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 i t forms with DNA have been elucidated with molecular dynamics simulati ons. Large TBP domain motions (bend and twist) are detected in the mon omer as well as in the DNA complexes; these motions can be important f or TBP binding of DNA. TBP interacts with guanine bases flanking the T ATA element in the simulations of the complex; these interactions may explain the preference for guanine observed at these DNA positions. Si de chains of some TBP residues at the binding interface display signif icant dynamic flexibility that results in 'flip-flop' contacts involvi ng multiple base pairs of the DNA. We discuss the possible functional significance of these observations.