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Solvents, interfaces and protein structure.

F M Richards, T Richmond

    Ciba Foundation Symposium
    |January 1, 1977
    PubMed
    Summary
    This summary is machine-generated.

    Protein packing densities are similar to organic solids, with variations influencing structural fluctuations. Minimizing solvent-accessible surface area drives protein folding and globular shapes, impacting free energy and ligand binding.

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    Area of Science:

    • Protein structure and biophysics
    • Molecular dynamics and thermodynamics
    • Computational biology and bioinformatics

    Background:

    • Protein interiors exhibit packing densities comparable to organic solids, with regional variations.
    • Molecular surface area is a key determinant of free energy changes during processes like solvent transfer and protein folding.
    • The hydrophobic effect, driven by surface area minimization, significantly influences protein conformation.

    Purpose of the Study:

    • To investigate the relationship between packing density, structural fluctuations, and molecular surface area in proteins.
    • To explore how changes in solvent-protein interfacial area during folding correlate with free energy.
    • To analyze the role of surface area changes in secondary and tertiary structure formation and protein-protein interactions.

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    Main Methods:

    • Analysis of protein packing densities and identification of packing defects.
    • Correlation of molecular surface areas with free energies of transfer.
    • Rank-ordering of amino acid propensities for secondary structure formation (alpha-helix and beta-sheet) based on area changes.
    • Development of a prediction scheme for helix-helix interactions.

    Main Results:

    • Substantial variations in packing density exist within protein interiors, potentially related to structural fluctuations.
    • Significant changes in solvent-protein interfacial area during folding lead to large free energy implications.
    • Amino acid tendencies for beta-sheet formation correlate well with non-polar area changes; alpha-helix formation shows correlation with some exceptions (glutamic acid, tyrosine).
    • Tertiary structure formation can be rank-ordered by area change, aiding in identifying nucleation sites.

    Conclusions:

    • Minimization of solvent-accessible surface area is a primary driving force for protein folding into globular structures.
    • Surface area changes provide a basis for understanding secondary and tertiary structure formation and predicting interactions.
    • Water in enzyme active site grooves may exhibit higher fugacity, contributing to ligand-binding energy beyond simple surface area reduction.