Crystal Structure of Swine Major Histocompatibility Complex Class I SLA-1*0401 and Identification of 2009 Pandemic Swine-Origin Influenza A H1N1 Virus Cytotoxic T Lymphocyte Epitope Peptides

Abstract

The presentation of viral epitopes to cytotoxic T lymphocytes (CTLs) by swine leukocyte antigen class I (SLA I) is crucial for swine immunity. To illustrate the structural basis of swine CTL epitope presentation, the first SLA crystal structures, SLA-1*0401, complexed with peptides derived from either 2009 pandemic H1N1 (pH1N1) swine-origin influenza A virus (S-OIV NW9 ; NSDTVGWSW) or Ebola virus (Ebola AY9 ; ATAAATEAY) were determined in this study. The overall peptide-SLA-1*0401 structures resemble, as expected, the general conformations of other structure-solved peptide major histocompatibility complexes (pMHC). The major distinction of SLA-1*0401 is that Arg 156 has a "one-ballot veto" function in peptide binding, due to its flexible side chain. S-OIV NW9 and Ebola AY9 bind SLA-1*0401 with similar conformations but employ different water molecules to stabilize their binding. The side chain of P7 residues in both peptides is exposed, indicating that the epitopes are "featured" peptides presented by this SLA. Further analyses showed that SLA-1*0401 and human leukocyte antigen (HLA) class I HLA-A*0101 can present the same peptides, but in different conformations, demonstrating cross-species epitope presentation. CTL epitope peptides derived from 2009 pandemic S-OIV were screened and evaluated by the in vitro refolding method. Three peptides were identified as potential cross-species influenza virus (IV) CTL epitopes. The binding motif of SLA-1*0401 was proposed, and thermostabilities of key peptide-SLA-1*0401 complexes were analyzed by circular dichroism spectra. Our results not only provide the structural basis of peptide presentation by SLA I but also identify some IV CTL epitope peptides. These results will benefit both vaccine development and swine organ-based xenotransplantation.

Structural Definition of Duck Major Histocompatibility Complex Class I Molecules That Might Explain Efficient Cytotoxic T Lymphocyte Immunity to Influenza A Virus

“…The gel filtration and SDS-PAGE results showed that the peak represented the complex of Anpl -UAA*01 and Anpl -β2m (Fig. 3), which is different from results of studies on cattle, pig, chicken, and horse pMHC I refolding (33, 39–41). This result could be due to the Cys 95 -Cys 112 disulfide bond of p Anpl -UAA*01.…”

The Structure of the MHC Class I Molecule of Bony Fishes Provides Insights into the Conserved Nature of the Antigen-Presenting System

“…Previously, we also found a peptide-selecting role for the D pocket of the swine MHC class I molecule p/SLA-1*0401 (Fig. 8C), although, like in some other p/MHC I with established roles of pocket D in peptide selection, in p/SLA-1*0401 other pockets also have an important anchor position role (10). In contrast, our current set of data indicate that in p/UAA-b2m the only dominant anchor position may be pocket D, which together with the hydrogen bond between pocket D Y99 and P3N (Fig.…”

“…The p/UAA-b2m crystal structure was solved by molecular replacement via the MOLREP program using SLA-1*0401 (Protein Data Bank [PDB] code: 3QQ3) as the search model (10). Extensive model building was manually performed with COOT (25), and restrained refinement was performed with REFMAC5.…”

“…To assemble p/UAA-b2m with each viral peptide, the peptide, Ctid-UAA, and Ctid-b2m were refolded according to the gradual dilution method (19). After a 48 h incubation at 4˚C, the remaining soluble portion of the complex was concentrated and purified by chromatography on a Superdex 200 16/60 column followed by Resource Q anion-exchange chromatography (GE Healthcare) as previously described (10,12). Three of the seven peptides formed p/UAA-b2m complexes and were recovered after gel filtration; p/UAA-b2m was recovered after anion-exchange chromatography (Fig.…”

“…Nearly all of these are from humans and mice (6), with scant data from monkeys (7), cattle (8,9), pigs (10), and chickens (11,12). The three-dimensional structures of p/MHC I reveal that the MHC class I H chain is composed of a1, a2, and a3 domains (13).…”