elelab / lc3c_ndp52_ge_mutant Goto Github PK

Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

Repository associated to the publication:

Di Rita A, Angelini DF, Maiorino T, Caputo V, Cascella R, Kumar M, Tiberti M, Lambrughi M, Wesch N, Löhr F, Dötsch V, Carinci M, D'Acunzo P, Chiurchiù V, Papaleo E, Rogov VV, Giardina E, Battistini L, Strappazzon F. Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy. Cell Death Differ. 2021 Aug;28(8):2499-2516. doi: 10.1038/s41418-021-00766-3. Epub 2021 Mar 15. PMID: 33723372; PMCID: PMC8329179.

contact person for the repository: Elena Papaleo, [email protected], [email protected]

The repository contains the input data for modeling and simulations, outputs from analyses and associated scripts to reproduce our data.

The MD trajectories have been deposited in OSF due to space limitation. They can be downloaded from here: https://osf.io/48wzq/

More detailed README files are in each subfolder to guide the user.

Please cite our publication if you use the material in this repository.

The main folders in the repository contains:

• modeller_data -> the files and scripts to generate the models of the complexes and the files and scripts to reproduce the model selection for simulations
• simulations_analysis -> folders, scripts, input and outputs to reproduce the analyses of md simulations or metadynamics
• plumednest -> the files to reproduce the metadynamics simulation associated with the publication. The files are deposited in the PLUMED-NEST project ID plumID:22.007 They can be downloaded from here: https://www.plumed-nest.org/eggs/22/007/

NOTES The numbering of the PDB and GRO file of the complex LC3C-NDP52 G->E mutant has been shifted of 100 amino acids with respect to what reported in UNIPROT for practical purposes. Thus E140 will be E240 in the PDB, XTC and GRO files, as an example to orient the reader.