Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating

If the data and/or scripts supplied in this dataset are used, please cite the following references: Simsive et al., Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating, JCIM (2025), https://doi.org/10.1021/acs.jcim.5c01365 Zdorevskyi et al. Catalytic relevance of quinol anion in biological energy conversion by respiratory complex I, bioRxiv (2024), https://doi.org/10.1101/2024.09.06.611712 Zdorevskyi et al. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I, Chem. Sci. (2023), https://doi.org/10.1039/d3sc01427d #################################################################################################################### The dataset lists all input files necessary for launching classical and QM/MM molecular dynamics simulations published in "Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating" by Luka Simsive, Oleksii Zdorevskyi and Vivek Sharma (UH, Finland), https://doi.org/10.1021/acs.jcim.5c01365. Every folder of the dataset represents the respective setup described in Tables S2-S5. Output trajectory files are also uploaded for the selected setups. Dataset structure Classical_MD 500ns_propka 500ns_L3 QM_MM_MD L L_US M M_prime M_prime_US M_US R_prime R_prime_US The simulation protocol is outlined in the Methods section. The folder “Classical_MD” contains 2 subfolders: 500ns_propka (classical MD simulations of the system with the protonation sates obtained from pKa estimates), and 500ns_L3, where protonation states correspond to setup L3, Table S2. Each subdirectory of “QM_MM_MD” contains the respective QM region: L (Table S2), M (Table S3), M_prime (Table S4), R_prime (Table S5). Subfolders “*_US” contain data from umbrella sampling simulations of the respective region.若使用本数据集提供的数据和/或脚本，请引用如下文献： Simsive等人，《呼吸复合物I中带电通道的质子传递：长程效应与构象门控》，《化学信息与建模杂志（Journal of Chemical Information and Modeling，简称JCIM）》，2025年，https://doi.org/10.1021/acs.jcim.5c01365 Zdorevskyi等人，《呼吸复合物I介导的生物能量转换中醌醇阴离子的催化相关性》，bioRxiv，2024年，https://doi.org/10.1101/2024.09.06.611712 Zdorevskyi等人，《线粒体呼吸复合物I中反向转运蛋白样亚基间的横向质子传递》，《化学科学（Chem. Sci.）》，2023年，https://doi.org/10.1039/d3sc01427d 本数据集包含启动经典分子动力学（classical molecular dynamics）与量子力学/分子力学（QM/MM）联合分子动力学模拟所需的全部输入文件，相关成果发表于卢卡·西姆西夫（Luka Simsive）、阿列克谢·兹多列夫斯基（Oleksii Zdorevskyi）与维韦克·夏尔马（Vivek Sharma）（芬兰赫尔辛基大学，UH）的《呼吸复合物I中带电通道的质子传递——长程效应与构象门控》，https://doi.org/10.1021/acs.jcim.5c01365。数据集内的每个文件夹对应表S2至S5中描述的相应模拟体系设置。本数据集还上传了部分选定设置对应的输出轨迹文件。 数据集结构 经典分子动力学（Classical_MD） 500ns_propka 500ns_L3 QM/MM联合分子动力学（QM_MM_MD） L L_US M M_prime M_prime_US M_US R_prime R_prime_US 模拟方案详见方法部分。“经典分子动力学”文件夹包含两个子文件夹：500ns_propka（基于pKa（酸解离常数）的估算值确定质子化状态的体系的经典分子动力学模拟）与500ns_L3，该文件夹内的质子化状态对应表S2中的设置L3。 “QM/MM联合分子动力学”下的每个子目录均对应相应的量子力学区域：L（表S2）、M（表S3）、M_prime（表S4）、R_prime（表S5）。带“*_US”后缀的子文件夹包含对应区域的伞形采样（umbrella sampling）模拟数据。