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.