Immune receptors
Contents
Leukocyte immunoglobulin-like receptorsLeukocyte immunoglobulin-like receptors (LIR) or CD85 have extracellular immunoglobulin domains. LIR modulates a variety of immune cells. LIR interacts with class I MHC molecules[1]. Leukocyte immunoglobulin-like receptor complex with class I MHC, β-2 microglobulin and POL polyprotein peptide (PDB entry 1p7q). Interactions between LIR and class I MHC, β-2 microglobulin. Cytokine receptorsTNF receptor superfamilyThe extracellular domain of TNFR contains 2 to 6 cysteine-rich domains (CRD). The CRD domains are ca. 40 amino-acid long and contain 4-6 cysteine residues. The CRDs are involved in binding of TNF[2]. Mg coordination site. Water molecules are shown as red spheres. TRAIL-R2 is called DR5. TRAIL trimer residues complex with death receptor-5 extracellular domain (1d0g). Colony-stimulating factor receptorThe kinase domain of M-CSFR interacts with a drug-designed inhibitor via the conserved kinase DFG motif (colored in salmon) and its gatekeeper threonine residue (colored in magenta)[3]. The structure of the complex between M-CSF and its receptor shows that a dimer of M-CSF binds to 2 molecules of the receptor. There are two binding sites between the molecules designated site I and site II[4]. All interactions. Type I cytokine receptorsThe EPO receptor of the blood marrow is part of the hematipoietic cytokine family. This receptor has a single transmembrane domain, that forms a homodimer complex until it is activated by the binding of EPO. This receptor is 484 amino acids long and weigh 52.6 kDa. Once the homodimer is formed after the binding, autophosphorlation of the Jak2 kinases, which activates other cellular processes. This transmembrane receptor has two extracellular domains. This receptor has two disulfide bonds that are formed from 4 cystine residues, Cys67 and Cys83 and Cys28 and Cys38. The intracellular domain of this receptor does not possess any enzymatic activity like other receptors. When EPO comes in contact with the extracellular domains form a ligand bond. The extracellular sinding site 1 and Binding site 2 are composed of D1 and D2. When EPO binds, all loops on D1 and D2 of binding site one form a bind with EPO. However loop 4 of D1 on binding site 2 does not participate in the binding of EPO [5]. After the biniding of EPO, 8 tyrosine residues are phosphoralated which activates the Jak2 kinase. This kinase helps regulate the transcription of different genes and expression of other proteins. Human erythropoietin receptor with erythropoietin (PDB code 1cn4).[6] Human prolactin receptor complex with prolactin, Na+ and Cl- (PDB code 3mzg). The interaction between PRLR and prolactin is strongly pH-dependent and is critically dependent on two histidine residues located at PRLP and on prolactin[7]. Water molecules are shown as red spheres. Na coordination site is situated between PRLR and prolactin. Type II cytokine receptorsInterferon receptors
All type I IFNs initiate signaling by binding to the same cell surface receptor composed of two subunits called IFNAR1 and IFNAR2. The intracellular domains (ICDs) of IFNAR1 and IFNAR2 are associated with the Janus kinases (Jaks) Tyk2 and Jak1, respectively. Upon ligand binding by the IFNAR chains and formation of the signaling complex, these tyrosine kinases trans-phosphorylate and thereby activate each other. Subsequently, the activated Jaks phosphorylate STAT transcription factors, which translocate into the nucleus and activate the expression of hundreds of IFN-stimulated genes. To gain insight into how type I IFNs engage their receptor chains, how the receptor system is able to recognize the large number of different ligands, and how different IFN ligands can evoke different physiological activities, we determined the crystal structures of unliganded IFNAR1 (SD1-SD3: sub-domains 1-3), the binary complex between IFNa2 and IFNAR2, and the ternary ligand-receptor complexes of IFNa2 and IFNw binding both receptor chains. A final theoretical ternary structure including the membrane-proximal sub-domain (SD4) of IFNAR1 was also created. These structures, in conjunction with biochemical and cellular experiments, reveal