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Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal

Estimating peptide-major histocompatibility complex (pMHC) binding using structural computational methods has an impact on understanding overall immune function triggering adaptive immune responses in MHC class II molecules. We developed a strategy for optimizing pMHC structure interacting with water molecules and for calculating the binding energy of receptor+ligand systems, such as HLA-DR1+HA, HLA-DR1+CLIP, HLA-DR2+MBP and HLA-DR3+CLIP as well as a mono-substitution panel. Taking pMHC's structural properties, we assumed that ∆H >> -T∆S would generate a linear model for estimating relative free energy change, using three semi-empirical quantum methods (PM6, PM7 and FMO-SCC-DFTB3) along with the implicit solvent models, and considering proteins in neutral and charged states. Likewise, we confirmed our approach's effectiveness in calculating binding energies having high correlation with experimental data and low RMSE (< 2 kcal/mol). All in all, our pipeline differentiates weak from strong peptide binders as a reliable method for studying pMHC interactions.