SELECTIVE BINDING OF THE TATA BOX-BINDING PROTEIN TO THE TATA BOX-CONTAINING PROMOTER - ANALYSIS OF STRUCTURAL AND ENERGETIC FACTORS

We report the results of an energy-based exploration of the components of selective recognition of the TATA box-binding protein (TBP) to a T ATA box sequence that includes 1) the interaction between the hydropho bic Leu, Pro, and Phe residues of TBP with the TA, AT, AA, TT, and CG steps, by ab initio quantum mechanical calculations; and 2) the free e nergy penalty, calculated from molecular dynamics/potential of mean fo rce simulations, for the conformational transition from A-DNA and B-DN A into the TA-DNA form of DNA observed in a complex with TBP. The GTAT , GATT, GAAT, and GTTT tetramers were explored. The results show that 1) the discrimination of TA, AT, AA, TT, or CG steps by TBP cannot res t on their interaction with the inserting Phe side chains; 2) the ster ic clash between the bulky and hydrophobic Pro and Leu residues and th e protruding -NH2 group of guanine is responsible for the observed sel ectivity against any Gua-containing basepair; 3) the Pro and Leu resid ues cannot selectively discriminate among TA, AT, AA, or TT steps; and 4) the calculated energy required to achieve the TA-DNA conformation of DNA that is observed in the complex with TBP appears to be a key de terminant for the observed selectivity against the AT, AA, and TT step s. The simulations also indicate that only the TA step can form a very efficient interbase hydrogen bond network in the TA-DNA conformation. Such an energetically stabilizing network is not achievable in the AA and TT steps. While it is viable in the AT step, structural constrain ts render the hydrogen bonding network energetically ineffective there .