Key Points
There are cross-species features of the N-terminal extension of peptides bound by MHC class I.
The polymorphic A pocket residues have pros and cons to the peptide extension.
The N-terminal extension of the peptide does not exceed three residues.
Visual Abstract
Abstract
Antigenic peptide presentation by the MHC is essential for activating T cells. The current view is that the peptide termini are tethered within the closed Ag-binding groove of MHC class I (MHC-I). Recently, the N-terminal extension mode of peptide presentation has been observed in human MHC-I (HLA-I). In this study, we found that the N terminus of the long peptide can extend beyond the groove of swine MHC-I (SLA-1*0401), confirming that this phenomenon can occur across species. Removal of the N-terminal extra (P-1) residue of the RW12 peptide significantly reduced the folding efficiency of the complex, but truncation of the second half of the peptide did not. Consistent with previous reports, the second (P1) residue of the peptide is twisted, and its side chain is inserted into the A pocket to form two hydrogen bonds with polymorphic E63 and conserved Y159. Mutations of E63 disrupt the binding of the peptide, indicating that E63 is necessary for this peptide-binding mode. Compared with W167, which exists in most MHC-Is, SLA-I–specific S167 ensures an open N-terminal groove of SLA-1*0401, enabling the P-1 residue to extend from the groove. In this MHC class II–like peptide-binding mode, the A pocket is restrictive to the P1 residue and is affected by the polymorphic residues. The peptidomes and refolding data indicated that the open N-terminal groove of SLA-1*0401 allows one to three residues to extend out of the Ag-binding groove. These cross-species comparisons can help us better understand the characteristics of this N-terminal extension presentation mode.
Footnotes
This work was supported by grants from the National Natural Science Foundation of China (31830097 and 31201887), the Natural Science Foundation of Beijing Municipality (6182029), the Major Science and Technology Project of Liaoning Province (2020JH1/10200003), the 2115 Talent Development Program of China Agricultural University, and the National Key Research and Development Program of China (2021YFD1800100).
N.Z. designed the study and supervised the project; X.W. performed the experiments and analyzed the data; Song Wang and Suqiu Wang assisted in the experiments; X.W. and Suqiu Wang solved the structure; X.X. provided guidance on data analysis; X.W. and N.Z. wrote the paper.
The coordinate and structure factors presented in this article have been submitted to the Protein Data Bank under accession number 6LF8 and the mass spectrometry proteomics data have been submitted to the ProteomeXchange Consortium under accession number PXD020818.
The online version of this article contains supplemental material.
Abbreviations used in this article
- CD
- circular dichroism
- MHC-I
- MHC class I
- MHC-II
- MHC class II
- MS
- mass spectrometry
- PDB
- Protein Data Bank
- sβ2m
- swine β-2-microglobulin
- TFA
- trifluoroacetic acid
- Tm
- midpoint transition temperature
- Received October 26, 2020.
- Accepted November 5, 2021.
- Copyright © 2022 by The American Association of Immunologists, Inc.
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