that the type I IFN receptor uses a mode of ligand interaction that is unique among cytokine receptors, but conserved between different IFNs. Furthermore, ligand discrimination occurs through distinct energetics of shared receptor contacts, and differential IFN signaling is mediated by specific ligand-receptor interface chemistries that lead to different ternary complex stabilities. Interferon interacts primarily with the D1 domain of IFNAR2. Arg33(IFN) appears to be the single most important residue for the interaction of the IFN ligand with IFNAR2. It forms an extensive hydrogen-bonding network with the main chain carbonyl oxygen atoms of Ile45(IFNAR2) and Glu50(IFNAR2) and the side chain of Thr44(IFNAR2). This residue is present in IFNa, IFNw, IFNb and IFNe. Two hydrophobic interaction clusters are part of the IFNa-IFNAR2 interface: the first one is formed between Leu15 and Met16 of the IFN molecule and Trp100 and Ile103 of IFNAR2; the second one comprises Leu26, Phe27, Leu30 and Val142 of the ligand and Met46, Leu52, Val80 and the methyl group of Thr44 of the receptor. Replacing Leu30(IFN) with alanine reduces affinity by three orders of magnitude (the second most important residue for binding). This is surprising, as it is not engaged in any intimate contacts with IFNAR2 residues. One reason for its importance might be a stabilizing effect on the position of Arg33(IFN). Most of the residues involved in the IFNa2-IFNAR2 interaction are also found in the IFNw-IFNAR2 interface of the IFNw ternary complex. A significant difference in the IFNAR2 interface between IFNa2 and IFNw is related to Arg149 in IFNa2, which is replaced with Lys152 in IFNw. In the IFNw-IFNAR2 interface, this residue forms an intramolecular salt bridge with Glu149(IFN), but does not contact Glu77 of the receptor. Because of the lower resolution of the IFNa ternary complex, we focused on the IFNw complex in our analysis of the IFN-IFNAR1 interface. In the IFNw-IFNAR1 complex, the ligand-binding site of IFNAR1 only contains two hotspot residues we could experimentally confirm, Tyr70(IFNAR1) and Phe238(IFNAR1). Substituting these residues by alanine reduces the affinity to all tested IFN ligands by more than 10-fold. On IFNw, mutation studies have shown that a charge-reversal mutation of Arg123 (Arg 120 on IFNa) leads to a total loss of activity. Indeed, this residue forms a salt bridge with Asp132(IFNAR1) in addition to a hydrogen bond with Ser182(IFNAR1). Substitution of glutamate for Arg123(IFN) would lead to electrostatic repulsion with Asp132(IFNAR1). The low affinity of IFNAR1 for the ligand appears to be functionally relevant, as weak binding to IFNAR1 is conserved between all alpha IFNs. Three amino acid substitutions on IFNa2 at positions His57, Glu58 and Ser61 to alanine or to Tyr, Asn, and Ser, respectively, confer tighter binding to IFNAR1, but leave the affinity to IFNAR2 essentially unaltered. IFNb exhibits 30% and 33% sequence identity with IFNw and IFNa2, respectively. Superimposing human IFNb onto IFNw in our ternary complex structure leads to only two clashes of side chains (Tyr92 and Tyr155) with the receptors, indicating that the IFNb ligand could be easily accommodated by the receptors in a position similar to IFNw and IFNa2. Furthermore, the superposition of IFNb onto IFNa2 in complex with IFNAR2 shows that Trp22 in IFNb and Ala19 in IFNa2 overlay onto each other. As a result, Ala19(IFN), when mutated to tryptophan, promotes an increased binding affinity to IFNAR2, which is a result of the contact made to Trp100 in IFNAR2 (as shown by double mutant cycle analysis). One of the more controversial aspects of cytokine signaling is whether receptor binding is sufficient to generate activity, or if it has to be accompanied by structural perturbations. The type I interferon signaling complex is a rare example of a cytokine receptor complex were the structures of all the components making up the biologically active complex were determined to high resolution in both their free and bound forms. A comparison of the unbound NMR structure with the ternary complex structure of interferon shows a small expansion during complex formation. Both