Pin1 is a Prolyl Isomerase that catalyzes cis-trans isomerization of peptides with pSer/Thr-Pro motifs in many cell signaling proteins. This conformational switch is implicated in diseases. Pin1 activity is considered a target for therapeutic applications. Pin1 targets motifs by its N-terminal WW-binding domain. A C-terminal PPIase domain is responsible for catalysis. To understand how Pin1 coordinates its enzymatic activities, it is necessary to probe how the domains behave in the presence of substrates. Here, we used novel (Histone H1 and Sic1) and other existing peptides to characterize the dynamics of Pin1 and impact of substrate binding on inter-domain interactions. Pin1- peptide complexes have been used to show that peptide addition causes a conformational change in the two domains. 15N-relaxation data suggest that the flexibility of these domains depends on the substrate peptide We have constructed a hypothesis about which substrate residues may be important for conferring tight binding and inter-domain interactions.