Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations
Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations
复制标题
DOI：
10.1016/j.bbagen.2016.04.006
复制
发表时间：
2016-07-01
影响因子：
3
通讯作者：
Chillemi, Giovanni
中科院分区：
文献类型：
--
作者：
Chandramouli, Balasubramanian;Silvestri, Valentina;Chillemi, Giovanni
背景：人类赖氨酸甲基转移酶Smyd3是SET和MyND结构域蛋白家族的成员，在组蛋白和非组蛋白靶标上都具有严格调控的甲基化活性。Smyd3如何动态调节底物识别的机制尚不完全清楚。方法：我们对全长的人Smyd3进行了分子动力学模拟，在存在(全息)和不存在(Apo)S-腺苷甲硫氨酸(ADOMet)辅助因子的情况下，进行了总计1.2u秒的模拟。通过对Smyd3的几何性质和静电性质的考察，比较了Smyd3在apo和holo两种状态下的动力学特征。结果：Smyd3的C-末端结构域(CTD)在两种状态下具有明显的动力学特征。在脱脂状态下，CTD经历一个大的铰链状的运动，并采样更开放的构型，从而像一个松动的夹子，导致扩大的底物结合缝隙。在全息状态下，CTD表现出受限的运动，而整体结构保持紧凑，类似于一个闭合的夹具。这导致底物结合裂解处的负电位局部增加。此外，目标赖氨酸通道上关键残基的溶剂可及性增加，这对甲基化活性至关重要。结论：我们假设Adobe Met辅助因子起到了钥匙的作用，并将Smyd3锁定在一个封闭的构象中。实际上，辅因子结合限制了CTD的弹性，呈现出一个紧密的具有高负电势的底物结合裂隙，这可能对底物通过远程静电募集产生影响。一般意义：Smyd3中CTD的缺失已被证明取消了组蛋白甲基化的基础活性。我们的研究强调了CTD弹性在形成识别底物结合部位方面的重要性，并支持先前提出的CTD在稳定甲基化活性部位方面的作用。(C)2016爱思唯尔B.V.保留所有权利。
Background: The human lysine methyltransferase Smyd3, a member of the SET and MYND domain containing protein family, harbors methylation activity on both histone and non-histone targets in a tightly regulated manner. The mechanism of how Smyd3 dynamically regulates substrate recognition is still not fully unveiled.Methods: Here, we employed molecular dynamics simulations on full length human Smyd3, performed to a total of 1.2 mu-second, in the presence (holo) and absence (apo) of the S-Adenosyl methionine (AdoMet) cofactor. The dynamical features of Smyd3 in apo and holo states have been examined and compared via examining geometrical and electrostatic properties.Results: The results show a distinct dynamics of the C-terminal domain (CTD) in the two states. In the apo state, the CTD undergoes a large hinge like motion and samples more opened configurations, thus acting like a loosened clamp and resulting in expanded substrate binding crevice. In the holo state, the CTD exhibits a restricted motion while the overall structure remains compact, mimicking a closed clamp. This leads to a localized increase in the negative potential at the substrate binding cleft. Further, solvent accessibility of critical residues at the target lysine access channel, important for methylation activity, is increased.Conclusions: We postulate that AdoMet cofactor acts like a key and locks Smyd3 in a closed conformation. In effect, the cofactor binding restricts the elasticity of the CTD, presenting a compact substrate binding cleft with high negative potential, which may have implications on substrate recruitment via long range electrostatics.General significance: The deletion of the CTD from Smyd3 has been shown to abolish the basal histone methylation activity. Our study highlights the importance of the CTD elasticity in shaping the substrate binding site for recognition and supports the previously proposed role of the CTD in stabilizing the active site for methylation activity. (C) 2016 Elsevier B.V. All rights reserved.