Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA.
Proteins. 2010 Feb 1;78(2):447-56. doi: 10.1002/prot.22565.
Targeted therapeutic intervention in receptor-ligand interactions of p53-mediated tumor suppression can impact progression of disease, aging, and variation in genetic expression. Here, we conducted a number of molecular simulations, based on structures of p53 in complex with its transcriptional coactivating CBP bromodomain, determined by NMR spectroscopy, to investigate the energetics of the binding complex. Building on the observation that acetylation of K382 in p53 serves as the essential triggering switch for a specific interaction with CBP, we assessed the differential effect of acetylation on binding from simulations of an octapeptide derived from p53 with acetylated and nonacetylated K382 (residues 379-386). Cluster analysis of the simulations shows that acetylation of the free peptide does not significantly change the population of the preferred conformation of the peptide in solution for binding to CBP. Conversion of the acetylated K382 to nonacetylated form with free energy perturbation (FEP) simulations of the p53 CBP complex and the free peptide showed that the relative contribution of the acetyl group to binding is 4.8 kcal/mol. An analysis of residue contributions to the binding energy using an MM-GBSA approach agrees with the FEP results and sheds additional light on the origin of selectivity in p53 binding to the CBP bromodomain.
靶向治疗干预 p53 介导的肿瘤抑制中受体-配体相互作用，可以影响疾病进展、衰老和遗传表达的变化。在这里，我们进行了一系列分子模拟，基于 NMR 光谱学确定的与 p53 转录共激活物 CBP 溴结构域复合物的 p53 结构，研究了结合复合物的能量学。基于观察到 p53 中的 K382 乙酰化作为与 CBP 特异性相互作用的基本触发开关，我们评估了来自具有乙酰化和非乙酰化 K382（残基 379-386）的 p53 衍生八肽的模拟中乙酰化对结合的差异影响。模拟的聚类分析表明，游离肽的乙酰化不会显著改变肽在溶液中与 CBP 结合的优选构象的种群。通过 p53 CBP 复合物和游离肽的自由能扰动 (FEP) 模拟将乙酰化的 K382 转化为非乙酰化形式，表明乙酰基对结合的相对贡献为 4.8 kcal/mol。使用 MM-GBSA 方法分析残基对结合能的贡献与 FEP 结果一致，并进一步阐明了 p53 与 CBP 溴结构域选择性结合的起源。
