Proteins containing phosphorylated Ser/Thr-Pro motifs play key roles in numerous regulatoryprocesses in the cell. The peptidyl prolyl
cis/trans isomerase Pin1 specifically catalyzes the conformationaltransition of phosphorylated Ser/Thr-Pro motifs. Here we report the direct analysis of the thermodynamicproperties of the interaction of the PPIase Pin1 with its substrate-analogue inhibitor Ac-Phe-
D-Thr(PO
3H
2)-Pip-Nal-Gln-NH
2 specifically targeted to the PPIase active site based on the combination ofisothermal titration calorimetry and studies on inhibition of enzymatic activity of wt Pin1 and active sitevariants. Determination of the thermodynamic parameters revealed an enthalpically and entropically favoredinteraction characterized by binding enthalpy
HITC of -6.3 ± 0.1 kcal mol
-1 and a
TSITC of 4.1 ± 0.1kcal mol
-1. The resulting dissociation constant
KD for binding of the peptidic inhibitor with 1.8 × 10
-8M resembles the dissociation constant of a Pin1 substrate in the transition state, suggesting a transitionstate analogue conformation of the bound inhibitor. The strongly decreased affinity of Pin1 for ligand atincreasing ionic strength implicates that the potential of bidentate binding of a substrate protein by thePPIase and the WW domain of Pin1 may be required to deploy improved efficiency and specificity ofPin1 under conditions of physiological ionic strength.