Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element Original Research Article

Abstract Background: We previously determined the co-crystal structure of the zinc finger region of transcription factor YY1 (YY1Δ) bound to the initiator element (Inr) of the adenoassociated virus (AAV) P5 gene promoter [Houbaviy, H.B. et al. (1996) Proc. Natl. Acad. Sci. USA 93, 13577–13582]. Our structure explained both binding specificity and the ability of YY1 to support specific, unidirectional transcription initiation. Results: To further understand Inr recognition by YY1, we analyzed the YY1Δ–Inr interaction by isothermal titration calorimetry (ITC) and used limited proteolysis, DNase I footprinting and missing nucleoside experiments to show that YY1Δ and full-length YY1 (YY1WT) have indistinguishable DNA binding properties. Conclusions: YY1 binding occurs at an equilibrium dissociation constant (Kd) of about 1 μM, and exhibits a large negative heat capacity change (ΔCp). We analyzed the thermodynamic behavior of YY1Δ in terms of buried solvent-accessible surface area resulting from interaction of two rigid bodies, which could not explain our measured value of ΔCp. We must, therefore, postulate conformational changes in YY1 and/or the Inr or question the validity of current ΔCp analysis methods for protein–DNA interactions. Article Outline * 1. Introduction