Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide
复制标题
结合使用复制交换分子动力学和魔角旋转固态核磁共振波谱模拟来确定膜结合肽的结构和方向
DOI：
10.1021/jp205290t
复制
发表时间：
2011
期刊：
影响因子：
3.3
通讯作者：
and Toshimichi Fujiwara
中科院分区：
文献类型：
--
作者：
Keisuke Ikeda;Tomoshi Kameda;Erisa Harada;Hideo Akutsu;and Toshimichi Fujiwara
我们报道了一种通过魔角旋转固体核磁共振和分子动力学模拟来确定膜肽和膜蛋白复合物结构的方法。首先，低能量结构的mastoparan-X，黄蜂毒液肽，在脂质双层的合奏产生的复制交换分子动力学（REMD）模拟与隐式膜/溶剂模型。接下来，从系综中选择与实验13 C α、Cβ和C′化学位移相容的肽结构。仅13 C α化学位移就足以从实验确定的结构中选择骨架Rmsd为1.08的结构。肽质子和脂质2 H/31 P核之间的偶极耦合是从13 C-取代的2 H/31 P-选择性1H-退磁实验中获得的，用于选择相对于膜的主链和侧链结构。模拟结构与实验结构在深度和方向上一致。REMD模拟可用于补充从固态NMR谱可获得的有限的结构约束。
We report an approach to determining membrane peptides and membrane protein complex structures by magic-angle-spinning solid-state NMR and molecular dynamics simulation. First, an ensemble of low energy structures of mastoparan-X, a wasp venom peptide, in lipid bilayers was generated by replica exchange molecular dynamics (REMD) simulation with the implicit membrane/solvent model. Next, peptide structures compatible with experimental13Cα, Cβ, and C′ chemical shifts were selected from the ensemble. The13Cαchemical shifts alone were sufficient for the selection with backbone rmsd's of ∼0.8 Å from the experimentally determined structure. The dipolar couplings between the peptide protons and lipid2H/31P nuclei were obtained from the13C-observed2H/31P-selective1H-demagnetization experiments for selecting the backbone and side chain structures relative to the membrane. The simulated structure agreed with the experimental one in the depth and orientation. The REMD simulation can be used for supplementing the limited structural constraints obtainable from the solid-state NMR spectra.