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The partial dissociation of MHC class I bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1: ERAP1 trimming of MHC I-bound peptides

The partial dissociation of MHC class I bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1: ERAP1 trimming of MHC I-bound peptides
The partial dissociation of MHC class I bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1: ERAP1 trimming of MHC I-bound peptides
Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 process N-terminally extended antigenic precursors for optimal loading onto major histocompatibility complex class I (MHC I) molecules. We and others have demonstrated that ERAP1 processes peptides bound to MHC I, but the underlying mechanism is unknown. To this end, we utilized single-chain trimers (SCT) of the ovalbumin-derived epitope SIINFEKL (SL8) tethered to the H2-Kb MHC I determinant from mouse and introduced three substitutions, E63A, K66A, and W167A, at the A-pocket of the peptide-binding groove in the MHC I heavy chain, which interact with the N termini of peptides. These variants significantly decreased SL8-presenting SCT at the cell surface in the presence of ERAP1, but did not affect overall SCT expression, indicating that ERAP1 trims the SL8 N terminus. Comparison of the X-ray crystal structures of WT and three variant SCTs revealed only minor perturbations of the peptide-binding domain in the variants. However, molecular dynamics simulations suggested that SL8 can dissociate partially within a sub-microsecond timescale, exposing its N terminus to the solvent. We also found that the C terminus of MHC I–bound SL8 remains deeply buried in the F-pocket of MHC I. Furthermore, free-energy calculations revealed that the three SCT variants exhibit lower free-energy barriers of N terminus dissociation than the WT Kb. Taken together, our results are consistent with a previously observed model in which the partial dissociation of bound peptides from MHC I exposes their N terminus to trimming by ERAP1, while their C terminus is anchored at the F-pocket.
Antigen processing, antigen presentation, Major Histocompatibility Complex, H2-Kb, single chain trimer, X-ray crystallography, ERAP1, molecular, free energy calculations, peptide trimming
Papakyriakou, Athanasios
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Reeves, Emma
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Beton, Mary
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Mikolajek, Halina
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Douglas, Leon
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Cooper, Grace
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Elliott, Timothy
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Werner, Jorn M.
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James, Edward
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Papakyriakou, Athanasios
939bc8c9-1693-4530-9099-c55772b22f1d
Reeves, Emma
bd61ff0c-6555-47fd-884f-74dc6105e846
Beton, Mary
2b3c8add-0da9-4405-892b-f4dfbfd4ad9d
Mikolajek, Halina
c394c255-9248-4217-ace9-4a0382bfc0c5
Douglas, Leon
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Cooper, Grace
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Elliott, Timothy
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Werner, Jorn M.
1b02513a-8310-4f4f-adac-dc2a466bd115
James, Edward
7dc1afb7-d326-4050-89fc-1f4e2a1a19a4

Papakyriakou, Athanasios, Reeves, Emma, Beton, Mary, Mikolajek, Halina, Douglas, Leon, Cooper, Grace, Elliott, Timothy, Werner, Jorn M. and James, Edward (2018) The partial dissociation of MHC class I bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1: ERAP1 trimming of MHC I-bound peptides. The Journal of Biological Chemistry. (doi:10.1074/jbc.RA117.000313).

Record type: Article

Abstract

Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 process N-terminally extended antigenic precursors for optimal loading onto major histocompatibility complex class I (MHC I) molecules. We and others have demonstrated that ERAP1 processes peptides bound to MHC I, but the underlying mechanism is unknown. To this end, we utilized single-chain trimers (SCT) of the ovalbumin-derived epitope SIINFEKL (SL8) tethered to the H2-Kb MHC I determinant from mouse and introduced three substitutions, E63A, K66A, and W167A, at the A-pocket of the peptide-binding groove in the MHC I heavy chain, which interact with the N termini of peptides. These variants significantly decreased SL8-presenting SCT at the cell surface in the presence of ERAP1, but did not affect overall SCT expression, indicating that ERAP1 trims the SL8 N terminus. Comparison of the X-ray crystal structures of WT and three variant SCTs revealed only minor perturbations of the peptide-binding domain in the variants. However, molecular dynamics simulations suggested that SL8 can dissociate partially within a sub-microsecond timescale, exposing its N terminus to the solvent. We also found that the C terminus of MHC I–bound SL8 remains deeply buried in the F-pocket of MHC I. Furthermore, free-energy calculations revealed that the three SCT variants exhibit lower free-energy barriers of N terminus dissociation than the WT Kb. Taken together, our results are consistent with a previously observed model in which the partial dissociation of bound peptides from MHC I exposes their N terminus to trimming by ERAP1, while their C terminus is anchored at the F-pocket.

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J. Biol. Chem.-2018-Papakyriakou-jbc.RA117.000313 - Accepted Manuscript
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Accepted/In Press date: 22 March 2018
e-pub ahead of print date: 29 March 2018
Keywords: Antigen processing, antigen presentation, Major Histocompatibility Complex, H2-Kb, single chain trimer, X-ray crystallography, ERAP1, molecular, free energy calculations, peptide trimming

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Local EPrints ID: 420200
URI: https://eprints.soton.ac.uk/id/eprint/420200
PURE UUID: 1b906b15-6e1a-44ff-9d27-a9cdae45b8e3
ORCID for Athanasios Papakyriakou: ORCID iD orcid.org/0000-0003-3931-6232
ORCID for Halina Mikolajek: ORCID iD orcid.org/0000-0003-0776-9974
ORCID for Timothy Elliott: ORCID iD orcid.org/0000-0003-1097-0222
ORCID for Jorn M. Werner: ORCID iD orcid.org/0000-0002-4712-1833

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Date deposited: 02 May 2018 16:30
Last modified: 29 Mar 2019 05:01

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Contributors

Author: Athanasios Papakyriakou ORCID iD
Author: Emma Reeves
Author: Mary Beton
Author: Leon Douglas
Author: Grace Cooper
Author: Timothy Elliott ORCID iD
Author: Jorn M. Werner ORCID iD
Author: Edward James

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