Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response

Xuelu Huan,Ziyi Zhuo,Ziwei Xiao,Ee Chee Ren

doi:10.1038/s41598-019-53201-6

Xuelu Huan, Ziyi Zhuo + Show 2 more

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https://doi.org/10.1038/s41598-019-53201-6

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Abstract

Peptides presented by Human leukocyte antigen (HLA) class-I molecules are generally 8–10 amino acids in length. However, the predominant pool of peptide fragments generated by proteasomes is less than 8 amino acids in length. Using the Epstein - Barr virus (EBV) Rta-epitope (ATIGTAMYK, residues 134–142) restricted by HLA-A*11:01 which generates a strong immunodominant response, we investigated the minimum length of a viral peptide that can constitute a viral epitope recognition by CD8 T cells. The results showed that Peripheral blood mononuclear cells (PBMCs) from healthy donors can be stimulated by a viral peptide fragment as short as 4-mer (AMYK), together with a 5-mer (ATIGT) to recapitulate the full length EBV Rta epitope. This was confirmed by generating crystals of the tetra-complex (2 peptides, HLA and β2-microglobulin). The solved crystal structure of HLA-A*11:01 in complex with these two short peptides revealed that they can bind in the same orientation similar to parental peptide (9-mer) and the free ends of two short peptides acquires a bulged conformation that is directed towards the T cell receptor. Our data shows that suboptimal length of 4-mer and 5-mer peptides can complement each other to form a stable peptide-MHC (pMHC) complex.

Highlights

Human leukocyte antigen class-I (HLA-I) molecules are responsible for presenting endogenous peptides mainly generated by proteolytic machinery on the surfaces of cytotoxic CD8+ T lymphocytes[1,2,3]
To evaluate the functionality of the shorter truncated peptides (ATIGT-5-mer and AMYK4-mer) deduced from the lytic phase of Epstein-Barr Virus (EBV)-Rta epitope (ATIGTAMYK, 134–142), Peripheral blood mononuclear cells (PBMCs) from two HLAA*11:01 donors were pulsed with these peptides singly or in combination, and were cultured for 14-days
Several structural studies had previously demonstrated that long peptides (>11-mer) binding to HLA class I alleles displayed high flexibility in www.nature.com/scientificreports the super bulged central region. These results suggest that the free ends of two short peptides acquire a bulged conformation that is directed towards the T cell receptor (Supplementary Fig. 1)

Summary

Introduction

Human leukocyte antigen class-I (HLA-I) molecules are responsible for presenting endogenous peptides mainly generated by proteolytic machinery on the surfaces of cytotoxic CD8+ T lymphocytes[1,2,3]. We employed a well characterized HLA-A*11:01-EBV restricted peptide ATIGTAMYK derived from BRLF1 protein product Rta (134–142)[28] to investigate the stability of HLA-A*11:01 molecule in complex with shorter peptides (

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