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Socket: a program for identifying and analysing coiled-coil motifs within protein structures.

J Walshaw1, D N Woolfson

  • 1Centre for Biomolecular Design and Drug Development, School of Biological Sciences, University of Sussex, Falmer, East Sussex, BN1 9QG, UK.

Journal of Molecular Biology
|April 9, 2001
PubMed
Summary

We developed SOCKET, a program to identify coiled-coil protein structures by their characteristic packing. This tool aids in analyzing coiled-coil diversity and assembly principles.

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Area of Science:

  • Structural biology
  • Bioinformatics

Background:

  • Coiled coils are simple, ubiquitous protein motifs facilitating protein-protein interactions.
  • They feature alpha-helices forming supercoils, often with a heptad repeat sequence pattern.
  • Coiled coils exhibit structural diversity in helix arrangement and oligomerization states.

Purpose of the Study:

  • To develop a computational tool for automated identification of coiled-coil motifs in protein structures.
  • To create a comprehensive database of coiled-coil structures for further analysis.
  • To aid in understanding coiled-coil assembly, prediction, and design.

Main Methods:

  • Developed SOCKET, a computer program that identifies coiled coils based on side-chain packing (knobs-into-holes).
  • Used SOCKET to collect a dataset of unambiguous coiled-coil structures from the RCSB Protein Data Bank.

Related Experiment Videos

  • Algorithm distinguishes coiled coils from other helix-helix packing arrangements in globular domains.

    • Main Results:

    • SOCKET accurately identifies coiled-coil helix boundaries, oligomerization states, and orientations.
    • The program assigns heptad registers, crucial for understanding coiled-coil sequences.
    • A diverse set of coiled-coil structures, including parallel and anti-parallel arrangements and various oligomeric states, was collected.

    Conclusions:

    • The SOCKET program and the curated structural database facilitate the study of coiled-coil structural diversity and assembly.
    • The gathered data can be used to identify principles for coiled-coil prediction and design.
    • Sequence and structural analyses are enabled, providing amino acid profiles for different coiled-coil motifs.