Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1

Abstract

Chemokines interact with their G protein–coupled receptors (GPCRs) through a two-step, two-site mechanism and, through this interaction, mediate various homeostatic and immune response mechanisms. Upon initial recognition of the chemokine by the receptor, the amino terminus of the chemokine inserts into the orthosteric pocket of the GPCR, causing conformational changes that trigger intracellular signaling. There is considerable structural and functional evidence to suggest that the amino acid composition and length of the chemokine amino terminus is critical for GPCR activation, complementing the size and amino acid composition of the orthosteric pocket. However, very few structures of a native chemokine-receptor complex have been solved. Here, we used a hybrid approach that combines structure-function data with Rosetta modeling to describe key contacts within a chemokine-GPCR interface. We found that the extreme amino-terminal residues of the chemokine XCL1 (Val1, Gly2, Ser3, and Glu4) contribute a large fraction of the binding energy to its receptor XCR1, whereas residues near the disulfide bond–forming residue Cys11 modulate XCR1 activation. Alterations in the XCL1 amino terminus changed XCR1 activation, as determined by assessing inositol triphosphate accumulation, intracellular calcium release, and directed cell migration. Computational analysis of XCL1-XCR1 interactions revealed functional contacts involving Glu4 of XCL1 and Tyr117 and Arg273 of XCR1. Subsequent mutation of Tyr117 and Arg273 led to diminished binding and activation of XCR1 by XCL1. These findings demonstrate the utility of a hybrid approach, using biological data and homology modeling, to study chemokine-GPCR interactions.

Transcriptome Profiling Reveals a Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Yellow Drum, Nibea albiflora

“…Xcr1 is a receptor for chemokines SCYC1 and SCYC2. A previous study suggested that Xcr1 transduced signals by increasing the intracellular calcium ion level [ 45 ]. Therefore, Xcr1 may be an important signal transduction molecule in the osmotic regulation mechanism of the yellow drums.…”

Role of chemokine systems in cancer and inflammatory diseases

“…Most of the functional studies published in recent years have shown that the chemokine ligand axis conforms the classical GPCR activation paradigm. 18 , 19 , 20 Once the ligand is stimulated, the G protein dissociates from the corresponding receptor and initiates different signaling events downstream of ligand binding that can eventually lead to various responses, such as cell proliferation, survival, invasion, migration, and gene transcription. 2 , 8 , 17 All chemokines are small, with approximately 20–50% identical sequences between individual chemokines, suggesting homology in their gene sequences and amino acid sequences.…”

“…The chemokine network is composed of nearly 50 chemokine ligands, 20 GPCRs, and four ACKRs, 17 which play significant roles in the body's immune homeostasis, inflammatory response, viral infection, and tumor progression (Figure 1). Most of the functional studies published in recent years have shown that the chemokine ligand axis conforms the classical GPCR activation paradigm 18–20 . Once the ligand is stimulated, the G protein dissociates from the corresponding receptor and initiates different signaling events downstream of ligand binding that can eventually lead to various responses, such as cell proliferation, survival, invasion, migration, and gene transcription 2,8,17 .…”

Efficient targeting of NY-ESO-1 tumor antigen to human cDC1s by lymphotactin results in cross-presentation and antigen-specific T cell expansion

“… 9 XCL1 is thus able to modulate the spatial location and function of both T cells and DCs. Binding of XCL1 to the orthosteric site of XCR1 triggers Ca 2+ efflux from the endoplasmic reticulum (ER), leading to cytoskeleton remodeling and cell migration, 10 followed by XCR1 desensitization and internalization to early endosomes. 11 It is hypothesized that by following a XCL1 chemotactic gradient, XCR1 + cDC1s can migrate toward the site of inflammation, where they take up antigens.…”