Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7363, USA.
J Am Chem Soc. 2011 Apr 13;133(14):5357-62. doi: 10.1021/ja110432e. Epub 2011 Mar 23.
Histone lysine methylation (Kme) encodes essential information modulating many biological processes including gene expression and transcriptional regulation. However, the atomic-level recognition mechanisms of methylated histones by their respective adaptor proteins are still elusive. For instance, it is unclear how L3MBTL1, a methyl-lysine histone code reader, recognizes equally well both mono- and dimethyl marks but ignores unmodified and trimethylated lysine residues. We made use of molecular dynamics (MD) and free energy perturbation (FEP) techniques in order to investigate the energetics and dynamics of the methyl-lysine recognition. Isothermal titration calorimetry (ITC) was employed to experimentally validate the computational findings. Both computational and experimental methods were applied to a set of designed "biophysical" probes that mimic the shape of a single lysine residue and reproduce the binding affinities of cognate histone peptides. Our results suggest that, besides forming favorable interactions, the L3MBTL1 binding pocket energetically penalizes both methylation states and has most probably evolved as a "compromise" that nonoptimally fits to both mono- and dimethyl-lysine marks.
组蛋白赖氨酸甲基化 (Kme) 编码了调节许多生物过程的重要信息，包括基因表达和转录调控。然而，甲基化组蛋白与其各自的衔接蛋白之间的原子水平识别机制仍然难以捉摸。例如，目前尚不清楚 L3MBTL1（一种甲基赖氨酸组蛋白编码阅读器）如何能够同样好地识别单甲基和二甲基标记，而忽略未修饰和三甲基化的赖氨酸残基。我们利用分子动力学 (MD) 和自由能微扰 (FEP) 技术来研究甲基赖氨酸的识别的能量和动力学。等温滴定量热法 (ITC) 被用于实验验证计算结果。计算和实验方法都应用于一组设计的“生物物理”探针，这些探针模拟单个赖氨酸残基的形状，并再现同源组蛋白肽的结合亲和力。我们的结果表明，除了形成有利的相互作用外，L3MBTL1 结合口袋在能量上惩罚两种甲基化状态，并且很可能是作为一种“妥协”而进化，这种“妥协”不能最佳地适应单甲基和二甲基赖氨酸标记。