IFNAR1 and IFNAR2, however, undergo significant domain movements upon binding. Using the D1 domain as anchor, a clear outwards movement of the D2 domain of IFNAR2 upon binding, on a scale of 6-12 Å, is observed (comparison of the unbound receptor (1n6u) with the binary IFNa2-IFNAR2 complex). The superimposition of the IFNa2-IFNAR2 binary complex with IFN-IFNAR2 in the ternary complexes reveals an additional domain movement of 6-9 Å, and even between the ternary IFNa and IFNw complexes a movement of 3-5 Å is observed. The D2 domain is engaged in crystal contacts in all three structures, and it remains an open question if the conformational changes in IFNAR2 are physiologically relevant. Still, these movements could change the proximity or orientation of the ICDs and associated Jaks within the cell. The low-affinity receptor chain, IFNAR1, also undergoes major conformational changes upon ligand binding. When using D1 as anchor, D3 is moving inwards (toward the ligand) by ~15 Å. This would generate an even larger movement of the membrane-proximal SD4 domain and the transmembrane helix. The conformational changes in IFNAR1 are necessary to form the full spectrum of interactions with the IFN ligand, and to form a stable signaling complex that is able to instigate downstream signaling. In contrast to SD3, SD4 seems to be highly flexible (even more than D2 of IFNAR2). One might suggest that the conformational changes in IFNAR1 by itself will be responsible for a reduced binding affinity of IFNAR1 and may slow down the rate of ligand association to IFNAR1 directly from solution. Classical MS pathology has been characterized by white matter plaques, shown in the image above, which are typically located in the subcortical or periventricular white matter, optic nerve sheaths, brain stem, and spinal cord. The lesions that occur in these regions are generally identified by perivascular infiltrates that contain clonally expanded CD8+ T cells (two ectodomains shown, 3qzw), as well as a smaller amount of CD4+ T cells (3t0e), monocytes (2ra4), and rare B cells (4e96) and plasma cells (2wq9). Pathologists disagree on whether there are different mechanisms for the inflammatory and degenerative components of MS, especially given that older patients have generally progressed further along with their degeneration. There are many proposed degeneration mechanisms including Wallerian degeneration secondary to demyelination, and axonal transection, damage from reactive oxygen species and nitric oxide, or energy failure from mitochondrial dysfunction. Many antigens have been investigated to determine whether they are the cause of T cell autoreactivity (extracellular domain shown, 1tcr) in the hopes to determine a single culprit including: myelin basic protein (MBP, 1bx2) with a peptide shown; proteolipid protein (PLP, 2xpg) with peptide shown; oligodendrocyte glycoprotein (MOG, 3csp); oligodendroglia-specific enzyme transaldolase, and heat shock protein alphaB crystallin (2y1z). Interesting discoveries have been made on possible inhibitors of myelin repair functions within the body, with an obvious application to MS treatment. The structure of the lingo-1 ectodomain is a module implicated in central nervous system repair inhibition. The interactions of lingo-1 with receptors lead to neurite and axonal collapse. Lingo-1 also regulates oligodendrocyte differentiation and myelination, thus leading to the suggestion that pharmacological modulation of Lingo-1 function could be a novel approach for nerve repair and remyelination therapies. A protein growth factor that stimulates an antiviral defense interferon-beta is one of the only two known vertebrate structural genes that lacks introns. Interferon-β is a relatively simple biological response modifier, with several identifiable regions. It consists of five alpha helices, as well as multiple interconnecting loop regions. Helices A, B and D run parallel to one another, and helices C and E run anti-parallel to the other three helices, but parallel to one another. Helix A consists of residues 6-23; Helix B consists of residues 49-65; Helix C consists of residues 77-91; Helix D consists of residues 112-131; and