How the TATA Box Selects Its Protein Partner

The TATA box-binding protein (TBP) binds in the minor groove of the TATA promoter sequence, drastically bending and unwinding the DNA helix. To explore the role of the TATA sequence in determining the specificity of TBP binding to DNA, we studied the solution structure and dynamics of 7 DNA dodecamer sequences, 6 of which bind to TBP. Molecular dynamics simulations were carried out with the CHARMM23 potential, explicit waters, one Na+/phosphate, and periodic boundary conditions. A comparison of the structural parameters of these dodecamers with DNA in the crystal structures of TBP/DNA complexes shows that the probability of various sequences for adopting transient conformations mimicking the distortions required for TBP binding, correlates with TBP-binding ability. The results indicate how the propensity of various TATA sequences to prepare structurally for TBP binding, constitutes a key selectivity determinant.