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

Carlos A. Ortiz-Mahecha, Hugo J. Bohórquez, William A. Agudelo, Manuel A. Patarroyo, Manuel E. Patarroyo, Carlos F. Suárez

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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 monosubstitution panel. Taking pMHC's structural properties, we assumed that ΔH ≫ -TΔS would generate a linear model for estimating relative free energy change, using three semiempirical 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 root-mean-square error (<2 kcal/mol). All in all, our pipeline differentiates weak from strong peptide binders as a reliable method for studying pMHC interactions.

Original languageEnglish (US)
JournalJournal of Chemical Information and Modeling
StatePublished - Nov 20 2019

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Chemical Engineering
  • Computer Science Applications
  • Library and Information Sciences


Dive into the research topics of 'Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal'. Together they form a unique fingerprint.

Cite this