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Related Experiment Videos

Solvent accessibility, protein surfaces, and protein folding

A M Lesk, C Chothia

    Biophysical Journal
    |October 1, 1980
    PubMed
    Summary

    Protein folding intermediates may form through interactions between secondary structures. Hydrophobic and van der Waals forces guide helix association, with parallel conformations favored before final native structure formation.

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    Area of Science:

    • Protein structure and folding dynamics
    • Computational biophysics and biochemistry

    Background:

    • Native protein structures are stabilized by known forces, but folding intermediates remain hypothetical.
    • A common assumption is that intermediates retain native-like secondary and tertiary structures.

    Purpose of the Study:

    • To investigate the formation of protein folding intermediates through the association of secondary structural elements.
    • To identify stabilizing interactions available to such intermediates using computational methods.

    Main Methods:

    • Calculated accessible surface area to quantify hydrophobic stabilization.
    • Employed parameterized nonbonded energy calculations to assess van der Waals forces.
    • Analyzed buried surface area contributions from secondary structure formation and interactions.

    Main Results:

    • Formation of secondary structure alone buries approximately half the surface area compared to the complete native structure.
    • Analysis of two alpha-helices approaching each other revealed solvent effects on orientation and van der Waals forces driving close packing.
    • A stable, non-specific complex can form via hydrophobic interactions before final native geometry is achieved, with parallel helix conformations favored under solvent-exclusion dominance.

    Conclusions:

    • Intermediates may form via interactions between secondary structural elements, stabilized by hydrophobic and van der Waals forces.
    • The study provides insights into the forces governing the association of protein structural units during folding.
    • Native geometry is only the most stable in the final stages of approach, suggesting alternative stable conformations exist earlier in folding.

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