Unbinding of the auto-inhibitory loop from the bromodomain in the CREB-Binding Protein

The CBP (or CREB-Binding Protein, CREBBP) and p300 paralog proteins are histone acetyltransferases (HATs) and contitute a family of transcriptional co-activators with a central role in gene expression. It has emerged that the long loop of CBP/p300 (also called the autoinhibitory loop, or AIL) participates in the control of their function. The AIL is a 63-residue-long lysine-rich loop that stems from the HAT domain. When de-acetylated, it binds an electronegative patch close to the HAT catalytic site, blocking its activity. When the AIL lysines are acetylated, it has been proposed that they become ligands of the bromodomain on the same molecule, thus competing with histone tails (the known ligands of the bromodomain). The negative regulation of bromodomain activity would allow the CBP catalytic core to detach from chromatin and interrupt transcription.

The movie shows a simulation of the CBP catalytic core dynamics, to analyze the kinetic stability of the AIL bound to the bromodomain. We started from the crystal structure of the CBP catalytic core (PDB ID: 5U7G) and reconstructed the disordered AIL which could not be crystallized. We employed all-atom molecular dynamics (MD) simulations in dihedral angle space and in implicit solvent. The CBP catalytic core is represented as a cartoon, with the AIL colored in yellow, and the other fully flexible segments (the bromodomain binding site loops and the hinges connecting the individual domains) in red. The acetylated lysine of the AIL (K1595ac) is shown in sticks. The single explicit water molecule is represented as a blue sphere and the two structural zinc ions as cyan spheres.

In the reference paper, we elucidate the process of AIL unbinding from the bromodomain and provide the unbinding kinetics. We find that intramolecular unbinding is one order of magnitude faster than intermolecular unbinding, which indicates that the AIL is not a substrate of the bromodomain on the same molecule.