Table · dataset · 2026
KIMMDY_COLLAGEN_HAT_input_files
Listed in Edmond
Description
These files were originally generated by Eric Hartmann and uploaded for data availability in this dataset. Gromacs Structure Files for Collagen Fibrils as used in doi.org/10.1101/2025.07.02.662624 github.com/graeter-group/kimmdy-examples/tree/main/collagen_HAT Simulations of consecutive HAT reactions are conducted with an all-atom model of a Rattus norvegicus collagen fibril (PDB ID: 3HR2) comprised of 41 triple helices spanning one central overlap and one gap region for a total of roughly 320 000 pro- tein atoms.
ColBuilder [1] was used to generate a model with N- and C-terminal PYD crosslinks with a connectivity of 9.C-5.B-944.B and 1047.C-1047.A-98.B, respec- tively. Furthermore, all Phe and Tyr residues were randomly mutated to either DOPA deprotonated at the Cϵ (DO1) or Cζ (DO2) hydroxy group. Since no quantitative experimental data of the oxidation state of Phe and Tyr residues has been published, these mutations serve to treat all potential DOPA sites as equally strong radical scavengers.
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The fibril was solvated, salt ions were added to neutralize the system and reach a concentration of 150 mM. After an energy minimization using the steepest descent method, a 10 ns NVT equilibration and then a 10 ns NpT equilibration were performed. Homolytic breaks at the previously identified PYD short-arm Cα-Cβ sacrificial bond ([2]) were introduced to the equilibrated structure using KIMMDY.
Overall, 12 structures with different break patterns of four breaks each for the 16 PYD crosslinks were generated, taking care to include each residue three times and excluding crosslinks within 40 ˚A of each other or on the same triple helix. The radical-containing structures were equilibrated in the NpT ensemble for another 10 ns. [1] Obarska-Kosinska, A., Rennekamp, B., ¨Unal, A. & Gr¨ater, F. Colbuilder: A server to build collagen fibril models.
Biophysical Journal 120, 3544–3549 (2021). URL sciencedirect.com/science/article/pii/S0006349521005610. [2] Rennekamp, B. et al. Collagen breaks at weak sacrificial bonds taming its mechanoradicals.
Nature Communications 14, 2075 (2023).
Links
Where it is published
- Dataverse dataset page edmond.mpg.de/dataset.xhtml?persistentId=doi%3A10.17617%2F3.X50DK9 ↗
landing page · from edmond mpdl mpg de
- DOI doi.org/10.17617/3.x50dk9 ↗
DOI / persistent id · from edmond mpdl mpg de
Catalogue records · 1
- Dataverse API edmond.mpg.de/api/datasets/:persistentId/?persistentId=doi%3A10.17617%2F3.X5… ↗
metadata API · from edmond mpdl mpg de
Topics
Provenance · 2 source records, 19 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Edmond | doi:10.17617/3.X50DK9 | 11 d ago | JSON v1 |
| Edmond | doi:10.17617/3.X50DK9 | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].local:field:astronomy | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:materials-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:physics | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · edmond mpg de | connector:edmond_mpg_de@1.0.0 | /subjects |
| created_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| description | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /description |
| publication_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| title | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | /name |
| updated_date | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 | |
| version_label | source · edmond mpdl mpg de | connector:edmond_mpdl_mpg_de@1.0.0 |