cited by 37
Guiding Biomolecular Interactions in Cells Using de Novo Protein–Protein Interfaces
Smith, A. J., Thomas, F., Shoemark, D. K., Woolfson, D. N., & Savery, N. J. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00501 · Cited by 37
Self-citationThe golgin family exhibits a propensity to form condensates in living cells
Ziltener, P., Rebane, A. A., Graham, M. M., Ernst, A. M., & Rothman, J. E. (2020) · FEBS Letters · doi:10.1002/1873-3468.13884 · Cited by 36 · cited 1×
“Moving out of the nucleus, the coiled-coil golgi protein GM130 and other members of the golgin family have been shown to undergo LLPS in vitro and when overexpressed in HeLa cells (262, 265).”
Differential sensing with arrays of de novo designed peptide assemblies
Dawson, W., Shelley, K. L., Fletcher, J. M., Scott, D. A., Lombardi, L., Rhys, G. G., LaGambina, T. J., Obst, U., Burton, A. J., Cross, J. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36024-y · Cited by 36 · cited 1×
“…dyes and lipophilic biomarkers that bind within the channels with μ M af fi nities (179) and using this as the basis for a differential biosensor (180); redesigning water-soluble α HBs to produce a membrane-spanning ion channel with high conductance and selectivity (181); and designing a system…”
Self-citationCrooks, 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 · cited 2×
“…de novo coiled-coil modules have been CC-Di-AB (92) and related heterodimeric systems, such as Hodges ’ E/K peptides (117, 118), Keating ’ s SYNZIP systems (124), and others from Jerala (91, 94), Mason (93, 182), O ’ Shea JBC REVIEWS: Understanding α -helical coiled coils (116), and Vinson (183).”
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 · cited 1×
“…of Self-Assembled peptide Fi-bers, SAFs (164), and hydrogel-forming variants of these, hSAFs (165); the templated assembly of bacterial collagens (166); the design of Self-Assembled peptide caGEs, SAGEs (167) and the applications of these in cell delivery and vaccine development (168, 169); the…”
Self-citationMembrane-spanning α-helical barrels as tractable protein-design targets
Niitsu, A., Heal, J. W., Fauland, K., Thomson, A. R., & Woolfson, D. N. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0213 · Cited by 34 · cited 1×
“As discussed in previous sections, α HBs have expanded our understanding and our reach into coiled-coil structural space, and they have inspired new protein designs (13, 140, 245).”
Self-citationDe novo design of a reversible phosphorylation-dependent switch for membrane targeting
Harrington, L., Fletcher, J. M., Heermann, T., Woolfson, D. N., & Schwille, P. (2021) · Nature Communications · doi:10.1038/s41467-021-21622-5 · Cited by 34 · cited 2×
“…of functioning hotspot residues from natural protein – protein interactions (173); the direction of protein – protein interactions at synthetic (174) and biological (175) membranes and controlling the former by incorporating phosphorylation-based switches into the designs (174); and, most…”
Self-citationInvestigating 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 · cited 1×
“They result in further left-handed, some right-handed, and even “ straight ” coiled coils (19, 55 – 58).”
Self-citationConformational Dynamics of Asparagine at Coiled-Coil Interfaces
Thomas, F., Niitsu, A., Oregioni, A., Bartlett, G. J., & Woolfson, D. N. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00848 · Cited by 33 · cited 1×
“However,asshown by reasoning, analysis, modeling, and experiments (86 – 88), this interaction cannot be made in alternate states such as antipar-allel dimers and parallel trimers.”
Self-citationDunker, A. K., & Zaleske, D. J. (1977) · Biochemical Journal · doi:10.1042/bj1630045 · Cited by 32 · cited 1×
“…residues at e and g sites progressively become involved in coiled-coil interfaces with increasing oligomeric state was fi rst formalized by Wal-shaw (96, 97), though Dunker and Zaleske considered the more general problem earlier (98), as did DeGrado et al. (99) at about the same time as Walshaw.”
