Abstract
The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD–MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.
Highlights
The major histocompatibility complex (MHC) is a large genetic region that can encode a wide variety of molecules and consists of the highly polymorphic classical MHC class I (MHC-I) and MHC class II (MHC-II), which are central to the adaptive immune response [1]
The high degree of micropolymorphisms enables MHC-I molecules to present a wide range of antigenic peptides and activate T-cell immune responses, and even a single residue mutation can drastically alter the peptide presentation of the MHC-I molecule and further affect disease resistance [18, 20,21,22, 25]
LC-mass spectrometry (MS)/MS was widely used to survey the eluted immunopeptidome of MHC-I [28], and the influence of the HLA-I micropolymorphism could be determined by an improved method combining LC-MS/MS and CRISPR technology [2, 29]
Summary
The major histocompatibility complex (MHC) is a large genetic region that can encode a wide variety of molecules and consists of the highly polymorphic classical MHC class I (MHC-I) and MHC class II (MHC-II), which are central to the adaptive immune response [1]. The sequence diversity found in MHC-I ranges from micropolymorphisms, which contain just a few different amino acids, to differences of more than 30 amino acids in more distantly related allomorphs [2]. This feature determines that the peptide-binding characteristics of individual MHC-I molecules are variable. Peptides anchor the antigen binding groove (ABG) via interactions between peptide residues and pockets, denoted A–F [3]. The landscape of these pockets is usually determined by the composition of nearby amino acids. Polymorphisms alter the stereo- and electrochemical environment of the pockets, dictating their ability to accommodate different peptide residues, thereby influencing the nature and quantity of the bound peptides [4,5,6]
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