A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology
Open accessAbstract
Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.
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The free energy landscape of coiled coils is complex, consisting of multiple local, energetically close minima.
“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 [33]
The burial of more than two Asn residues at the hydrophobic peptide core is not tolerated in higher oligomerization states, rendering the trimer and tetramer states less favorable.
“However, the burial of more than two Asn residues is not tolerated in higher oligomerization states, rendering the trimer and tetramer states less favorable.33,112”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [33]
The Asn17-Asn17 hydrogen bond in CC-Di and the Asp@e-Arg@a hydrogen bonds/salt bridges in apCC-Di determine the formation of parallel and antiparallel dimers, respectively.
“Of notable importance are the Asn17-Asn17 hydrogen bond in CC-Di, and the Asp@e-Arg@a hydrogen bonds/salt bridges in apCC-Di, which determine the formation of parallel and antiparallel dimers, respectively.33,89”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [33]
In CC-Di, each monomer has an Asn residue at the a position of one of its central heptads, which strongly favors the parallel dimer state due to the formation of interhelical Asn-Asn hydrogen bonds.
“In the case of CC-Di, each monomer has an Asn residue at the a position of one of its central heptads, which strongly favors the parallel dimer state due to the formation of interhelical Asn–Asn hydrogen bonds.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [33]
Substitution of Asn to Ile results in a parallel trimer instead; therefore, the presence of the Asn residues confers high selectivity for the parallel dimer state.
“Notably, substitution of Asn to Ile, which is ordinarily present at the a position in coiled-coil dimers (and is present in all other a positions of the CC-Di sequence), results in a parallel trimer instead;33 therefore, the presence of the Asn residues confers high selectivity for the parallel dimer state.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [33]
The difference in ΔGbind,total°/helix values reflects the inherent stability of the complexes; CC-Di, CC-Tri and CC-Tet are hyper-stable coiled coils with high melting points, whereas the CC-Hex*-L24E system has increased plasticity to allow conformational switching upon changes in pH and consequently has a lower ΔGbind,total°/helix value.
“The difference in these values reflects the inherent stability of the complexes; CC-Di, CC-Tri and CC-Tet are hyper-stable coiled coils, with high melting points,33 whereas the CC-Hex*-L24E system has increased plasticity to allow conformational switching upon changes in the pH and consequently has a lower ΔGbind,total◦/helix value.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [33]
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- Authors
- 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., Thomson, A. R., & Woolfson, D. N.
- Affiliations
- University of Bristol (GB)
- Corresponding author
- Thomson, Andrew R.
- Woolfson, Derek N.
- ORCID
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-05-14
- Volume
- 1
- Issue
- 6
- Pages
- 240-250
- ISSN
- 2161-5063 (ISSN-L)
- OpenAlex
- W2073184464
- Cited by
- 262
- References
- 11
- Citations by year
- 2026: 10 · 2025: 24 · 2024: 23 · 2023: 25 · 2022: 20 · 2021: 29 · 2020: 13 · 2019: 23 · 2018: 19 · 2017: 24 · 2016: 20 · 2015: 7 · 2014: 11 · 2013: 7 · 2012: 7
- FWCI
- 4.12
- Type
- journal article
- Language
- en
- Open access
- Licence
- cc-by
- Locations
- ACS Synthetic Biology (publishedVersion)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Durham Research Online (Durham University) (submittedVersion, cc-by)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/G008833/1, BB/F007256/1, BB/J020087/1)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- coiled-coil peptides, de novo peptide design, coiled-coil dimerization
- MeSH terms
- Amino Acid Sequence, Models, Molecular, Peptides, Computer-Aided Design, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, X-Ray, Protein Structure, Quaternary, Protein Interaction Domains and Motifs, Protein Multimerization, Protein Stability, Biophysical Phenomena, Synthetic Biology
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