Kinetic analysis of acetylation-dependent Pb1 bromodomain-histone interactions

Stopped-flow fluorescence anisotropy was used to determine the kinetic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains are acetyllysine binding motifs found in many chromatin associated proteins. Individual bromodomains were derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin-remodeling complex that has six tandem bromodomains in the amino-terminal region. The average kon and koff values for the formation of high-affinity complexes are 275 M− 1 s− 1 and 0.41 × 10− 3 s− 1, respectively. The average kon and koff values for the formation of low-affinity complexes are 119 M− 1 s− 1 and 1.42 × 10− 3 s− 1, respectively. Analysis of the on- and off-rates yields acetylation site-dependent equilibrium dissociation constants averaging 1.4 and 12.9 μM for high- and low-affinity complexes, respectively. This work represents the first examination of kinetic mechanisms of acetylation-dependent bromodomain-histone interactions.