Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
SCAI-SuperComputing Applications and Innovation Department, CINECA ,Via dei Tizii 6, 00185 Rome, Italy.
J Chem Inf Model. 2016 Dec 27;56(12):2467-2475. doi: 10.1021/acs.jcim.6b00652. Epub 2016 Dec 13.
Smyd2, the SET and MYND domain containing protein lysine methyltransferase, targets histone and nonhistone substrates. Methylation of nonhistone substrates has direct implications in cancer development and progression. Dynamic regulation of Smyd2 activity and the structural basis of broad substrate specificity still remain elusive. Herein, we report on extensive molecular dynamics simulations on a full length Smyd2 in the presence and absence of AdoMet cofactor (covering together 1.3 μs of sampling), and the accompanying conformational transitions. Additionally, dynamics of the C-terminal domain (CTD) and structural features of substrate crevices of Smyd2 and Smyd3 are compared. The CTD of Smyd2 exhibits conformational flexibility in both states. In the holo form, however, it undergoes larger hinge motions resulting in more opened configurations than the apo form, which is confined around the partially open starting X-ray configuration. AdoMet binding triggers increased elasticity of the CTD leading Smyd2 to adopt fully opened configurations, which completely exposes the substrate binding crevice. These long-range concerted motions highlight Smyd2's ability to target substrates of varying sizes. Substrate crevices of Smyd2 and Smyd3 show distinct features in terms of spatial, hydration, and electrostatic properties that emphasize their characteristic modes of substrates interaction and entry pathways for inhibitor binding. On the whole, our study shows how the elasticity and hinge motion of the CTD regulate its functional role and underpin the basis of broad substrate specificity of Smyd2. We also highlight the specific structural principles that guide substrate and inhibitor binding to Smyd2 and Smyd3.
Smyd2 是一种含有 SET 和 MYND 结构域的赖氨酸甲基转移酶蛋白，其作用靶点为组蛋白和非组蛋白底物。非组蛋白底物的甲基化直接影响癌症的发生和发展。Smyd2 活性的动态调控和广泛的底物特异性的结构基础仍然难以捉摸。在此，我们报告了在存在和不存在 AdoMet 辅因子的情况下（总共涵盖 1.3μs 的采样），对全长 Smyd2 进行广泛的分子动力学模拟，以及伴随的构象转变。此外，还比较了 Smyd2 和 Smyd3 的 C 端结构域（CTD）的动力学和底物裂隙的结构特征。Smyd2 的 CTD 在两种状态下都表现出构象灵活性。然而，在全酶形式下，它经历更大的铰链运动，导致更开放的构象，而apo 形式则局限于部分开放的起始 X 射线构象。AdoMet 结合触发 CTD 的弹性增加，导致 Smyd2 采用完全开放的构象，完全暴露底物结合裂隙。这些长程协同运动突出了 Smyd2 靶向不同大小底物的能力。Smyd2 和 Smyd3 的底物裂隙在空间、水合和静电特性方面具有不同的特征，强调了它们与底物相互作用的特征模式和抑制剂结合的进入途径。总的来说，我们的研究表明 CTD 的弹性和铰链运动如何调节其功能作用，并为 Smyd2 广泛的底物特异性提供了基础。我们还强调了指导 Smyd2 和 Smyd3 底物和抑制剂结合的特定结构原则。
