Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element.
BACKGROUND
We previously determined the co-crystal structure of the zinc finger region of transcription factor YY1 (YY1Delta) 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 YY1Delta-Inr interaction by isothermal titration calorimetry (ITC) and used limited proteolysis, DNase I footprinting and missing nucleoside experiments to show that YY1Delta and full-length YY1 (YY1WT) have indistinguishable DNA binding properties.


CONCLUSIONS
YY1 binding occurs at an equilibrium dissociation constant (K(d)) of about 1 microM, and exhibits a large negative heat capacity change (DeltaC(p)). We analyzed the thermodynamic behavior of YY1Delta in terms of buried solvent-accessible surface area resulting from interaction of two rigid bodies, which could not explain our measured value of DeltaC(p). We must, therefore, postulate conformational changes in YY1 and/or the Inr or question the validity of current DeltaC(p) analysis methods for protein-DNA interactions.
Houbaviy
H B
HB
Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10021, USA.
Burley
S K
SK
D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000229:Dependovirus / Q000737:chemistry*; D050981:Erythroid-Specific DNA-Binding Factors; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D050986:YY1 Transcription Factor
D004268:DNA-Binding Proteins; D050981:Erythroid-Specific DNA-Binding Factors; D014157:Transcription Factors; D014764:Viral Proteins; D050986:YY1 Transcription Factor