Structural reorganization of the antigen-binding groove of human CD1b for presentation of mycobacterial sulfoglycolipids

Abstract

The mechanisms permitting nonpolymorphic CD1 molecules to present lipid antigens that differ considerably in polar head and aliphatic tails remain elusive. It is also unclear why hydrophobic motifs in the aliphatic tails of some antigens, which presumably embed inside CD1 pockets, contribute to determinants for T-cell recognition. The 1.9-Å crystal structure of an active complex of CD1b and a mycobacterial diacylsulfoglycolipid presented here provides some clues. Upon antigen binding, endogenous spacers of CD1b, which consist of a mixture of diradylglycerols, moved considerably within the lipid-binding groove. Spacer displacement was accompanied by F' pocket closure and an extensive rearrangement of residues exposed to T-cell receptors. Such structural reorganization resulted in reduction of the A' pocket capacity and led to incomplete embedding of the methyl-ramified portion of the phthioceranoyl chain of the antigen, explaining why such hydrophobic motifs are critical for T-cell receptor recognition. Mutagenesis experiments supported the functional importance of the observed structural alterations for T-cell stimulation. Overall, our data delineate a complex molecular mechanism combining spacer repositioning and ligandinduced conformational changes that, together with pocket intricacy, endows CD1b with the required molecular plasticity to present a broad range of structurally diverse antigens.three-dimensional structure | groove shrinking | diacylglycerol endogenous ligand | T lymphocyte activation | CD1b mutant transfectant T lymphocytes have developed the capacity to recognize as antigens a large variety of molecules including peptides, (glyco)lipids, and phosphorylated metabolites (1). Specific recognition of peptides or lipids by T-cell receptors (TCR) occurs when these molecules form antigenic complexes with dedicated antigen-presenting molecules belonging to MHC or CD1 families, respectively. Diversity has forced the immune system to develop appropriate strategies to present antigens in immunogenic form. Polymorphic MHC molecules cope with the peptide repertoire by constraining the ligand conformational space (2). Less clear is how the immune system adapts to the large glycolipid antigenic range and forms antigenic complexes using the functionally nonpolymorphic CD1 molecules.Human antigen-presenting cells (APC) display the CD1a, CD1b, CD1c, and CD1d proteins on their plasma membranes (1, 3). CD1 ectodomains consist of a heavy chain, which folds into three extracellular domains (α1-α3) noncovalently associated with β2-microglobulin (4). Antigen-binding grooves nestle between the α1 and α2 domains and are mostly lined by hydrophobic residues. This allows the antigenic lipids to be anchored via their hydrophobic chains, so that polar motifs protrude toward the aqueous milieu. Consequently, polar heads but not hydrophobic tails are assumed to establish stimulatory contacts with TCRs. Nevertheless, modifications in the lipid chains may also indirectly impact on TCR recognition (5).The number, shape, and conn...

Novel insights into lipid antigen presentation

“…Studies performed with recombinant soluble proteins revealed that CD1b, CD1c and CD1d are associated with different lipids [11][12][13][14][15][16][17], suggesting that CD1 molecules are not assembled with empty pockets (Table 1). Thus, lipids bound by CD1 during assembly in the ER might contribute to stabilisation of assembled molecules, resembling the binding of peptides to nascent MHC class I molecules …”

“…During loading with a well characterised antigenic sulfoglycolipid, CD1b undergoes a conformational change in the key residues, glutamic acid at position 80 and tyrosine at position 151, which approximate, thus closing the F 0 pocket. Lipid-antigen loading also induces a sliding of the spacer, which assumes a novel position and moves towards the A 0 pocket [16]. Importantly, spacers with different length can associate with CD1b, thereby lipid antigens with different alkyl chains can be optimally accommodated.…”

“…During antigen binding, CD1b also changes the position of a glutamine 152, as its lateral residue becomes oriented against the TCR [16]. Mutagenesis into alanine generates a gain of function CD1b molecule, capable of activating more efficiently specific T cells, but still in an antigendependent manner.…”

Donor-unrestricted T cells in the human CD1 system

“…However, the lipids might contribute in an indirect way to TCR activation even in the absence of TCR contact. Lipids can alter the surface of the CD1 protein by pushing outward on key residues or closing up loose ternary structures (Garcia-Alles et al 2006; McCarthy et al 2007; Garcia-Alles et al 2011; Mansour et al 2016). …”

Total synthesis, stereochemical elucidation and biological evaluation of Ac2SGL; a 1,3-methyl branched sulfoglycolipid from Mycobacterium tuberculosis

“…To investigate how the natural product 1 might be bound by CD1b, the CD1b-diacylsulfoglycolipid co-crystal structure (PDB code: 3T8X) 46 was used as a template to model the natural product into the deep binding pocket. 1 was manually docked into the binding groove, and the energy of the system minimized using the MAB force eld as implemented in the computer program MOLOC, 47 while keeping the protein coordinates xed.…”