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Scientific article
Open access
English

CC+ : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models

Published inProtein science, vol. 32, no. 11, e4789
Publication date2023-10-20
First online date2023-10-20
Abstract

α‐Helical coiled coils are common tertiary and quaternary elements of protein structure. In coiled coils, two or more α helices wrap around each other to form bundles. This apparently simple structural motif can generate many architectures and topologies. Coiled coil‐forming sequences can be predicted from heptad repeats of hydrophobic and polar residues, hpphppp , although this is not always reliable. Alternatively, coiled‐coil structures can be identified using the program SOCKET, which finds knobs‐into‐holes (KIH) packing between side chains of neighboring helices. SOCKET also classifies coiled‐coil architecture and topology, thus allowing sequence‐to‐structure relationships to be garnered. In 2009, we used SOCKET to create a relational database of coiled‐coil structures, CC + , from the RCSB Protein Data Bank (PDB). Here, we report an update of CC + following an update of SOCKET (to Socket2) and the recent explosion of structural data and the success of AlphaFold2 in predicting protein structures from genome sequences. With the most‐stringent SOCKET parameters, CC + contains ≈12,000 coiled‐coil assemblies from experimentally determined structures, and ≈120,000 potential coiled‐coil structures within single‐chain models predicted by AlphaFold2 across 48 proteomes. CC + allows these and other less‐stringently defined coiled coils to be searched at various levels of structure, sequence, and side‐chain interactions. The identified coiled coils can be viewed directly from CC + using the Socket2 application, and their associated data can be downloaded for further analyses. CC + is available freely at http://coiledcoils.chm.bris.ac.uk/CCPlus/Home.html . It will be updated automatically. We envisage that CC+ could be used to understand coiled‐coil assemblies and their sequence‐to‐structure relationships, and to aid protein design and engineering.

eng
Keywords
  • AlphaFold2
  • SOCKET
  • Socket2
  • Bioinformatics
  • Coiled coil
  • Protein assembly
  • Protein design
  • Protein engineering
  • Protein-structure analysis and modeling
  • Structural biology
  • Α helix
Affiliation Not a UNIGE publication
Funding
  • European Commission - Infinite Protein Self-Assembly in Health and Disease [819318]
  • UK Research and Innovation - BrisSynBio: Bristol Centre for Synthetic Biology [BB/L01386X/1]
  • European Commission - Alpha-helical Barrels: Exploring, Understanding and Exploiting a New Class of Protein Structure [340764]
  • European Commission - Barrel Array Diagnostics And SenSing [787173]
  • UK Research and Innovation - Rational computational protein design in ISAMBARD: new approaches, folds and functions [BB/R00661X/1]
  • Israel Science Foundation - [1452/18]
Citation (ISO format)
KUMAR, Prasun et al. CC<sup>+ </sup>: A searchable database of validated coiled coils in PDB structures and AlphaFold2 models. In: Protein science, 2023, vol. 32, n° 11, p. e4789. doi: 10.1002/pro.4789
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Article (Published version)
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ISSN of the journal0961-8368
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Technical informations

Creation04/23/2024 3:52:38 PM
First validation04/24/2024 12:14:38 PM
Update time04/24/2024 12:14:38 PM
Status update04/24/2024 12:14:38 PM
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