Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin.
Biochim Biophys Acta,
PubMed id: 20600625
BACKGROUND: Prerequisite for the design of tight binding protein inhibitors and
prediction of their properties is an in-depth understanding of the structural
and thermodynamic details of the binding process. A series of closely related
phosphonamidates was studied to elucidate the forces underlying their binding
affinity to thermolysin. The investigated inhibitors are identical except for
the parts penetrating into the hydrophobic S(1)'-pocket. METHODS: A correlation
of structural, kinetic and thermodynamic data was carried out by X-ray
crystallography, kinetic inhibition assay and isothermal titration calorimetry.
RESULTS & CONCLUSIONS: Binding affinity increases with larger ligand
hydrophobic P(1)'-moieties accommodating the S(1)'-pocket. Surprisingly, larger
P(1)'-side chain modifications are accompanied by an increase in the enthalpic
contribution to binding. In agreement with other studies, it is suggested that
the release of largely disorder waters from an imperfectly hydrated pocket
results in an enthalpically favourable integration of these water molecules into
bulk water upon inhibitor binding. This enthalpically favourable process
contributes more strongly to the binding energetics than the entropy increase
resulting from the release of water molecules from the S(1)'-pocket or the
formation of apolar interactions between protein and inhibitor. GENERAL
SIGNIFICANCE: Displacement of highly disordered water molecules from a rather
imperfectly hydrated and hydrophobic specificity pocket can reveal an enthalpic
signature of inhibitor binding.