Data analyzed for manuscript "Understanding Allosteric Stabilization of pMHC by Peptide Ligands Through Molecular Dynamics Simulations"

Description: This dataset supplements the manuscript "Understanding Allosteric Stabilization of pMHC by Peptide Ligands Through Molecular Dynamics Simulations", and contains data tables generated through analysis of molecular dynamics simulations trajectories of peptide-free and peptide-loaded HLA-A*02:01 structures loaded with three different 10mer peptides (PDB IDs: 3UTQ, 5N1Y, 5C0F). Please refer to the manuscript/publication for more details on the context of the study, and how these data were generated. Simulation conditions: Software: gromacs 2023.4 Force-field: AMBER99SB-ILDN Explicit solvent with neutralization with ions at 0.15M concentration. Time step: 4fs time-step (HMR) NPT ensemble (310K and 1 bar) Repeats: 3 Simulation length: each repeat for 750 ns Total simulation length: 9 microseconds Short descriptions of data frames (.csv files): df_rmsf_2024_12_30.csv: Root Mean Square Fluctuations (RMSFs) of alpha-carbons, following superposition of all alpha-carbon coordinates onto the initial conformation. df_rmsf_pep_2024_12_29.csv: RMSFs of peptide alpha-carbons, following superposition of peptide-binding groove conformations onto the initial conformation. df_cons_pairs_saved_2025_02_01.csv: "Consistent pairs" of residues exhibiting significantly similar interaction energies across replicas based on one-way ANOVA. In other words, pairs whose interaction energies did not differ significantly (p > 0.05) across replica simulations. p values are included as well. df_sig_aff_pairs_loaded_2025_02_01.csv: Consistent pairs that showed statistically-significant (p < 0.05, Student’s t-test) energy shifts with an absolute interaction energy difference of 2 kcal/mol upon peptide binding toward attractive or repulsive ranges. p values are included as well. df_bc_equil_2025_02_01.csv: Betweenness centralities (BCs) of each node (amino acids) in the constructed protein energy networks (PENs) in each conformation in each simulation trajectory. df_bc_equil_cons_resids_2025_02_01.csv: Betweenness centralities, also including "consistent BC residues" with consistent betweenness centralities (BCs) across replica simulations. Identified using the same procedure described above for df_cons_pairs_saved_2025_02_01.csv. p values are included as well. If no p value is listed, there respective residue is not a consistent BC residue. df_bc_sigaff_resids_2025_02_01.csv: Consistent BC residues with BC levels with statistically-significant BC shifts (p < 0.05, one-way ANOVA) upon peptide-binding. In other words, residues whose BCs did not differ significantly (p > 0.05) between peptide-free simulations and at least one peptide-loaded system simulation. p values are included as well. Please note that the lowest floating point number that can be computed by the machine on which the analyses were run is -1.7976931348623157e+308. Hence, if you see a p value of zero (0.0) in any data frame, this means the real value is below this lower threshold.