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Related Experiment Video

Updated: Jan 24, 2026

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
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Studying MHC Class II Peptide Loading and Editing In Vitro.

AeRyon Kim1, Isabel Emiko Ishizuka2, Isamu Z Hartman3

  • 1Department of Inflammation and Oncology, Amgen Research, Amgen Inc., South San Francisco, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|June 1, 2019
PubMed
Summary

Investigating human leukocyte antigen (HLA)-DM

Keywords:
BIAcore surface plasmon resonance (SPR)Fluorescent peptideGentle SDS-PAGE assayHLA-DM editingKinetic studiesPeptide binding to HLA-DRTryptophan fluorescence assay

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Area of Science:

  • Immunology
  • Molecular Biology
  • Biochemistry

Background:

  • Human leukocyte antigen (HLA)-DM plays a crucial role in selecting immunodominant epitopes.
  • Understanding epitope selection mechanisms requires examining the biophysical interactions of MHC class II molecules with antigenic peptides and the influence of HLA-DM.

Purpose of the Study:

  • To describe in vitro methods for measuring peptide binding to HLA-DR molecules.
  • To investigate the effects of HLA-DM on these peptide-MHC interactions.

Main Methods:

  • Gentle SDS-PAGE Assay for qualitative assessment of peptide-MHC class II complex formation.
  • Kinetic analysis using fluorescently labeled peptides and G50 spin columns.
  • Real-time kinetic analysis via BIAcore Surface Plasmon Resonance (SPR) with unlabeled peptides.
  • Intrinsic tryptophan fluorescence assay for studying HLA-DM and MHC class II transient interactions.

Main Results:

  • The study details methods to quantify peptide binding affinity and kinetics to HLA-DR molecules.
  • The impact of HLA-DM on peptide binding dynamics to MHC class II molecules can be assessed.
  • Transient interactions between HLA-DM and MHC class II molecules can be characterized.

Conclusions:

  • Established in vitro methods allow for detailed biophysical characterization of peptide-MHC class II interactions.
  • These methods facilitate the study of HLA-DM's role in modulating epitope selection.
  • A comprehensive understanding of these molecular mechanisms is essential for advancing immunology and related fields.