Navigating the Structural Landscape of De Novo α-Helical Bundles
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Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
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Experimental data suggest CC-Hex*-L24E forms a parallel hexamer at pH 2-6.5 and an antiparallel tetramer at pH > 7.
“Experimental data suggest CC-Hex*-L24E forms a parallel hexamer at pH 2–6.5 and an antiparallel tetramer at pH > 7.29”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [29]
CC-Hex*-L24E forms a parallel hexamer at pH 2-6.5 and an antiparallel tetramer with an offset at pH > 7.
“We then turned our attention to a pH-switchable system, CC-Hex*-L24E, which forms a parallel hexamer at pH 2–6.5 and an antiparallel tetramer with an offset at pH > 7 (Figure 2).29”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [29]
The CC-Hex*-L24E antiparallel tetramer does not have salt bridges or hydrogen bonds in its structure.
“The CC-Hex*-L24E antiparallel tetramer however does not have salt bridges or hydrogen bonds in its structure.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [29]
The monomer helicity calculations agree with experimental data which portray the CC-Hex*-L24E complex as highly helical at pH 3-5 and less helical at pH 6-7.
“These monomer helicity calculations agree with experimental data which portray the CC-Hex*-L24E complex as highly helical at pH 3–5 and less helical at pH 6–7.29”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [29]
The hexamer at low pH has E and F helices showing C-terminal fraying, with residues missing from the structure; as a consequence, the hexamer likely has increased conformational plasticity and has the potential to rearrange its helices in the bound state to maximize hydrogen bond formation at the core.
“With regards to the hexamer state, while at first glance a negative value seems counterintuitive given the hexamer at low pH is the experimentally observed structure, it should be noted that the E and F helices show C-terminal fraying, with residues missing from the structure;29 as a consequence, the hexamer likely has increased conformational plasticity and has the potential to rearrange its heli”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [29]
Cites
Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution
Sutton, R. B., Fasshauer, D., Jahn, R., & Brunger, A. T. (1998) · Nature · doi:10.1038/26412 · Cited by 2,417 · see citing works
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 · see citing works
Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts
Lawson, D. M., Artymiuk, P. J., Yewdall, S. J., Smith, J. M. A., Livingstone, J. C., Treffry, A., Luzzago, A., Levi, S., Arosio, P., Cesareni, G., et al. (1991) · Nature · doi:10.1038/349541a0 · Cited by 777 · see citing works
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 · see citing works
Self-citationCrystal structure of an isoleucine-zipper trimer
Harbury, P. B., Kim, P. S., & Alber, T. (1994) · Nature · doi:10.1038/371080a0 · Cited by 472 · see citing works
The HAMP Domain Structure Implies Helix Rotation in Transmembrane Signaling
Hulko, M., Berndt, F., Gruber, M., Linder, J. U., Truffault, V., Schultz, A., Martin, J., Schultz, J. E., Lupas, A. N., & Coles, M. (2006) · Cell · doi:10.1016/j.cell.2006.06.058 · Cited by 416 · see citing works
Walshaw, J., & Woolfson, D. N. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4545 · Cited by 357 · see citing works
Self-citationComputational 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 · see citing works
Self-citationThe Fourier transform of a coiled-coil
Crick, F. H. C. (1953) · Acta Crystallographica · doi:10.1107/s0365110x53001952 · Cited by 313 · see citing works
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 · see citing works
Coiled-Coil Design: Updated and Upgraded
Woolfson, D. N. (2017) · Subcellular Biochemistry · doi:10.1007/978-3-319-49674-0_2 · Cited by 149 · see citing works
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Understanding a protein fold: The physics, chemistry, and biology of α-helical coiled coils
Woolfson, D. N. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104579 · Cited by 106 · see citing works
Self-citationStructure of an endogenous mycobacterial MCE lipid transporter
Chen, J., Fruhauf, A., Fan, C., Ponce, J., Ueberheide, B., Bhabha, G., & Ekiert, D. C. (2023) · Nature · doi:10.1038/s41586-023-06366-0 · Cited by 69 · see citing works
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 · see citing works
Self-citationA Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
Blazhynska, M., Gumbart, J. C., Chen, H., Tajkhorshid, E., Roux, B., & Chipot, C. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00941 · Cited by 22 · see citing works
Notari, E., Wood, C. W., & Michel, J. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01695 · Cited by 4 · see citing works
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- Authors
- Rhys, G. G., Wood, C. W., Beesley, J. L., Zaccai, N. R., Burton, A. J., Brady, R. L., Thomson, A. R., & Woolfson, D. N.
- Affiliations
- University of Bristol (GB)
- Princeton University (US)
- Corresponding author
- Woolfson, Derek N.
- ORCID
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-05-08
- Volume
- 141
- Issue
- 22
- Pages
- 8787-8797
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2906649237
- Cited by
- 48
- References
- 11
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 3 · 2023: 13 · 2022: 4 · 2021: 12 · 2020: 7 · 2019: 3
- FWCI
- 2.15
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of the American Chemical Society (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion, other-oa)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion, cc-by-sa)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Explore Bristol Research (submittedVersion, other-oa)
- Funders
- Royal Society (WM140008)
- Research Councils UK (EP/G036764/1, BB/J014400/1, BB/R00661X/1)
- European Commission (340764)
- Wolfson Foundation (WM140008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Physical Sciences › Materials Science › Biomaterials › Supramolecular Self-Assembly in Materials
- Keywords
- alpha-helical coiled coil, de novo protein design, amphipathic helix, hydrophobic effect, synthetic peptides, protein stability, protein engineering, synthetic biology
- MeSH terms
- Protein Conformation, alpha-Helical, Amino Acid Sequence, Models, Molecular, Proteins, Water, Protein Folding, Hydrophobic and Hydrophilic Interactions
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