KIMMDY_COLLAGEN_HAT_input_files

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

https://doi.org/10.1101/2025.07.02.662624

https://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.
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
https://www.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).