Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.
Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.
复制标题
DOI：
10.1021/jp3110369
复制
发表时间：
2013-05-02
影响因子：
3.3
通讯作者：
Islam, Shahidul M.
中科院分区：
文献类型：
--
作者：
Roux, Benoit;Islam, Shahidul M.
DEER（双电子电子共振）光谱是一种强大的脉冲ESR（电子自旋共振）技术，允许在蛋白质的天然环境中确定定点氮氧标记位点之间的自旋-自旋距离直方图。然而，将ESR/DEER数据纳入结构细化是具有挑战性的，因为来自大量距离直方图的信息是复杂且高度耦合的。在这里，一种新的约束系综分子动力学模拟方法的发展，同时将信息从多个ESR/DEER距离直方图。对T4溶菌酶中插入的3个耦合自旋标记的说明性测试表明，该方法有效地将实验距离分布强加在该系统中。通过约束系综模拟研究了自旋标记中χ 1和χ 2二面体的不同旋光异构态。使用这种方法，它是希望从ESR/DEER实验的实验约束可以用来细化生物系统的结构特性。
DEER (double electron electron resonance) spectroscopy is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of spin-spin distance histograms between site-directed nitroxide label sites on a protein in their native environment. However, incorporating ESR/DEER data in structural refinement is challenging because the information from the large number of distance histograms is complex and highly coupled. Here, a novel restrained-ensemble molecular dynamics simulation method is developed to incorporate the information from multiple ESR/DEER distance histograms simultaneously. Illustrative tests on 3 coupled spin-labels inserted in T4 lysozyme show that the method efficiently imposes the experimental distance distribution in this system. Different rotameric states of the χ1 and χ2 dihedrals in the spin-labels are also explored by restrained ensemble simulations. Using this method, it is hoped that experimental restraints from ESR/DEER experiments can be used to refine structural properties of biological systems.
登录
查看更多内容
影响因子：
3.4
作者：
Kim, Taehoon;Jo, Sunhwan;Im, Wonpil
通讯作者：
Im, Wonpil
影响因子：
2.9
作者：
Mchaourab, HS;Kálai, T;Hubbell, WL
通讯作者：
Hubbell, WL
影响因子：
5.7
作者：
Mchaourab, Hassane S.;Steed, P. Ryan;Kazmier, Kelli
通讯作者：
Kazmier, Kelli
影响因子：
8
作者：
Guo, Zhefeng;Cascio, Duilio;Hubbell, Wayne L.
通讯作者：
Hubbell, Wayne L.
影响因子：
64.8
作者：
Lindorff-Larsen, K;Best, RB;Vendruscolo, M
通讯作者：
Vendruscolo, M