Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95.
Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95.
复制标题
DOI：
10.1038/s41467-018-06133-0
复制
发表时间：
2018-09-13
影响因子：
16.6
通讯作者：
Sanabria H
中科院分区：
文献类型：
--
作者：
Yanez Orozco IS;Mindlin FA;Ma J;Wang B;Levesque B;Spencer M;Rezaei Adariani S;Hamilton G;Ding F;Bowen ME;Sanabria H
先前对PSD-95的n端PDZ串联的研究产生了不同的模型，并且未能确定稳定结构的域间接触。我们使用集合和单分子FRET以及复制交换分子动力学来充分表征能量景观。模拟和实验确定了两种构象：一种是由盐桥稳定的小接触界面的开放构象，另一种是由表面暴露的疏水残留物稳定的大接触界面的封闭构象。两个界面均得到了实验验证。区域间接触靠近结合袋可以解释观察到的构象和结合之间的耦合。构象之间的低能垒允许亚毫秒级的动力学，这在以前的NMR和FRET研究中是时间平均的。此外，由于晶体结构在模拟中很少采样，小的接触界面可能被晶格接触覆盖。我们的混合方法可以识别多结构域蛋白中丰富但经常被动态平均所掩盖的瞬态结构域间相互作用。蛋白质内部生物相关的弱和瞬态结构域间相互作用很难分析。在这里，作者结合多尺度分子动力学模拟和高精度FRET实验来表征PSD-95串联PDZ结构域之间的相互作用，揭示了以前隐藏的构象状态。
Previous studies of the N-terminal PDZ tandem from PSD-95 produced divergent models and failed to identify interdomain contacts stabilizing the structure. We used ensemble and single-molecule FRET along with replica-exchange molecular dynamics to fully characterize the energy landscape. Simulations and experiments identified two conformations: an open-like conformation with a small contact interface stabilized by salt bridges, and a closed-like conformation with a larger contact interface stabilized by surface-exposed hydrophobic residues. Both interfaces were confirmed experimentally. Proximity of interdomain contacts to the binding pockets may explain the observed coupling between conformation and binding. The low-energy barrier between conformations allows submillisecond dynamics, which were time-averaged in previous NMR and FRET studies. Moreover, the small contact interfaces were likely overridden by lattice contacts as crystal structures were rarely sampled in simulations. Our hybrid approach can identify transient interdomain interactions, which are abundant in multidomain proteins yet often obscured by dynamic averaging. Biologically relevant weak and transient interdomain interactions within proteins are difficult to analyze. Here, the authors combine multiscale molecular dynamics simulations and high-precision FRET experiments to characterize interactions between the tandem PDZ domains of PSD-95, revealing previously hidden conformational states.
登录
查看更多内容
影响因子：
64.8
作者：
Bouvignies, Guillaume;Vallurupalli, Pramodh;Hansen, D. Flemming;Correia, Bruno E.;Lange, Oliver;Bah, Alaji;Vernon, Robert M.;Dahlquist, Frederick W.;Baker, David;Kay, Lewis E.
通讯作者：
Kay, Lewis E.
影响因子：
3.3
作者：
Kalinin, Stanislav;Valeri, Alessandro;Seidel, Claus A. M.
通讯作者：
Seidel, Claus A. M.
影响因子：
9.2
作者：
Fanning, AS;Anderson, JM
通讯作者：
Anderson, JM
影响因子：
14.7
作者：
Ha T;Tinnefeld P
通讯作者：
Tinnefeld P
影响因子：
46.9
作者：
通讯作者：
--