An acetyl-histone peptide library was used to determine the thermodynamic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains interact with histones by binding acetylated lysines. The bromodomain used in this study, BrD3, is derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin remodeling complex. Steady-state fluorescence anisotropy was used to examine the variations in specificity and affinity that drive molecular recognition. Temperature and salt concentration dependence studies demonstrate that the hydrophobic effect is the primary driving force, consistent with lysine acetylation being required for binding. An electrostatic effect was observed in only two complexes where the acetyl-lysine was adjacent to an arginine. The large change in heat capacity determined for the specific complex suggests that the dehydrated BrD3-histone interface forms a tightly bound, high-affinity complex with the target site. These explorations into the thermodynamic driving forces that confer acetylation site-dependent BrD3-histone interactions improve our understanding of how individual bromodomains work in isolation. Furthermore, this work will permit the development of hypotheses regarding how the native Pb1, and the broader class of bromodomain proteins, directs multisubunit chromatin remodeling complexes to specific acetyl-nucleosome sites in vivo.
KeywordsAcetyl-lysine; Histone acetylation; Polybromo; Histone code; Protein-protein interactions; Thermodynamics Histone acetylation is a key regulator of transcription; however, it is still a matter of debate as to whether the regulatory features are influenced by modification at specific lysine sites or it is the cumulative electrostatic consequences of random lysine acetylation. Mounting evidence indicates that large multiprotein chromatin remodeling complexes regulate transcription by localizing to certain chromatin sites through the interaction of bromodomain (BrD) 1 proteins with acetylated nucleosomes [1][2][3][4][5][6][7]. The BrD is a protein motif, approximately 100 amino acids in length, primarily associated with targeting subunits of chromatin remodeling complexes [8]. The biological role of the BrD centers on its ability to discriminate the acetylation state of lysine residues in histone proteins. In fact, there is growing evidence that the position of the acetyl-lysine is not random, but instead, the BrD requires acetylation at specific sites for highaffinity binding [9]. For example, fluorescence resonance energy transfer assays were used to show that the bromodomain protein Brd2 requires the interaction between its bromodomain and an acetyl-histone to amplify transcription in vivo [10]. To activate transcription after SAGA (Spt-Ada-Gcn5 acetyl-transferase) complex directed acetylation at specific nucleosomal locations, BrD proteins of the Swi2/Snf2 complex are required to displace acetyl-histones [11]. Likewise, the yeast RSC (remodels the structure of chromatin) complex requires multiple BrD...