DNA Binding by TATA-box Binding Protein (TBP): A Molecular Dynamics Computational Study

TATA-box binding protein (TBP) in a monomeric form and the complexes it forms with DNA have been elucidated with molecular dynamics simulations. Large TBP domain motions (bend and twist) are detected in the monomer as well as in the DNA complexes; these motions can be important for TBP binding of DNA. TBP interacts with guanine bases flanking the TATA element in the simulations of the complex; these interactions may explain the preference for guanine observed at these DNA positions. Side chains of some TBP residues at the binding interface display significant dynamic flexibility that results in 'flip-flop' contacts involving multiple base pairs of the DNA. We discuss the possible functional significance of these observations.