elelab / trap1_activity Goto Github PK

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

Repository associated to the publication:

S-nitrosylation affects TRAP1 structure and ATPase activity and contributes to mitochondrial homeostasis Fiorella Faienza, Matteo Lambrughi, Salvatore Rizza, Chiara Pecorari, Paola Giglio, Juan Salamanca Viloria, Maria Francesca Allega, Giovanni Chiappetta, Francesca Pacello, Andrea Battistoni, Andrea Rasola, Elena Papaleo, Giuseppe Filomeni, Biochem Pharmacol 2020 Jun;176:113869. doi: 10.1016/j.bcp.2020.113869.

contact person for the repository: Elena Papaleo, elenap-at-cancer.dk

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

The three main folders in the repository contains:

modeller -> the files and scripts to generate the models of the protomers simulations -> templates files for gromacs to run preparation and md along with bash scripts for the preparation steps. The corresponding tratrajectories are deposited in OSF with skipped frames due to size limitation (the full trajectories can be provided upon request) foldx -> input and outputs from foldx calculations psn -> the files and scripts for the protein structure network analysis pca-> the files and scripts for the principal component analysis

N.B. the topology, running input files and trajectories filtered on the protein atoms are available for download in the OSF repository: https://osf.io/wytg2/

N.B. the numbering in the trajectory is shifted so that C516 of Danio rerio (PDB numbering, 4IPE) is C432 in the gromacs files.