Helix E consists of residues 135-155. Since a PDB reference does not exist for interferon-β interacting with interferon receptors 1 or 2, and a multitude of files exist on interferon-α interacting with the receptor, a comparison to interferon-α will be made prior to demonstrating the types of bonding that occur between the interferon and its receptor. To see more information regarding interferons, please visit the Interferons site. Interferon-α has a 31% sequence homology to interferon-β. It too has many identifiable regions with two disulfide bonds: one between the N-terminus and Helix E, and the other between Loop AB and Helix G. It has seven alpha helices, as compared to the five of interferon-β, and therefore has more loop regions. The helices A, C, and F run parallel to one another, and anti-parallel to B, E, and G which run parallel to each other.Helix D does not run parallel or anti-parallel to either set, but rather runs at a 45-90 degree angle to them. Helix A consists of residues 10-12; Helix B of 40-43; Helix C of 53-68; Helix D of 70-75; Helix E of 78-100; Helix F of 109-132; and Helix G of 137-158. Interferons-α and -β interact with a receptor at the cell surface. This receptor has three domains: an N-domain, with two disulfide bonds, a C-domain, with one disulfide bond, and a linker region. The termini regions of the receptor have no secondary structure, allowing for some serious flexibility, leading to eight clashes amongst the domains, which are all illustrated on the N-terminus region. Interferon-α binds to an interferon receptor mainly with helices C and G. There are many residues, shown in ball-and-stick, within 4 angstroms of one another. These residues could form many different types of bonds, with hydrogen bonds illustrated in white dotted lines. Given that interferon-α does not undergo many structural changes upon binding to interferon receptor II, Quadt-Akabayov et al. have concluded that the binding mechanism is similar to that of a lock and key. While interferon-α and -β bind to the same receptors as one another, the affinities with which they bind to IFNAR1 and IFNAR2 differ. While the binding to IFNAR2 is stronger for both in comparison to IFNAR1, interferon-β has a much stronger affinity for IFNAR1 than interferon-α. Interleukin receptorsInterleukin-20 receptor:
IL-24 is associated with multiple diseases, including the promotion and amplification of inflammatory responses during autoimmune and chronic inflammation [12], psoriasis-like skin inflammation [13], epidermal inflammation induced by stresses [14], inflammatory bowel disease [15][16], and also with host defense during bacterial infection [17]. Some studies suggest anti-cancer activities that increased the interest in this molecule. One of the stable variants (IL-24B) was crystallized, its structure solved at 1.3 Å resolution and deposited to PDB under the code 6gg1. This structure together with the recently published crystal structure of the ternary complex of IL-24 fused to IL-22R1 and co-expressed with IL-20R2 (PDB ID 6df3[11]) allowed us to analyze the role of the mutated amino acid residues protein stability, flexibility, and binding to the cognate receptors. Structure comparison of the 6gg1 (green) and 6df3 (white). Based on the analysis, we expressed a series of variants back engineered from the PROSS designed variant by changing the critical residues back to their wild types. We revealed that re-introduction of a single IL-24 wild type residue (T198) to the patch interacting with receptors 1 restored 80 % of the binding affinity and signaling capacity accompanied by an acceptable drop in the protein stability by 9°C. Chemokine receptors, two of which acting as binding proteins for HIV (CXCR4 and CCR5). They are G protein-coupled receptorsCXCR4: Ligand binding cavity with antagonist citrulline (PDB code 3oe0). Ligand binding cavity with antagonist citrulline, receptor is in spacefill representation. Ligand binding cavity with antagonist citrulline, receptor surface is shown. T-cell receptorsT-cell receptor α chain, β chain complex with enterotoxin and Na+ ion (2xna) See also:
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