Self-assembled artificial viral capsids bearing coiled-coils at the surface
Fujita, S., & Matsuura, K. (2017) · Organic & Biomolecular Chemistry · doi:10.1039/c7ob00998d · Cited by 32 · cited 1×
“…on coiled-coil stability and orientation (185) and, similarly, coassembled fl uorescent proteins (186); constructing synthetic virus-like capsids (187) and motor proteins (188); examining for strand displacement in peptide – peptide interactions (189); exploring the mechanics of biomaterials…”
Modifying Self-Assembled Peptide Cages To Control Internalization into Mammalian Cells
Beesley, J. L., Baum, H. E., Hodgson, L. R., Verkade, P., Banting, G. S., & Woolfson, D. N. (2018) · Nano Letters · doi:10.1021/acs.nanolett.8b02633 · Cited by 32 · cited 1×
“…collagens (166); the design of Self-Assembled peptide caGEs, SAGEs (167) and the applications of these in cell delivery and vaccine development (168, 169); the construction of arti fi cial transcription factors (119, 170) and cytoscaffolds (171) that assemble and function in bacterial cells;…”
Self-citationSelective coordination of three transition metal ions within a coiled-coil peptide scaffold
Boyle, A. L., Rabe, M., Crone, N. S. A., Rhys, G. G., Soler, N., Voskamp, P., Pannu, N. S., & Kros, A. (2019) · Chemical Science · doi:10.1039/c9sc01165j · Cited by 31 · cited 1×
“…(206, 207) on oligo-meric protein scaffolds; in combination with metal coordination, to drive supramolecular assembly (208, 209); to design metalloproteins (210); and to explore the fundamentals of coiled-coil assembly (211), including the incorporation of nonproteinogenic amino acids (212).”
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 · cited 1×
“Despite some early successes (141), we found that CC-Hex often collapsed back to parallel tetramer and other states when altered.”
Self-citationA library of coiled-coil domains: from regular bundles to peculiar twists
Szczepaniak, K., Bukala, A., Neto, A. M. D. S., Ludwiczak, J., & Dunin-Horkawicz, S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1041 · Cited by 30 · cited 1×
“Indeed, I contend that we are close to a complete chemical understanding of coiled-coil structure and assembly, and others agree (51, 69, 70).”
De Novo Designed α‐Helical Coiled‐Coil Peptides as Scaffolds for Chemical Reactions
Rink, W. M., & Thomas, F. (2018) · Chemistry - A European Journal · doi:10.1002/chem.201802849 · Cited by 29
Coiled-Coil Motifs of RNA-Binding Proteins: Dynamicity in RNA Regulation
Ford, L. K., & Fioriti, L. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.607947 · Cited by 29
Kuster, D. J., Liu, C., Fang, Z., Ponder, J. W., & Marshall, G. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123146 · Cited by 28 · cited 1×
“This is because the energy well for the α helix is narrow and deep (53), and small deviations from α -helical parameters incur large energy penalties.”
Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils
Groth, M. C., Rink, W. M., Meyer, N. F., & Thomas, F. (2018) · Chemical Science · doi:10.1039/c7sc05342h · Cited by 27 · cited 1×
“…constructing synthetic virus-like capsids (187) and motor proteins (188); examining for strand displacement in peptide – peptide interactions (189); exploring the mechanics of biomaterials using biomolecular simulations and experiments (190 – 192); engineering hybrid (natural plus designed)…”
Folded‐unfolded cross‐predictions and protein evolution: The case study of coiled‐coils
Szappanos, B., Süveges, D., Nyitray, L., Perczel, A., & Gáspári, Z. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.03.026 · Cited by 26 · cited 1×
“[ Although there are examples of coiled-coil predictions within IDRs and vice versa (20, 256, 257).]”
