Epistructural Tension Promotes Protein Associations

Epistructural tension is the reversible work per unit area required to span the aqueous interface of a soluble protein structure. The parameter accounts for the free-energy cost of imperfect hydration, involving water molecules with a shortage of hydrogen-bonding partnerships relative to bulk levels. The binding hot spots along protein-protein interfaces are identified with residues that contribute significantly to the epistructural tension in the free subunits. Upon association, such residues either displace or become deprived of low-coordination vicinal water molecules.

Figure 1

Interfacial water exclusion upon complex formation in human insulin (PDB.3E7Y). The ribbon rendering of the chain conformations (upper left) are an aid to the eye. The free (uncomplexed) chains ($A$ in magenta, $B$ in blue) are shown on the lower left. The backbone is represented as virtual bonds joining the $\alpha$-carbons of residues along the chain, with well-shielded backbone hydrogen bonds and dehydrons shown as segments sustained between the paired residues in grey and green, respectively. The location of hot interfacial water molecules is marked by asterisks and relative to the hydration vicinity of dehydrons in the free chains. The hot interfacial water molecules are excluded upon complex formation, as shown on the right, and the dehydrons vicinal to hot water molecules in the free chains turn into well-shielded hydrogen bonds (green to grey) within the complex. The intermolecular water exclusion patterns are marked by thin blue lines joining the residue that excludes water upon binding and the center of the hydrogen bond whose vicinity is deprived of interfacial water upon association. All hot interfacial water molecules with $g^{*}<3.5$ are excluded upon complexation.

Figure 2

Comparison between alanine scanning and variational analysis of protein-protein interfaces combining the $\Delta \Delta G_a$ classifier (upper entries) and the $g^{*}$-classifier (lower entries) of interfacial residues. Hot-spot residues marked in dark grey (bold font), white, and light grey correspond to the ranges $\Delta \Delta G_a\ge 3\mathrm{kcal}/\mathrm{mol}$, $1\mathrm{kcal}/\mathrm{mol}\le \Delta \Delta G_a<3\mathrm{kcal}/\mathrm{mol}$, and $\Delta \Delta G_a<1\mathrm{kcal}/\mathrm{mol}$, respectively, (upper rows for each PP interface). According to the second classifier (lower rows), residues are marked in dark grey (bold font), white, and light grey if their vicinal water lies in the ranges $g^{*}<3$, $3\le g^{*}<4$, $g=4$, respectively. The interfacial effect of the association upon the hydration vicinity of a residue is represented by “$X$” if water is displaced, “$\#$” if the residue displaces water intermolecularly as a result of its side-chain penetration into the vicinity of another residue across the PP interface, “$S$” if an intermolecular salt bridge is formed across the PP interface, and “blank space” if the hydration vicinity is unaltered.