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NMR spectroscopy reveals unexpected structural variation at the protein–protein interface in MHC class I molecules

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Abstract

β2-Microglobulin (β2m) is a small, monomorphic protein non-covalently bound to the heavy chain (HC) in polymorphic major histocompatibility complex (MHC) class I molecules. Given the high evolutionary conservation of structural features of β2m in various MHC molecules as shown by X-ray crystallography, β2m is often considered as a mere scaffolding protein. Using nuclear magnetic resonance (NMR) spectroscopy, we investigate here whether β2m residues at the interface to the HC exhibit changes depending on HC polymorphisms and the peptides bound to the complex in solution. First we show that human β2m can effectively be produced in deuterated form using high-cell-density-fermentation and we employ the NMR resonance assignments obtained for triple-labeled β2m bound to the HLA-B*27:09 HC to examine the β2m-HC interface. We then proceed to compare the resonances of β2m in two minimally distinct subtypes, HLA-B*27:09 and HLA-B*27:05, that are differentially associated with the spondyloarthropathy Ankylosing Spondylitis. Each of these subtypes is complexed with four distinct peptides for which structural information is already available. We find that only the resonances at the β2m-HC interface show a variation of their chemical shifts between the different complexes. This indicates the existence of an unexpected plasticity that enables β2m to accommodate changes that depend on HC polymorphism as well as on the bound peptide through subtle structural variations of the protein-protein interface.

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Abbreviations

OD600nm :

Optical density of the culture at 600 nm

MHC:

Major histocompatibility complex

HLA:

Human leucocyte antigen

β2m:

Beta-2-microglobulin

HC:

Heavy chain of an MHC class I molecule

TROSY:

Transverse relaxation optimized spectroscopy

HSQC:

Heteronuclear single quantum correlation

NMR:

Nuclear magnetic resonance

HCDF:

High cell density fermentation

BMRB:

BioMagResBank

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Acknowledgments

We thank Dr. B. Loll (Freie Universität Berlin) for providing us with unpublished information on β2m residues in an X-ray structure obtained at room temperature and Dr. M. Dorn for help with improving the HCDF. Support from the Leibniz-Institut für Molekulare Pharmakologie (FMP) is gratefully acknowledged. The work was funded by the Deutsche Forschungsgemeinschaft (SCHM880/9-1, UC8/2-1).

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Authors and Affiliations

  1. Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany

    Monika Beerbaum, Martin Ballaschk, Natalja Erdmann, Anne Diehl & Peter Schmieder

  2. Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Thielallee 73, 14195, Berlin, Germany

    Christina Schnick, Barbara Uchanska-Ziegler & Andreas Ziegler

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  1. Monika Beerbaum
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  2. Martin Ballaschk
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  3. Natalja Erdmann
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  4. Christina Schnick
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  5. Anne Diehl
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  6. Barbara Uchanska-Ziegler
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  7. Andreas Ziegler
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  8. Peter Schmieder
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Correspondence to Peter Schmieder.

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Beerbaum, M., Ballaschk, M., Erdmann, N. et al. NMR spectroscopy reveals unexpected structural variation at the protein–protein interface in MHC class I molecules. J Biomol NMR 57, 167–178 (2013). https://doi.org/10.1007/s10858-013-9777-z

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  • DOI: https://doi.org/10.1007/s10858-013-9777-z

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