Computational Prediction and Design for Creating Iteratively Larger Heterospecific Coiled Coil Sets
Crooks, R. O., Lathbridge, A., Panek, A. S., & Mason, J. M. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00047 · Cited by 26
Structural determinants of coiled coil mechanics
López‐García, P., Goktas, M., Bergues-Pupo, A. E., Koksch, B., Silva, D. V., & Blank, K. G. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp00665f · Cited by 25
Coiled‐Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection
Mueller, C., & Grossmann, T. N. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201811515 · Cited by 25 · cited 1×
“…plus designed) arti fi cial transcription factors in Escherichia coli (193); designing molecular switches (beacons) for detecting natural proteins (194); masking therapeutic antibodies that can be activated by proteolysis of the coiled coils (195); and appending them to natural bacterial proteins…”
Structural resolution of switchable states of a de novo peptide assembly
Dawson, W., Lang, E. J. M., Rhys, G. G., Shelley, K. L., Williams, C., Brady, R. L., Crump, M. P., Mulholland, A. J., & Woolfson, D. N. (2021) · Nature Communications · doi:10.1038/s41467-021-21851-8 · Cited by 25 · cited 4×
“5 B ) and in solution (145).”
InfluentialSelf-citationSynthetic biology principles for the design of protein with novel structures and functions
Zhou, W., Šmidlehner, T., & Jerala, R. (2020) · FEBS Letters · doi:10.1002/1873-3468.13796 · Cited by 25 · cited 3×
“Moreover, they have been used widely as rules for protein design by many groups to deliver many de novo – designed coiled-coil peptides and proteins (12, 14, 51, 70, 80), which are described in more detail below.”
De novo design of obligate ABC-type heterotrimeric proteins
Bermeo, S., Favor, A., Chang, Y., Norris, A. S., Boyken, S. E., Hsia, Y., Haddox, H. K., Xu, C., Brunette, T., Wysocki, V. H., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00879-4 · Cited by 25 · cited 3×
“This target has been revisited by Baker et al. using parametric design in Rosetta (122).”
InfluentialFrom peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles
Naudin, E. A., Albanese, K. I., Smith, A. J., Mylemans, B., Baker, E. G., Weiner, O. D., Andrews, D. M., Tigue, N. J., Savery, N. J., & Woolfson, D. N. (2022) · Chemical Science · doi:10.1039/d2sc04479j · Cited by 25
Self-citationCritical assessment of coiled-coil predictions based on protein structure data
Simm, D., Hatje, K., Waack, S., & Kollmar, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-91886-w · Cited by 24 · cited 1×
“There is a cautionary note here, however, coiled-coil predictions at scale can be (234).”
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322003576 · Cited by 24
Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers
Miller, J. G., Hughes, S. A., Modlin, C., & Conticello, V. P. (2022) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583522000014 · Cited by 24 · cited 1×
“Conticello et al. have written a comprehensive review on such structures (108).”
Applying graph theory to protein structures: an Atlas of coiled coils
Heal, J. W., Bartlett, G. J., Wood, C. W., Thomson, A. R., & Woolfson, D. N. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty347 · Cited by 23
Self-citationSpencer, R. K., & Hochbaum, A. I. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00201 · Cited by 22 · cited 1×
“…and the α HBs, others have employed these to engineer antiparallel hexamers with aromatic cores that might be suitable for electron transfer (82, 83); to direct the assembly of reversible protein condensates in living cells (213, 214); to encapsulate carbon nanotubes with these…”
Sušjan, P., Roškar, S., & Hafner‐Bratkovič, I. (2017) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2017.01.008 · Cited by 22
De Novo Designed Protein-Interaction Modules for In-Cell Applications
Edgell, C. L., Smith, A. J., Beesley, J. L., Savery, N. J., & Woolfson, D. N. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00453 · Cited by 22 · cited 3×
“…polyproline-II helix followed packing with an α helix (290); three hetero-oligomeric coiled coils formed from acidic (A, red ) and basic (B, blue ) peptide chains (92, 119); an 8-helix bundle formed exclusively from 3 10 helices (52); and a single-chain 4-helix coiled coil based on apCC-Tet* (148).”
