N-Glycosylation effects on T cell receptor kinetics
Data files
Dec 03, 2021 version files 861.25 MB
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aglyco_50ns_cmap.csv
90.43 MB
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aglyco_50ns_hmap.csv
979.66 KB
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aglyco_50ns.gro
577.02 KB
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aglyco_60ns_cmap.csv
24.53 MB
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aglyco_60ns_hmap.csv
223.21 KB
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aglyco_60ns.gro
577.02 KB
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aglyco_70ns_cmap.csv
51.16 MB
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aglyco_70ns_hmap.csv
519.97 KB
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aglyco_70ns.gro
577.02 KB
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glyco_50ns_cmap.csv
467.75 MB
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glyco_50ns_hmap.csv
6.37 MB
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glyco_50ns.gro
673.28 KB
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glyco_60ns_cmap.csv
107.54 MB
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glyco_60ns_hmap.csv
1.26 MB
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glyco_60ns.gro
673.28 KB
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glyco_70ns_cmap.csv
105.40 MB
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glyco_70ns_hmap.csv
1.29 MB
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glyco_70ns.gro
673.28 KB
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RMSF_Stats.xlsx
16.02 KB
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Total_HBonds_Contacts_Stats_Para1.xlsx
18.86 KB
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).
Data was collected and processed on high performance computers (hpc1/hpc2) at the University of California, Davis College of Engineering.
- 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
- 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
- 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
- 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
- Parwise Tukey HSD Post-Hoc Analysis
- Total_HBonds_Contacts_Stats_Para1.xlsx
- RMSF_stats.xlsx