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Related Experiment Videos

Periodicity in alpha-helix lengths and C-capping preferences.

S Penel1, R G Morrison, R J Mortishire-Smith

  • 1Department of Biomolecular Sciences, UMIST, Manchester, M60 1QD, UK.

Journal of Molecular Biology
|November 5, 1999
PubMed
Summary

Protein alpha-helices exhibit preferred lengths, influencing their capping and surface accessibility. These findings suggest incorporating helix length into predictive algorithms for protein structure.

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Area of Science:

  • Structural Biology
  • Protein Biochemistry
  • Computational Biology

Background:

  • Alpha-helices are fundamental protein secondary structures.
  • Helix length and capping motifs play crucial roles in protein folding and function.
  • Predictive algorithms for protein structure often overlook helix length as a key parameter.

Purpose of the Study:

  • To investigate the distribution of alpha-helix lengths in protein crystal structures.
  • To analyze the relationship between helix length and N- and C-terminal capping preferences.
  • To provide insights for improving computational prediction of helices and capping motifs.

Main Methods:

  • Surveyed 299 high-resolution, non-homologous protein crystal structures.
  • Analyzed alpha-helix lengths and identified preferred and disfavored residue counts.

Related Experiment Videos

  • Examined amino acid preferences at N- and C-termini and C-capping motifs (Schellman, alphaL).

    • Main Results:

    • Alpha-helices show a preference for lengths close to an integral number of turns.
    • Specific residue counts (e.g., 6, 7, 10, 11) are favored, while others (e.g., 8, 9, 12) are disfavored.
    • Favored length helices display distinct C-capping preferences (non-polar at C4, polar at C2) compared to disfavored lengths (non-polar at C2).
    • Periodic trends in C-capping motifs correlate with side-chain burial preferences.

    Conclusions:

    • Helix length is a significant factor influencing alpha-helix structure and capping.
    • Favored helix lengths facilitate surface exposure through specific capping strategies.
    • Algorithms for predicting protein helices and C-capping should incorporate helix length as a predictive feature.