Self-citationEvaluation of de novo-designed coiled coils as off-the-shelf components for protein assembly
Cristie‐David, A. S., Sciore, A., Badieyan, S., Escheweiler, J. D., Koldewey, P., Bardwell, J. C. A., Ruotolo, B. T., & Marsh, E. N. G. (2017) · Molecular Systems Design & Engineering · doi:10.1039/c7me00012j · Cited by 21 · cited 2×
“…to the original basis set of CC-Di, CC-Tri, and CC-Tet, others have used these to make standards for protein oligomers, for instance GFP fusions (197, 198), though there are cautionary tales here too (see below); to construct arti fi cial cages by appending CC-Tri, CC-Tet, or CC-Pent to natural…”
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 · cited 1×
“The design of antiparallel coiled-coil dimers has been pursued by others for some time; for examples, see the work of Hodges, Oakley, Gellman, Keating, and others (152 – 159).”
Self-citationThe Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation
Spencer, R. K., & Hochbaum, A. I. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00756 · Cited by 19 · cited 1×
“…and the α HBs, others have employed these to engineer antiparallel hexamers with aromatic cores that might be suitable for electron transfer (82, 83); to direct the assembly of reversible protein condensates in living cells (213, 214); to encapsulate carbon nanotubes with these water-soluble…”
Fibrous Protein Structures: Hierarchy, History and Heroes
Squire, J. M., & Parry, D. A. D. (2017) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-319-49674-0_1 · Cited by 19 · cited 4×
“For more complete historical perspectives on the conceptual origins of α -helical coiled coils, please see reviews by Squire and Parry and by Lupas et al. (19 – 21).”
InfluentialMolecular mechanism for kinesin-1 direct membrane recognition
Antón, Z., Weijman, J. F., Williams, C., Moody, E. R. R., Mantell, J., Yip, Y. Y., Cross, J. A., Williams, T. A., Steiner, R. A., Crump, M. P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg6636 · Cited by 19
Self-citationMajerle, A., Hadži, S., Aupič, J., Satler, T., Lapenta, F., Strmšek, Ž., Lah, J., Loris, R., & Jerala, R. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021899118 · Cited by 19 · cited 1×
“However, only one of these has been con fi rmed by a high-resolution X-ray crystal structure (160).”
Scheib, K. A., Tavenor, N. A., Lawless, M. J., Saxena, S., & Horne, W. S. (2019) · Chemical Communications · doi:10.1039/c9cc03496j · Cited by 18 · cited 1×
“…and functional proteins (206, 207) on oligo-meric protein scaffolds; in combination with metal coordination, to drive supramolecular assembly (208, 209); to design metalloproteins (210); and to explore the fundamentals of coiled-coil assembly (211), including the incorporation of…”
Coiled coil exposure and histidine tags drive function of an intracellular protein drug carrier
Dhankher, A., Lv, W., Studstill, W. T., & Champion, J. A. (2021) · Journal of Controlled Release · doi:10.1016/j.jconrel.2021.09.026 · Cited by 18
Coiled coil structures and transcription: an analysis of the S. cerevisiae coilome
Barbara, K. E., Willis, K. A., Haley, T. M., Deminoff, S. J., & Santangelo, G. M. (2007) · Molecular Genetics and Genomics · doi:10.1007/s00438-007-0237-x · Cited by 17
Determining the Stoichiometry of Small Protein Oligomers Using Steady-State Fluorescence Anisotropy
Heckmeier, P. J., Agam, G. N., Teese, M. G., Hoyer, M., Stehle, R., Lamb, D. C., & Langosch, D. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.05.025 · Cited by 17 · cited 2×
“Indeed, we have observed this for CC-Tet and some α HB systems (89, 100, 109, 144, 145, 181), and others have reported changes in oligomer states when incorporating some of the modules into larger fusion proteins (197, 198).”
