Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania, 18015.
J Comput Chem. 2020 Feb 15;41(5):415-420. doi: 10.1002/jcc.26032. Epub 2019 Jul 22.
The double electron-electron resonance (DEER) is a powerful structural biology technique to obtain distance information in the range of 18 to 80 å by measuring the dipolar coupling between two unpaired electron spins. The distance distributions obtained from the experiment provide valuable structural information about the protein in its native environment that can be exploited using restrained ensemble molecular dynamics (reMD) simulations. We present a new tool DEER Facilitator in CHARMM-GUI that consists of two modules Spin-Pair Distributor and reMD Prepper to setup simulations that utilize information from DEER experiments. Spin-Pair Distributor provides a web-based interface to calculate the spin-pair distance distribution of labeled sites in a protein using MD simulations. The calculated distribution can be used to guide the selection of the labeling sites in experiments as well as validate different protein structure models. reMD Prepper facilities the setup of reMD simulations using different types of spin labels in four different environments including vacuum, solution, micelle, and bilayer. The applications of these two modules are demonstrated with several test cases. Spin-Pair Distributor and reMD Prepper are available at http://www.charmm-gui.org/input/deer and http://www.charmm-gui.org/input/deerre. DEER Facilitator is expected to facilitate advanced biomolecular modeling and simulation, thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems based on experimental DEER data. © 2019 Wiley Periodicals, Inc.
双电子电子共振（DEER）是一种强大的结构生物学技术，通过测量两个未配对电子自旋之间的偶极耦合，可以获得 18 至 80Å范围内的距离信息。从实验中获得的距离分布提供了关于蛋白质在其天然环境中的有价值的结构信息，可以利用约束整体分子动力学（reMD）模拟来利用这些信息。我们在 CHARMM-GUI 中引入了一种新的工具 DEER Facilitator，它由两个模块 Spin-Pair Distributor 和 reMD Prepper 组成，用于设置利用 DEER 实验信息的模拟。Spin-Pair Distributor 提供了一个基于网络的界面，可使用 MD 模拟计算蛋白质中标记位点的自旋对距离分布。计算出的分布可用于指导实验中标记位点的选择，也可用于验证不同的蛋白质结构模型。reMD Prepper 可在包括真空、溶液、胶束和双层在内的四种不同环境中使用不同类型的自旋标记设置 reMD 模拟。通过几个测试案例演示了这两个模块的应用。Spin-Pair Distributor 和 reMD Prepper 可在 http://www.charmm-gui.org/input/deer 和 http://www.charmm-gui.org/input/deerre 获得。DEER Facilitator 有望促进高级生物分子建模和模拟，从而基于实验 DEER 数据提高对复杂生物分子系统的结构和动态的理解。© 2019 威立出版社
