Molecular dynamics trajectories of pYEEI:SH2 recognition, unbiased, at all-atom resolution.

Set of 772 all-atom trajectories simulated from an unbound (apo) configuration of the human p56 -lck tyrosine kinase SH2 domain with its high-specificity phosphopeptide recognition substrate pYEEI (initial structure based on PDB:1LKK ).  Approximately 24 trajectories spontaneously reach a bound state with ligand RMSD < 2 Â from the crystal. System building and run details are described in [1].

A preliminary version of this dataset have been analyzed and discussed in [1] (approx 200 ns per trajectory were available and used in [1]). 

The trajectories provided here are extended to ~800 ns each, for a total of ~640 μs sampled time. The full dataset is analyzed in [2] with a SOM-based technique.

Notes

These are all-atom simulations (with TIP3P water). Water molecules have been stripped off from these files (filtered).

Not all trajectories have the same length. Some are cut short due to the distributed computing setup.

Frame-to-frame interval is 1 ns.

Acknowledgments

We thank the volunteers of the GPUGRID.net project for donating computing time.

References

[1]  T. Giorgino, I. Buch, and G. De Fabritiis. Visualizing the Induced Binding of SH2-Phosphopeptide, J. Chem. Theory Comput. 2012, 8, 4, 1171-1175. doi:10.1021/ct300003f

[2] Lara Callea, Camilla Caprai, Laura Bonati, Toni Giorgino, Stefano Motta.  Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics. J. Chem. Phys, 2024. https://doi.org/10.1063/5.0225183