Salutari Ilaria, Caflisch Amedeo
Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland.
J Chem Inf Model. 2022 Feb 28;62(4):1014-1024. doi: 10.1021/acs.jcim.1c01423. Epub 2022 Feb 4.
The tight control of transcriptional coactivators is a fundamental aspect of gene expression in cells. The regulation of the CREB-binding protein (CBP) and p300 coactivators, two paralog multidomain proteins, involves an autoinhibitory loop (AIL) of the histone acetyltransferase (HAT) domain. There is experimental evidence for the AIL engaging with the HAT binding site, thus interrupting the acetylation of histone tails or other proteins. Both CBP and p300 contain a domain of about 110 residues (called the bromodomain) that recognizes histone tails with one or more acetylated lysine side chains. Here, we investigate by molecular dynamics simulations whether the AIL of CBP (residues 1556-1618) acetylated at the side chain of Lys1595 can bind to the bromodomain. The structural instability and fast unbinding kinetics of the AIL from the bromodomain pocket suggest that the AIL is not a ligand of the bromodomain on the same protein chain. This is further supported by the absence of strong and persistent contacts at the binding interface. Furthermore, the simulations of unbinding show an initial fast detachment of the acetylated lysine and a slower phase necessary for complete AIL dissociation. We provide further evidence for the instability of the AIL intramolecular binding by comparison with a natural ligand, the histone peptide H3K56ac, which shows higher stability in the pocket.
转录共激活因子的严格调控是细胞基因表达的一个基本方面。对CREB结合蛋白（CBP）和p300共激活因子这两种旁系同源多结构域蛋白的调控涉及组蛋白乙酰转移酶（HAT）结构域的自抑制环（AIL）。有实验证据表明AIL与HAT结合位点相互作用，从而中断组蛋白尾巴或其他蛋白质的乙酰化。CBP和p300都含有一个约110个残基的结构域（称为溴结构域），该结构域可识别带有一个或多个乙酰化赖氨酸侧链的组蛋白尾巴。在这里，我们通过分子动力学模拟研究在赖氨酸1595侧链乙酰化的CBP的AIL（第1556 - 1618位残基）是否能与溴结构域结合。AIL从溴结构域口袋的结构不稳定性和快速解离动力学表明，AIL不是同一蛋白质链上溴结构域的配体。结合界面缺乏强烈且持久的接触进一步支持了这一点。此外，解离模拟显示乙酰化赖氨酸最初快速脱离，而AIL完全解离需要一个较慢的阶段。通过与天然配体组蛋白肽H3K56ac比较，我们为AIL分子内结合的不稳定性提供了进一步证据，H3K56ac在口袋中显示出更高的稳定性。