Szefczyk, M., Szulc, N., Gąsior‐Głogowska, M., Modrak‐Wójcik, A., Bzowska, A., Majstrzyk, W., Taube, M., Kozak, M., Gotszalk, T. P., Rudzińska‐Szostak, E., et al. (2021) · Nanoscale · doi:10.1039/d0nr04313c · Cited by 17
Segregated Protein–Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons
Ramberg, K. O., Guagnini, F., Engilberge, S., Wrońska, M. A., Rennie, M. L., Pérez, J., & Crowley, P. B. (2021) · Chemistry - A European Journal · doi:10.1002/chem.202103025 · Cited by 17 · cited 1×
“…fi ned oligomers of photosynthetic reaction centers in membranes (203); to display multiple sugar moieties (204), small-molecule – binding peptides (205), membrane-active peptides (175), and functional proteins (206, 207) on oligo-meric protein scaffolds; in combination with metal coordination, to…”
iPEP: peptides designed and selected for interfering with protein interaction and function
Mason, J. M., Müller, K. M., & Arndt, K. M. (2008) · Biochemical Society Transactions · doi:10.1042/bst0361442 · Cited by 15
Construction of a Chassis for a Tripartite Protein-Based Molecular Motor
Small, L. S. R., Bruning, M., Thomson, A. R., Boyle, A. L., Davies, R. B., Curmi, P. M. G., Forde, N. R., Linke, H., Woolfson, D. N., & Bromley, E. H. C. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00037 · Cited by 15 · cited 1×
“…and orientation (185) and, similarly, coassembled fl uorescent proteins (186); constructing synthetic virus-like capsids (187) and motor proteins (188); examining for strand displacement in peptide – peptide interactions (189); exploring the mechanics of biomaterials using biomolecular…”
Self-citationCell-penetrating Alphabody protein scaffolds for intracellular drug targeting
Pannecoucke, E., Trimpont, M. V., Desmet, J., Pieters, T., Reunes, L., Demoen, L., Vuylsteke, M., Loverix, S., Vandenbroucke, K., Alard, P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe1682 · Cited by 15 · cited 1×
“However, recent reports show considerable promise for making de novo coiled-coil peptides and proteins that penetrate mammalian cells to seek out and bind speci fi ed targets (162, 284).”
From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles
Naudin, E. A., Albanese, K. I., Smith, A. J., Mylemans, B., Baker, E. G., Weiner, O., Andrews, D., Tigue, N. J., Savery, N., & Woolfson, D. (2022) · bioRxiv · doi:10.1101/2022.08.04.502660 · Cited by 15 · cited 4×
“…polyproline-II helix followed packing with an α helix (290); three hetero-oligomeric coiled coils formed from acidic (A, red ) and basic (B, blue ) peptide chains (92, 119); an 8-helix bundle formed exclusively from 3 10 helices (52); and a single-chain 4-helix coiled coil based on apCC-Tet* (148).”
InfluentialSelf-citationControlling the Assembly of Coiled–Coil Peptide Nanotubes
Thomas, F., Burgess, N. C., Thomson, A. R., & Woolfson, D. N. (2015) · Angewandte Chemie · doi:10.1002/ange.201509304 · Cited by 15
Self-citationRobust De Novo-Designed Homotetrameric Coiled Coils
Edgell, C. L., Savery, N. J., & Woolfson, D. N. (2020) · Biochemistry · doi:10.1021/acs.biochem.0c00082 · Cited by 14 · cited 2×
“…parallel dimers and trimer, these salt bridges can form between residues at g on one helix and residues at e of the next heptad in the neighboring helix, i.e. g → e ’ +1 (89); in parallel pentamers and above, they are at c → b ’ +1 (34); and parallel tetramers fall between these extremes (143).”
Self-citationTertiary motifs as building blocks for the design of protein‐binding peptides
Swanson, S., Sivaraman, V., Grigoryan, G., & Keating, A. E. (2022) · Protein Science · doi:10.1002/pro.4322 · Cited by 14 · cited 2×
“Of course, along with other challenges (280, 281), rigid coiled-coil scaffolds may not be optimal for binding.”
Protein grafting of p53TAD onto a leucine zipper scaffold generates a potent HDM dual inhibitor
Lee, J., Kang, E., Lee, J., Kim, J., Lee, K. H., Han, J., Kang, H. Y., Ahn, S.-S., Oh, Y., Shin, D., et al. (2014) · Nature Communications · doi:10.1038/ncomms4814 · Cited by 13 · cited 1×
“…coils, progress is being made here by grafting hotspot residues from natural protein – protein interactions onto nat-ural and de novo – designed coiled-coil peptides (173, 282) and by using de novo – designed, single-chain coiled coils ( “ Alpha-bodies ” ) to present binding-site libraries (283).”
