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.

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