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Structural heterogeneity in protein crystals.

J L Smith, W A Hendrickson, R B Honzatko

    Biochemistry
    |September 9, 1986
    PubMed
    Summary
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    High-resolution protein crystallography reveals extensive conformational heterogeneity in multiple proteins. This structural flexibility, observed in side chains and backbones, indicates proteins exist in discrete substates.

    Area of Science:

    • Structural Biology
    • Biophysics
    • Protein Crystallography

    Background:

    • Proteins exhibit conformational flexibility, crucial for their function.
    • Understanding protein dynamics at atomic resolution is challenging.
    • Crystallography provides snapshots of protein structures.

    Purpose of the Study:

    • To investigate conformational heterogeneity in highly refined protein crystal structures.
    • To quantify the extent of multiple conformations in amino acid side chains and backbones.
    • To explore the implications of observed heterogeneity for protein dynamics in solution.

    Main Methods:

    • Analysis of X-ray diffraction data for four proteins (crambin, erabutoxin, myohemerythrin, lamprey hemoglobin) to spacings of 0.945–2.0 Å.
    • High-resolution crystallographic refinement of protein structures.

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  • Detailed examination of electron density maps to identify multiple conformations and solvent networks.

    • Main Results:

    • Extensive conformational heterogeneity observed in 6–13% of amino acid side chains across four proteins.
    • Structural heterogeneity includes flexible surface and buried side chains, and occasional backbone variations.
    • Multiple discrete conformations, rather than continuous flexibility, are preferred.
    • Numerous solvent sites exhibit multiplet conformations and form mutually exclusive networks.

    Conclusions:

    • Highly refined protein crystal structures reveal significant conformational heterogeneity.
    • This heterogeneity reflects discrete conformational substates accessible to proteins.
    • Observed heterogeneity sets a lower bound for protein conformational substates in solution.
    • High-resolution data suggests small fluctuations lead to discrete substates, with unresolved conformers contributing to thermal parameters.