Characterization and Control of Dynamic Rearrangement in a Self-Assembled Antibody Carrier
Dhankher, A., Hernandez, M. E., Howard, H. C., & Champion, J. A. (2020) · Biomacromolecules · doi:10.1021/acs.biomac.9b01712 · Cited by 13
Watson, M. D., Peran, I., & Raleigh, D. P. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00270 · Cited by 12 · cited 1×
“…following: designing self-sorting heterodimers (184); developing a fl uorescence-quencher pair that reports on coiled-coil stability and orientation (185) and, similarly, coassembled fl uorescent proteins (186); constructing synthetic virus-like capsids (187) and motor proteins (188); examining for…”
Stability profile of vimentin rod domain
Lilina, A. V., Leekens, S., Hashim, H. M., et al. (2022) · Protein Science · doi:10.1002/pro.4505 · Cited by 12
Miyamoto, T., Hayashi, Y., Yoshida, K., Watanabe, H., Uchihashi, T., Yonezawa, K., Shimizu, N., Kamikubo, H., & Hirota, S. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00019 · Cited by 11
Swainsbury, D. J. K., Harniman, R. L., Bartolo, N. D. D., Liu, J., Harper, W. F. M., Corrie, A. S., & Jones, M. R. (2016) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2016.09.002 · Cited by 11 · cited 1×
“…CC-Pent to natural proteins with complementary symmetries (199 – 202); to form de fi ned oligomers of photosynthetic reaction centers in membranes (203); to display multiple sugar moieties (204), small-molecule – binding peptides (205), membrane-active peptides (175), and functional proteins…”
Lv, W., & Champion, J. A. (2020) · Nanomedicine Nanotechnology Biology and Medicine · doi:10.1016/j.nano.2020.102315 · Cited by 11 · cited 1×
“Finally, in an impressive series of studies, Champion et al. have shown that the original CC-Hex sequence can be complexed with IgG to promote the cellular uptake and cytosolic delivery of these antibodies (220 – 223).”
Guidelines for the assembly of novel coiled-coil structures: α-sheets and α-cylinders
Walshaw, J., Shipway, J. M., & Woolfson, D. N. (2001) · Biochemical Society Symposia · doi:10.1042/bss0680111 · Cited by 9 · cited 1×
“The resulting helices are no longer simple amphiphiles, they are bifaceted with the potential to form high-order structures (97, 99, 101, 102).”
Self-citationHow Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues
Rhys, G. G., Dawson, W., Beesley, J. L., Martin, F. J. O., Brady, R. L., Thomson, A. R., & Woolfson, D. N. (2021) · Biomacromolecules · doi:10.1021/acs.biomac.1c00131 · Cited by 9
Self-citationBiok, N. A., Passow, A. D., Wang, C., Bingman, C. A., Abbott, N. L., & Gellman, S. H. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00668 · Cited by 9 · cited 1×
“…(206, 207) on oligo-meric protein scaffolds; in combination with metal coordination, to drive supramolecular assembly (208, 209); to design metalloproteins (210); and to explore the fundamentals of coiled-coil assembly (211), including the incorporation of nonproteinogenic amino acids (212).”
An M protein coiled coil unfurls and exposes its hydrophobic core to capture LL-37
Kolesiński, P., Wang, K.-C., Hirose, Y., Nizet, V., & Ghosh, P. (2022) · eLife · doi:10.7554/elife.77989 · Cited by 8
Yan, W., Chen, G., & Li, J. (2022) · The FASEB Journal · doi:10.1096/fj.202200403rr · Cited by 7
Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold
Morellet, N., Hardouin, P., Assrir, N., van Heijenoort, C., & Golinelli-Pimpaneau, B. (2022) · Biomolecules · doi:10.3390/biom12121798 · Cited by 7
Coiled‐Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection
Mueller, C., & Grossmann, T. N. (2018) · Angewandte Chemie · doi:10.1002/ange.201811515 · Cited by 7
Sztatelman, O., Kopeć, K., Pędziwiatr, M., Trojnar, M., Worch, R., Wielgus‐Kutrowska, B., Jemioła‐Rzemińska, M., Bzowska, A., & Grzyb, J. (2019) · Biochimie · doi:10.1016/j.biochi.2019.09.015 · Cited by 6 · cited 1×
“…a fl uorescence-quencher pair that reports on coiled-coil stability and orientation (185) and, similarly, coassembled fl uorescent proteins (186); constructing synthetic virus-like capsids (187) and motor proteins (188); examining for strand displacement in peptide – peptide interactions…”
Gisdon, F. J., Kynast, J. P., Ayyildiz, M., Hine, A. V., Plückthun, A., & Höcker, B. (2022) · Biological Chemistry · doi:10.1515/hsz-2021-0384 · Cited by 6 · cited 1×
“I have not touched on this in my perspective, but there are excellent reviews from these groups (110, 111, 285 – 287).”
