DOI: 10.25338/b8q05w
title: N-Glycosylation effects on T cell receptor kinetics

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