Extended knobs-into-holes packing in classical and complex coiled-coil assemblies☆
Abstract
This year marks the 50th anniversary of Crick's seminal paper on the packing of alpha-helices into coiled-coil structures. The central tenet of Crick's work is the interdigitation of side chains, which directs the helix-helix interactions; so called knobs-into-holes packing. Subsequent determinations of coiled-coil-protein sequences and structures confirmed the key features of Crick's model and established it as a fundamental concept in structural biology. Recently, we developed a program, SOCKET, to recognise knobs-into-holes packing in protein structures, which we applied to the Protein Data Bank to compile a database of coiled-coil structures. In addition to classic structures, the database reveals 4-helix bundles and larger helical assemblies. Here, we describe how the more-complex structures can be understood by extending Crick's principles for classic coiled coils. In the simplest case, each helix of a 2-stranded structure contributes a single seam of (core) knobs-into-holes to the helical interface. 3-, 4-, and 5-Stranded structures, however, are best considered as rings of helices with cycles of knobs-into-holes. These higher-order oligomers make additional (peripheral) knobs-into-holes that broaden the helical contacts. Combinations of core and peripheral knobs may be assigned to different sequence repeats offset within the same helix. Such multiple repeats lead to multi-faceted helices, which explain structures above dimers. For instance, coiled-coil oligomer state correlates with the offset of the different repeats along a sequence. In addition, certain multi-helix assemblies can be considered as conjoined coiled coils in which multi-faceted helices participate in more than one coiled-coil motif.
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Further helices can be recruited to the assembly via the expansion of the hydrophobic interface, achieved by introducing hydrophobic residues at the e and g positions.
“Further helices can be recruited to the assembly via the expansion of the hydrophobic interface, achieved by introducing hydrophobic residues at the e and g positions.10”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [10]
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- Authors
- Walshaw, J., & Woolfson, D. N.
- Affiliations
- University of Sussex (GB)
- Corresponding author
- Woolfson, Derek N.
- Venue
- Journal of Structural Biology
- Publisher
- Elsevier BV
- Published
- 2003-12
- Volume
- 144
- Issue
- 3
- Pages
- 349-361
- ISSN
- 1047-8477 (ISSN-L)
- OpenAlex
- W2110361885
- Cited by
- 104
- References
- 43
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 4 · 2023: 6 · 2022: 3 · 2021: 3 · 2020: 4 · 2019: 3 · 2018: 4 · 2017: 7 · 2016: 3 · 2015: 3 · 2014: 3 · 2013: 5 · 2012: 6
- FWCI
- 1.72
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Structural Biology (publishedVersion)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- coiled coil, alpha-helix packing, helical oligomers, helix-helix interactions, sequence repeats
- MeSH terms
- Algorithms, Models, Molecular, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Software, Protein Structure, Secondary, Amino Acid Motifs
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