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All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric Peptide.

ABSTRACT: Natural killer (NK) cells, an important part of the innate immune system, can clear a wide variety of pathological challenges, including tumor, senescent, and virally infected cells. They express various activating and inhibitory receptors on their surface, and the balance of interactions between them and specific ligands displayed on the surface of target cells is critical for NK cell cytolytic function and target cell protection. The CD94/NKG2A heterodimer is one of the inhibitory receptors that interacts with its trimeric ligand consisting of HLA-E, β2m, and a nonameric peptide. Here, multi-microsecond-long all-atom molecular dynamics simulations of eight immune complexes elucidate the subtleties of receptor (NKG2A/CD94)-ligand (HLA-E/β2m/peptide) molecular recognition that mediate the NK cell protection from a geometric and energetic perspective. We identify key differences in the interactions between the receptor and ligand complexes, which are via an entangled network of hydrogen bonds fine-tuned by the ligand-specific nonameric peptide. We further reveal that the receptor protein NKG2A regulates the NK cell activity, while its CD94 partner forms the majority of the energetically important interactions with the ligand. This knowledge rationalizes the atomistic details of the fundamental NK cell protection mechanism and may enable a variety of opportunities in rational-based drug discovery for diverse pathologies including viral infections and cancer and elimination of senescent cells associated with potential treatment of many age-related diseases.

SUBMITTER: Prasnikar E

PROVIDER: S-EPMC8389527 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:MHC class I antigen E (HLA-E), a ligand for the inhibitory NKG2A/CD94 receptor of the immune system, is responsible for evading the immune surveillance in several settings, including senescent cell accumulation and tumor persistence. The formation of this ligand-receptor interaction promotes the inhibition of the cytolytic action of immune system natural killer (NK) cells and CD8+ T-cells expressing this receptor. The final outcome of the HLA-E/NKG2A/CD94 interaction on target cells is also highly dependent on the identity of the nonameric peptide incorporated into the HLA-E ligand. To better understand the role played by a nonameric peptide in these immune complexes, we performed a series of multi-microsecond all-atom molecular dynamics simulations. We generated natural and alternative variants of the nonameric peptide bound to the HLA-E ligand alone or in the HLA-E/NKG2A/CD94 complexes. A systematic study of molecular recognition between HLA-E and peptides led to the development of new variants that differ at the strategic 6th position (P6) of the peptide and have favorable in silico properties comparable to those of natural binding peptides. Further examination of a selected subset of peptides in full complexes revealed a new variant that, according to our previously derived atomistic model, can interfere with the signal transduction via HLA-E/NKG2A/CD94 and thus prevent the target cell from evading immune clearance by NK and CD8+ T-cells. These simulations provide an atomistic picture of how a small change in amino acid sequence can lead to a profound effect on binding and molecular recognition. Furthermore, our study also provides new data on the peptide interaction motifs as well as the energetic and conformational properties of the binding interface, laying the structure-based foundation for future development of potential therapeutic peptides, peptidomimetics, or even small molecules that would bind to the HLA-E ligand and abrogate NKG2A/CD94 recognition. Such external intervention would be useful in the emerging field of targeting senescent cells in a variety of age-related diseases, as well as in novel cancer immunotherapies.

Project description:Natural killer (NK) cell therapies are a tool to antagonize a dysfunctional immune system. NK cells recognize malignant cells, traffic to a tumor location, and infiltrate the solid tumor. The immune checkpoint molecule human leukocyte antigen (HLA)-G is upregulated on malignant cells but not on healthy surrounding cells, the requirement of understanding the basis of receptor mediated events at the HLA-G/NK cell interface becomes obvious. The NK cell receptors ILT2 and KIR2DL4 have been described to bind to HLA-G; however, their differential function and expression levels on NK cell subsets suggest the existence of an unreported receptor. Here, we performed a ligand-based receptor capture on living cells utilizing sHLA-G*01:01 molecules coupled to TriCEPS and bound to NK cells followed by mass spectrometric analyses. We could define NKG2A/CD94 as a cognate receptor of HLA-G. To verify the results, we used the reciprocal method by expressing recombinant soluble heterodimeric NKG2A/CD94 molecules and used them to target HLA-G*01:01 expressing cells. NKG2A/CD94 could be confirmed as an immune receptor of HLA-G*01:01. Despite HLA-G is marginal polymorphic, we could previously demonstrate that the most common allelic subtypes HLA-G*01:01/01:03 and 01:04 differ in peptide repertoire, their engagement to NK cells, their catalyzation of dNK cell proliferation and their impact on NK cell development. Continuing these studies with regard to NKG2A/CD94 engagement we engineered recombinant single antigen presenting K562 cells and targeted the surface expressed HLA-G*01:01, 01:03 or 01:04 molecules with NKG2A/CD94. Specificity and sensitivity of HLA-G*01:04/NKG2A/CD94 engagement could be significantly verified. The binding affinity decreases when using K562-G*01:03 or K562-G*01:01 cells as targets. These results demonstrate that the ligand-receptor assignment between HLA-G and NKG2A/CD94 is dependent of the amino acid composition in the HLA-G heavy chain. Understanding the biophysical basis of receptor-mediated events that lead to NK cell inhibition would help to remove non-tumor reactive cells and support personalized mild autologous NK cell therapies.

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All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric Peptide.

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