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N-Glycosylation effects on T cell receptor kinetics

Citation

Rollins, Zachary; Harris, Bradley; George, Steven; Faller, Roland (2021), N-Glycosylation effects on T cell receptor kinetics, Dryad, Dataset, https://doi.org/10.25338/B8Q05W

Abstract

This methodology is an atomic-level investigation of the physiochemical effects of glycosylation on TCR dissociation kinetics. The force-dependent bond lifetime and bond strength of the DMF5 T Cell Receptor (TCR) to the MART1 peptide-Major Histocompatibility Complexes (pMHCs) were simulated using Steered Molecular Dynamics. N-glycsoylated and aglycosylated configurations were compared in triplicate.  This data set contains atomic structure of the TCR and pMHC (.gro files), atomic interactions between the TCR and pMHC (hmap & cmap .csv files), and rendered trajecories of the pulling simulations (.mp4).

Methods

Data was collected and processed on high performance computers (hpc1/hpc2) at the University of California, Davis College of Engineering.

Usage Notes

  1. The trajectories for the SMD pulling simulations were compiled into videos with 10 ps time steps including the raw trajectory and the projected princriple component trajectories
    • aglyco_trj_50ns.mp4, aglyco_pc1_50ns.mp4, aglyco_pc2_50ns.mp4, aglyco_pc3_50ns.mp4
    • aglyco_trj_60ns.mp4, aglyco_pc1_60ns.mp4, aglyco_pc2_60ns.mp4, aglyco_pc3_60ns.mp4
    • aglyco_trj_70ns.mp4, aglyco_pc1_70ns.mp4, aglyco_pc2_70ns.mp4, aglyco_pc3_70ns.mp4
    • glyco_trj_50ns.mp4, glyco_pc1_50ns.mp4, glyco_pc2_50ns.mp4, glyco_pc3_50ns.mp4
    • glyco_trj_60ns.mp4, glyco_pc1_60ns.mp4, glyco_pc2_60ns.mp4, glyco_pc3_60ns.mp4
    • glyco_trj_70ns.mp4, glyco_pc1_70ns.mp4, glyco_pc2_70ns.mp4, glyco_pc3_70ns.mp4
  2. High resolution hydrogen bond maps (function of simulation time and reaction coordinate) and corresponding CSV files with all interactions
    • aglyco_50ns_hbond_occupancy_t.png, aglyco_50ns_hbond_occupancy_x.png, aglyco_50ns_hmap.csv
    • aglyco_60ns_hbond_occupancy_t.png, aglyco_60ns_hbond_occupancy_x.png, aglyco_60ns_hmap.csv
    • aglyco_70ns_hbond_occupancy_t.png, aglyco_70ns_hbond_occupancy_x.png, aglyco_70ns_hmap.csv
    • glyco_50ns_hbond_occupancy_t.png, glyco_50ns_hbond_occupancy_x.png, glyco_50ns_hmap.csv
    • glyco_60ns_hbond_occupancy_t.png, glyco_60ns_hbond_occupancy_x.png, glyco_60ns_hmap.csv
    • glyco_70ns_hbond_occupancy_t.png, glyco_70ns_hbond_occupancy_x.png, glyco_70ns_hmap.csv
  3. High resolution Lennard-Jones contact maps (function of simulation time and reaction coordinate) and corresponding CSV files with all interactions
    • aglyco_50ns_contact_occupancy_t.png, aglyco_50ns_contact_occupancy_x.png, aglyco_50ns_cmap.csv
    • aglyco_60ns_contact_occupancy_t.png, aglyco_60ns_contact_occupancy_x.png, aglyco_60ns_cmap.csv
    • aglyco_70ns_contact_occupancy_t.png, aglyco_70ns_contact_occupancy_x.png, aglyco_70ns_cmap.csv
    • glyco_50ns_contact_occupancy_t.png, glyco_50ns_contact_occupancy_x.png, glyco_50ns_cmap.csv
    • glyco_60ns_contact_occupancy_t.png, glyco_60ns_contact_occupancy_x.png, glyco_60ns_cmap.csv
    • glyco_70ns_contact_occupancy_t.png, glyco_70ns_contact_occupancy_x.png, glyco_70ns_cmap.csv
  4. Starting configurations for SMD of aglycosylated and N-glycosylated structures. These structures can be visualized using any standard molecular viewing software (e.g., VMD, Chimera, PyMOL, etc.).
    • aglyco_50ns.gro, aglyco_60ns.gro, aglyco_70ns.gro
    • glyco_50ns.gro, glyco_60ns.gro, glyco_70ns.gro
  5. Parwise Tukey HSD Post-Hoc Analysis
    • Total_HBonds_Contacts_Stats_Para1.xlsx
    • RMSF_stats.xlsx