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Abualrous ET, Stolzenberg S, Sticht J, Wieczorek M, Roske Y, Günther M, Dähn S, Boesen BB, Calvo MM, Biese C, Kuppler F, Medina-García Á, Álvaro-Benito M, Höfer T, Noé F, Freund C. MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Nat Chem Biol 2023; 19:1196-1204. [PMID: 37142807 PMCID: PMC10522485 DOI: 10.1038/s41589-023-01316-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 03/17/2023] [Indexed: 05/06/2023]
Abstract
Presentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide-MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.
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Affiliation(s)
- Esam T Abualrous
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sebastian Stolzenberg
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marek Wieczorek
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Matthias Günther
- Theoretische Systembiologie (B086), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Steffen Dähn
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benedikt B Boesen
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcos Martínez Calvo
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Charlotte Biese
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Frank Kuppler
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Álvaro Medina-García
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Thomas Höfer
- Theoretische Systembiologie (B086), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
- Microsoft Research AI4Science, Berlin, Germany.
- Department of Physics, Freie Universität Berlin, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, USA.
| | - Christian Freund
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
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