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| Item Type: | Dataset |
|---|---|
| Title: | Data for manuscript: Integrative modelling reveals the structure of the human Mic60-Mic19 subcomplex and its role as a diffusion barrier in mitochondria |
| Creators: |
Rolando, Edoardo  ORCID: https://orcid.org/0009-0001-8276-1406, Nathanail, Evangelia ORCID: https://orcid.org/0009-0004-9579-8074, Clementi, Cecilia ORCID: https://orcid.org/0000-0001-9221-2358 and Daumke, Oliver ORCID: https://orcid.org/0000-0002-6190-1414
|
| Abstract: | The data is provided as a part of the manuscript "Integrative modelling reveals the structure of the human Mic60-Mic19 subcomplex and its role as a diffusion barrier in mitochondria". This dataset contains the initial (input) and final (output) atomic structures for the molecular dynamics simulations reported in [biorxiv link], organized by simulation campaign. Where a simulation was restrained against an artificial catenoid/cylinder membrane-neck surface (a set of dummy "UNK" atoms), that surface is included merged into the same PDB file as extra atoms, so it can be visualized together with the protein in any structure viewer (e.g. PyMOL, VMD). main_model_all_atom/ — Main model, all-atom representation. input_modeller.pdb is the MODELLER-built starting structure. Two production ensembles (30 replicas each) branch from it: output_free/ (flat membrane, no curvature restraint) and input_crista//output_crista/ (curved "crista" branch, restrained against a fixed catenoid surface, included in these files). main_model_calpha/ — Main model, Cα (one bead per residue) representation, restrained against the same crista/catenoid geometry as main_model_all_atom. input/ and output/ each hold 30 structures (one per independent replica), catenoid included. main_model_mlcg/ — Main model, machine-learned coarse-grained (MLCG) representation. input_modeller_5beads.pdb is the CG-mapped starting structure; output/ holds the final structure of each of 5 independent trajectories. alternative_model_all_atom/ — Alternative model, all-atom representation. input_modeller.pdb is the starting structure; output/ holds the final structure of each of 5 independent replicas. cter_martini/ — MARTINI coarse-grained C-terminal steered-dynamics and umbrella-sampling campaign on a curved membrane. input_flat.pdb and input_curved.pdb are the protein+membrane structure before and after the curvature-inducing bending transform; equilibrated_final.pdb is the structure after membrane/solvent equilibration; umbrella_windows/input/ and umbrella_windows/output/ hold the initial and final structure of each of the 60 umbrella-sampling windows; paper_picture_final_snapshot_nowater.pdb is the specific snapshot used for the paper figure. No catenoid restraint is used here — the membrane curvature is physically simulated. diffusion_barrier_calpha/ — Cα diffusion-barrier scan, 14 independent windows varying a restraint-sphere radius (0.25–3.5 nm) used to probe the energetic cost of crossing the crista neck. input/ and output/ each hold one structure per window, catenoid included. Files are named to indicate their campaign, replica/window index, and whether they are an input or output structure. |
| Keywords: | MD simulations, Mic60-Mic19 complex, MICOS complex, Crista junctions, Coarse-grained modeling |
| Source: | Zenodo |
| Publisher: | CERN |
| Date: | 10 August 2026 |
| Official Publication: | https://doi.org/10.5281/zenodo.21871798 |
| Related to: |
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