Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers
Molecular dynamics simulation of NMR relaxation rates and slow dynamics in lipid bilayers
复制标题
DOI：
10.1063/1.1389469
复制
发表时间：
2001-09-08
影响因子：
4.4
通讯作者：
Edholm, O
中科院分区：
文献类型：
--
作者：
Lindahl, E;Edholm, O
通过对二棕榈酰磷脂酰胆碱脂质双层进行 100 ns 分子动力学模拟，我们能够计算烃链 C-H 向量的完整旋转相关函数，并高精度地确定整个脂质分子的旋转扩散。模拟弛豫在 0.1 ps 的时间尺度上已经是强非指数的。相关函数的傅立叶变换产生的数据在 H-2 和 C-13 NMR 实验可访问的相对较窄的频率范围内与报道的自旋晶格弛豫率的 1/根 omega 依赖性一致。发现模拟的弛豫动力学比实验的稍快，我们认为这是由于当前力场的二面角势的有限精度来解释的。通过引入局部参考系，链运动被分为局部二面角转变和整体脂质重新定向。内链异构化主导弛豫，并且可以通过幂律很好地描述。小分子重新取向对衰变的贡献是指数级的，对于脂质长轴的运动（D-垂直于 = 2.9 x 10(7) s(-1)）和绕其旋转（D-平行于 = 3.8 x 10(8) s(-1)）的单独时间尺度而言。超过 100 ns 的均方横向位移（针对层的相对运动进行校正）对应于 323 K 时的长期平移扩散系数 D-lat = 1.2 x 10(-7) cm(2) s(-1)。(C) 2001 美国物理研究所。
By performing a 100 ns molecular dynamics simulation of a dipalmitoylphosphatidylcholine lipid bilayer we are able to calculate the full rotational correlation functions of the hydrocarbon chain C-H vectors and determine rotational diffusion of entire lipid molecules with high accuracy. The simulated relaxation is strongly nonexponential already on time scales from 0.1 ps. Fourier transformation of the correlation functions yields data that in the relatively narrow frequency range accessible to H-2 and C-13 NMR experiments are consistent with the reported 1/root omega dependence of spin-lattice relaxation rates. The simulated relaxation dynamics is found to be slightly faster than experimental, which we suggest is explained by the limited accuracy in dihedral potentials of present force fields. By introducing a local frame of reference, the chain motion is separated into local dihedral transitions and overall lipid reorientation. The internal chain isomerization dominates the relaxation and is well-described by power laws. The small molecular reorientation contribution to the decay is exponential with separate time scales for motions of the lipid long axis (D-perpendicular to = 2.9 x 10(7) s(-1)) and spinning rotation around it (D-parallel to = 3.8 x 10(8) s(-1)). The mean square lateral displacement over 100 ns, corrected for the relative motions of the layers, corresponds to a long-time translational diffusion coefficient of D-lat = 1.2 x 10(-7) cm(2) s(-1) at 323 K. (C) 2001 American Institute of Physics.