Rational Design and Self-Assembly of Coiled-Coil Linked SasG Protein Fibrils
Jasaitis, L., Silver, C. D., Rawlings, A. E., Peters, D. T., Whelan, F., Regan, L., Pasquina-Lemonche, L., Potts, J. R., Johnson, S., & Staniland, S. S. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00156 · Cited by 4
Direct Phasing of Coiled-Coil Protein Crystals
Fu, R., Su, W.-P., & He, H. (2022) · Crystals · doi:10.3390/cryst12111674 · Cited by 4
Coiled coil type neoglycoproteins presenting three lactose residues
Sweeney, S., Bullen, G. A., Gillis, R. B., Adams, G. G., Rowe, A. J., Harding, S. E., Tucker, J. H. R., Peacock, A. F. A., & Murphy, P. V. (2016) · Tetrahedron Letters · doi:10.1016/j.tetlet.2016.02.005 · Cited by 2 · cited 1×
“…symmetries (199 – 202); to form de fi ned oligomers of photosynthetic reaction centers in membranes (203); to display multiple sugar moieties (204), small-molecule – binding peptides (205), membrane-active peptides (175), and functional proteins (206, 207) on oligo-meric protein scaffolds;…”
THE SOLUTION STRUCTURE OF A LEUCINE-ZIPPER MOTIF PEPTIDE: 1zta
Saudek, V., Pastore, A., Morelli, M. A. C., Frank, R., Gausepohl, H., & Gibson, T. (1990) · Worldwide Protein Data Bank · doi:10.2210/pdb1zta/pdb
REFINEMENT OF THE INFLUENZA VIRUS HEMAGGLUTININ BY SIMULATED ANNEALING: 5hmg
Weis, W. I., Bruenger, A. T., Skehel, J. J., & Wiley, D. C. (1989) · Worldwide Protein Data Bank · doi:10.2210/pdb5hmg/pdb
Engineering protein stability with atomic precision in a monomeric miniprotein: 5lo3
Baker, E. G., Hudson, K. L., Williams, C., Bartlett, G. G., Heal, J. W., Sessions, R. B., Crump, M. P., & Woolfson, D. N. (2017) · Worldwide Protein Data Bank · doi:10.2210/pdb5lo3/pdb
Self-citationX-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A TWO-STRANDED, PARALLEL COILED COIL: 2zta
O'Shea, E. K., Klemm, J. D., Kim, P. S., et al. (1991) · Worldwide Protein Data Bank · doi:10.2210/pdb2zta/pdb
Coiled Coil Domains: Stability, Specificity, and Biological Implications
Mason, J. M., & Arndt, K. M. (2004) · ChemInform · doi:10.1002/chin.200415270
Sticky-end assembly of a designed peptide fibre provides insight into protein fibrillogenesis
Pandya, M. J., Spooner, G. M., Thorpe, J. R., Rodger, A., & Woolfson, D. N. (2000) · Biochemical Society Transactions · doi:10.1042/bst028a074a
Self-citationCorrection to Modifying Self-Assembled Peptide Cages To Control Internalization into Mammalian Cells
Beesley, J. L., Baum, H. E., Hodgson, L. R., Verkade, P., Banting, G. S., & Woolfson, D. N. (2019) · Nano Letters · doi:10.1021/acs.nanolett.9b01133
Self-citationGuiding biomolecular interactions in cells using de novo protein-protein interfaces
Smith, A. J., Thomas, F., Shoemark, D., Woolfson, D. N., & Savery, N. J. (2018) · doi:10.1101/486902
Self-citationMolecular mechanism for kinesin-1 direct membrane recognition
Antón, Z., Weijman, J. F., Williams, C., Moody, E. R. R., Mantell, J., Yip, Y. Y., Cross, J. A., Williams, T. A., Steiner, R. A., Crump, M., et al. (2021) · doi:10.1101/2021.01.20.427326
Self-citationRational Design of Helical Nanotubes from Self-assembly of Coiled-coil Lock Washers
Xu, C., Wright, E. R., Mehta, A., Ser-pell, L. C., Zuo, X., Wall, J. S., & Conticello, V. P. (2013) · Microscopy and Microanalysis · doi:10.1017/s143192761300370x
