טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentFaiger Hana
SubjectThe Mechanism of Protein/DNA Structural Recognition in the
Model System of TATA Binding Protein/TATA-Box
Interaction
DepartmentDepartment of Biology
Supervisor Professor Tali Haran


Abstract

The TATA binding protein (TBP) is one of the most important proteins involved in transcriptional regulation in all eukaryotes. The TBP binding of an eight base-pair segment of DNA called TATA box is the first step in the initiation of transcription, leading to protein synthesis. The recognition of TATA boxes by TBP involves indirect reading of the DNA sequence, which means recognition of the intrinsic structure of the DNA target or its ability to deform upon complex formation. I have studied the interaction of TBP with TATA box to explore the molecular mechanisms underlying indirect reading of DNA by proteins in general and in this system in particular. In these studies, I have observed a correlation between the kinetic stability of TBP/TATA-box complexes and the identity of a last base pair in some TATA boxes but not in others. I suggest that a possible source for this difference may lie in the different structural properties of these TATA boxes. The analysis of kinetic data revealed a biphasic dissociation process of TBP from all TATA-box variants with two independent processes occurring simultaneously during dissociation of the TBP/TATA-box complex. I suggest a multistep TBP/TATA-box interaction mechanism to explain this kinetic behavior. Furthermore, I have studied the effect of sequences flanking the TATA box on TBP/TATA-box interaction, using in vitro selection method. I found that this effect is dependent on structural properties of TATA boxes. The effect is more significant in governing dissociation kinetics of TBP/TATA-box complexes than their thermodynamic stability.