Brd4 belongs to the BET family. It is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. With its tandem bromodomains, Brd4 avidly binds to diacetylated H4-AcK5/K12 and H3-AcK9/K14 peptides. Solution structure of the second bromodomain (BD) is reported in this research. In addition to the piD-helix, which is special for BET members, an incompact alphaZ' distinct from Brd2 BD2 is found, although they have identical sequences in this region. Both BD1 and BD2 bind to monoacetylated H4-AcK5 and H4-AcK12 peptides, but with subtle differences. An NMR perturbation study and mutational analysis identified the binding interface and revealed several residues important for binding specificity. By molecular dynamics simulations, a complex model composed of H4-AcK5/K12 and two molecules of BD2 is presented. Relaxation data and internal motions of BD2 are also discussed. Unlike Brd2 BD1, the two bromodomains of Brd4 are mainly monomeric in solution. They do not form heterodimers like TAFII250. It suggests that Brd4 should have its own mechanism to reinforce its chromatin association both in mitotic retention and related cellular regulation.
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