Structural Determinants of Coiled Coil Mechanics
Lopez-Garcia, P., Goktas, M., Bergues-Pupo, A. E., Koksch, B., Silva, D. V., & Blank, K. G. (2019) · doi:10.1101/530873
Flagged first, then by citations
Research works printed but not linked: 1
- Plaper, 2021, De novo designed parallel heterodimeric coiled-coil peptide pairs with high affinity for use in mammalian cells, FEBS Open Biol., 11, 269
Cited by
Sorted by citations
De novo protein design—From new structures to programmable functions
Kortemme, T. (2024) · Cell · doi:10.1016/j.cell.2023.12.028 · Cited by 383
“Generalizing this idea, a systematic exploration of alpha-helical coiled-coils led to the design of novel architectures and development of principles to exploit these architectures for diverse functions 55 .”
An atlas of protein homo-oligomerization across domains of life
Schweke, H., Pacesa, M., Levin, T., Goverde, C. A., Kumar, P., Duhoo, Y., Dornfeld, L. J., Dubreuil, B., Georgeon, S., Ovchinnikov, S., et al. (2024) · Cell · doi:10.1016/j.cell.2024.01.022 · Cited by 144
Self-citationBlueprinting extendable nanomaterials with standardized protein blocks
Huddy, T. F., Hsia, Y., Kibler, R. D., Xu, J., Bethel, N. P., Nagarajan, D., Redler, R. L., Leung, P. J. Y., Weidle, C., Courbet, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07188-4 · Cited by 69
“There is a rich history of designing coiled coils using simple geometric principles; this extensibility and designability have made them widely used constituents of designed protein materials 15 .”
Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models
Ramirez, D. A., Hough, L. E., & Shirts, M. R. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.02.007 · Cited by 53
Diversity of Bioinspired Hydrogels: From Structure to Applications
Lupu, A., Grădinaru, L. M., Grădinaru, V. R., & Bercea, M. (2023) · Gels · doi:10.3390/gels9050376 · Cited by 47
“Many efforts have been focused on peptides folding into β-sheets (amyloid-like structures [22]) and also on the rational design of α-helical folding (proteins/peptide stabilization) [23].”
Background
Metadata
- Authors
- Woolfson, D. N.
- Affiliations
- University of Bristol (GB)
- Corresponding author
- Woolfson, Derek N.
- ORCID
- Woolfson, Derek N.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2023-04
- Volume
- 299
- Issue
- 4
- Pages
- 104579
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC10124910
- OpenAlex
- W4323276421
- Semantic Scholar
- e4a88b334ce7fa373dec876f2a178f521ccd9503
- Cited by
- 106
- References
- 292
- Citations by year
- 2026: 24 · 2025: 39 · 2024: 29 · 2023: 14
- FWCI
- 2.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Explore Bristol Research (submittedVersion, cc-by-nc-nd)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/S002820/1, BB/V004220/1, BB/V006231/1)
- Royal Society (WM140008)
- University of Bristol
- 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
- alpha-helical coiled coil, coiled-coil stability, synthetic biology, protein design, protein folding
- MeSH terms
- Protein Domains, Protein Conformation, alpha-Helical, Biology, Physics, Proteins, Protein Folding
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