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Extended secondary structures in proteins.

Léo Degrève, Carlos A Fuzo, Antonio Caliri

    Biochimica Et Biophysica Acta
    |February 12, 2014
    PubMed
    Summary

    Extended secondary structures (ESSs) are common in globular proteins, stabilizing protein structures. These fused secondary structures involve about 30% of residues, enhancing conformational stability and protein folding.

    Area of Science:

    • Protein structure and folding
    • Structural bioinformatics
    • Biophysics

    Background:

    • Super secondary structures are known but often overlooked beyond basic identification.
    • Deeper fusion of secondary structures in globular proteins requires further investigation.

    Purpose of the Study:

    • To demonstrate that associated secondary structures sharing backbone residues, termed extended secondary structures (ESSs), are common in globular proteins.
    • To investigate the role of ESSs in stabilizing secondary and tertiary protein structures.

    Main Methods:

    • Statistical analysis of 163 randomly selected proteins from the Protein Data Bank.
    • Detailed structural analysis of specific protein cases.
    • Molecular Dynamics (MD) simulations of protein-aqueous solvent systems to analyze ESS stability.

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    Main Results:

    • Approximately 30% of residues in a protein participate in ESS on average.
    • MD simulations showed high conformational stability for ESSs, indicated by narrow root mean squared deviation distributions.
    • ESSs form stable aggregates that significantly enhance protein conformational stability.

    Conclusions:

    • Extended secondary structures (ESSs) are a ubiquitous and specific feature in globular proteins.
    • ESSs play a crucial role in stabilizing protein structures and may be involved in domain formation.
    • Further research into the function and significance of ESSs in protein architecture is warranted.