Protein–protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area

Authors

  • Jieming Chen,

    1. Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520
    2. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
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  • Nicholas Sawyer,

    1. Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520
    2. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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  • Lynne Regan

    Corresponding author
    1. Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520
    2. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520
    3. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
    4. Department of Chemistry, Yale University, New Haven, Connecticut 06520
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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Abstract

Protein–protein interactions play key roles in many cellular processes and their affinities and specificities are finely tuned to the functions they perform. Here, we present a study on the relationship between binding affinity and the size and chemical nature of protein–protein interfaces. Our analysis focuses on heterodimers and includes curated structural and thermodynamic data for 113 complexes. We observe a direct correlation between binding affinity and the amount of surface area buried at the interface. For a given amount of surface area buried, the binding affinity spans four orders of magnitude in terms of the dissociation constant (Kd). Across the entire dataset, we observe no obvious relationship between binding affinity and the chemical composition of the interface. We also calculate the free energy per unit surface area buried, or “surface energy density,” of each heterodimer. For interfacial surface areas between 500 and 2000 Å2, the surface energy density decreases as the buried surface area increases. As the buried surface area increases beyond about 2000 Å2, the surface energy density levels off to a constant value. We believe that these analyses and data will be useful for researchers with an interest in understanding, designing or inhibiting protein–protein interfaces.

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