The repository contains data for modelling of slightly oxidized model mitochondrial membrane. Here we put models of monohydroperoxides of tetralinoleoyl cardiolipin as well as models of two BODIPY-based dyes sensitive to lipid peroxidation.
The deposited data supplements the original research:
K. G. Lyamzaev, N. V. Sumbatyan, A. M. Nesterenko, E. G. Kholina, V. Natalia, S. Heinz-Jürgen, A. Y. Mulkidjanian, and B. V. Chernyak, Mitoclox: A novel mitochondria-targeted fluorescent probe for tracing lipid peroxidation, Oxidative Medicine and Cellular Longevity, vol. 2019, p. 9710208, 2019. [doi]
This is an example system containing PLPC, PSLPE, POPC, oxidized TCLC and MitoCLOx dye.
Into the ff.construction folder we put the protocols for parametrization for BODIPY-based dye and hydroperoxide of lynoleic acid. The forcefield folder contains ready GROMACS topologies and all files needed for compiling GROMACS binary file with the sample system. In the model.bilayers there are many subfolders with different types of mitochondrial model membranes, which differs with the type of lynoleic acid hydroperoxides in the TLCL molecules.
Alexey Nesterenko
- ResearcherID: C-8646-2012
- Scholar Profile: A.M. Nesterenko
- RG profile: Alexey Nesterenko
Ekaterina Kholina
- ResearcherID: F-8720-2018