Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding

Abstract

Bats are natural reservoir hosts, harboring more than 100 viruses, some of which are lethal to humans. The asymptomatic coexistence with viruses is thought to be connected to the unique immune system of bats. MHC class I (MHC I) presentation is closely related to cytotoxic lymphocyte immunity, which plays an important role in viral resistance. To investigate the characteristics of MHC I presentation in bats, the crystal structures of peptide–MHC I complexes of Pteropus alecto, Ptal-N*01:01/HEV-1 (DFANTFLP) and Ptal-N*01:01/HEV-2 (DYINTNLVP), and two related mutants, Ptal-N*01:01/HEV-1PΩL (DFANTFLL) and Ptal-N*01:01ΔMDL/HEV-1, were determined. Through structural analysis, we found that Ptal-N*01:01 had a multi-Ala–assembled pocket B and a flexible hydrophobic pocket F, which could accommodate variable anchor residues and allow Ptal-N*01:01 to bind numerous peptides. Three sequential amino acids, Met, Asp, and Leu, absent from the α1 domain of the H chain in other mammals, were present in this domain in the bat. Upon deleting these amino acids and determining the structure in p/Ptal-N*01:01ΔMDL/HEV-1, we found they helped form an extra salt-bridge chain between the H chain and the N-terminal aspartic acid of the peptide. By introducing an MHC I random peptide library for de novo liquid chromatography–tandem mass spectrometry analysis, we found that this insertion module, present in all types of bats, can promote MHC I presentation of peptides with high affinity during the peptide exchange process. This study will help us better understand how bat MHC I presents high-affinity peptides from an extensive binding peptidome and provides a foundation to understand the cellular immunity of bats.

Novel Insights Into Immune Systems of Bats

“…This study showed that bat MHC molecules can accommodate larger peptides, compared to other mammals and have unique consensus-binding motifs, potentially as a result of their co-evolution with viruses (125). The MHC class I protein complexes (126) in P. alecto were recently crystallized, revealing three additional amino acids in bat MHC class I (methionine, aspartic acid and leucine), compared to other selected mammals (127). The three amino acids formed an additional salt bridge that could potentially present high affinity peptides during the peptide exchange process in bat cells facilitating an efficient cell-mediated immune response.…”

COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes

“…We identified 174 potential SARS-CoV-2 vaccine candidate peptides, out of which 48 have been previously deposited in IEDB following various studies (Qu et al 2019;Blicher et al 2005;Sylvester-Hvid et al 2004;Harndahl et al 2006;Sidney et al 2006;Ishizuka et al 2009) . The majority of the previously deposited peptides were measured in one or multiple affinity assays and reached low Kd (<50 nM) values, indicating strong affinity.…”

A Glimpse of the Peptide Profile Presentation by Xenopus laevis MHC Class I: Crystal Structure of pXela-UAA Reveals a Distinct Peptide-Binding Groove

“…The nonapeptides used in the study (see Supplemental Table I) and one synthetic random peptide library, Ran_9X splitted (9X, XXXXXXXXX, where X is a random amino acid other than cysteine), were synthesized and purified by reverse-phase HPLC and mass spectrometry (MS) (SciLight Biotechnology) with .95% purity. The lyophilized peptides were stored at 280˚C and dissolved in DMSO at a concentration of 25 mg/ml before use as previously described (31).…”