Interferon: Difference between revisions

'''Interferons''' were the first cytokines discovered and were identified by Isaacs and Lindenmann. These proteins were classified as interferons because they interfered with virus growth.<ref name="Isaacs" /> The initial experiments performed poorly characterized the interferons, and was based merely on bioactivity. Advances in scientific instrumentation and technique have allowed for greater understanding and visualization of not only the structure but also the mechanisms of the various types of inteferons.<ref name="Structure">PMID:2413490</ref> The interferons were originally classified as leukocyte ('''interferon-α'''), fibroblast ('''interferon-β'''), and immune ('''interferon-γ'''), although today they are classified into types I (α, β, ε, κ, ω), II (γ), and III (λ).<ref name="Isaacs" /><ref name="Structure" />

Type I interferons are homologous helical cytokines that effect a wide variety of cells pleiotropically. These effects range from antiviral activity to antibacterial, antiprozoal, immunodulatory, and cell growth regulatory functions. Without Type I interferons, the survival of the higher vertebrates would be impossible. Because of their strong antiviral and antiproliferative effects, these interferons are used in the treatment of numerous cancers, hepatitis C, and multiple sclerosis. See [[Multiple sclerosis]].

 

See more details in [[IntronA (Interferon alpha 2b)]]

A protein growth factor that stimulates an antiviral defense <scene name='Multiple_sclerosis/Interferon_beta/9'>interferon-beta</scene> is one of the only two known vertebrate structural genes that lacks introns.<ref name="Biochem Text">Voet, D., Voet, J.G., and C. Pratt. ''Fundamentals of Biochemistry'' 3rd Edition. Hoboken, NJ: John Wiley and Sons, 2008. Print.</ref> Interferon-β has a 31% sequence homology to interferon-α . It is a relatively simple biological response modifier, with several <scene name='Multiple_sclerosis/Interferon_beta_labeled/1'>identifiable regions</scene>. It consists of five <scene name='Multiple_sclerosis/Ifnb_helices_in_color/1'>alpha helices</scene>, as compared to the seven of interferon-α, as well as multiple interconnecting <scene name='Multiple_sclerosis/Interferon_beta_loops/2'>loop regions</scene>. Helices A, B and D run <scene name='Multiple_sclerosis/Ifnb_parallel_abd/3'>parallel to one another</scene>, and helices C and E run <scene name='Multiple_sclerosis/Ifnb_antiparallel/1'>anti-parallel</scene> to the other three helices, but <scene name='Multiple_sclerosis/Ifnb_antiparallel_ce/3'>parallel</scene> 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.<ref name="Structure Ifn B">PMID:20616576</ref><ref name="UniProt">http://www.uniprot.org/uniprot/P00784</ref>.  

*<scene name='Interferon/Ifn_alpha/5'>Interferon Alpha</scene>

*<scene name='Interferon/Interferon_beta/4'>Interferon Beta</scene>

*<scene name='Interferon/Ifn_gamma/5'>Interferon Gamma</scene>

=== Structural linkage between ligand discrimination and receptor activation by type I interferons <ref>DOI 10.1016/j.cell.2011.06.048</ref>===

===Introduction===

All <scene name='User:David_Canner/Workbench/Opening_ifna/2'>type I IFNs</scene> initiate signaling by binding to the same cell surface receptor composed of two subunits called <scene name='User:David_Canner/Workbench/Opening_ifnar1/3'>IFNAR1</scene> and <scene name='User:David_Canner/Workbench/Opening_ifnar2/2'>IFNAR2</scene>. 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 <scene name='User:David_Canner/Workbench/Opening_ifnar1_alone/2'>IFNAR1 (SD1-SD3: sub-domains 1-3)</scene>, the binary complex <scene name='User:David_Canner/Workbench/Opening_ifnar2_binary/1'>between IFNa2 and IFNAR2</scene>, and the ternary ligand-receptor complexes of <scene name='User:David_Canner/Workbench/Opening_ternary_alpha/2'>IFNa2</scene> and <scene name='User:David_Canner/Workbench/Opening_ternary_gamma/3'>IFNw</scene> binding both receptor chains. A final theoretical ternary structure including <scene name='User:David_Canner/Workbench/Opening_sd4_ternary/1'>the membrane-proximal sub-domain (SD4) of IFNAR1</scene> 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.

===Interactions Between IFNAR & IFN===

<scene name='User:David_Canner/Workbench/Opening_ifna/2'>Interferon</scene> interacts primarily with the <scene name='User:David_Canner/Workbench2/Ifn_ifnar2_interaction/1'>D1 domain of IFNAR2</scene>. Arg33(IFN) appears to be the <scene name='User:David_Canner/Workbench2/Ifn_arg_33/1'>single most important residue</scene> 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 <scene name='User:David_Canner/Workbench2/Ifn_ifnar2_leu_30/1'>Leu30(IFN) with alanine</scene> 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 <scene name='User:David_Canner/Workbench2/Ifn_ifnar2_arg_stabilized/1'>stabilizing effect on the position of Arg33(IFN)</scene>.

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 <scene name='User:David_Canner/Workbench2/Ifn_ifnar2_interaction_dif/5'>IFNa2</scene> and IFNw is related to <scene name='User:David_Canner/Workbench2/Ifn_ifnar2_interaction_salt/1'>Arg149 in IFNa2</scene>, which is replaced with Lys152 in <scene name='User:David_Canner/Workbench2/Ifnw_ifnar21_structure/3'>IFNw</scene>. In the <scene name='User:David_Canner/Workbench2/Ifnw_ifnar2_interface/3'>IFNw-IFNAR2 interface</scene>, this residue forms an <scene name='User:David_Canner/Workbench2/Ifnw_ifnar2_salt/1'>intramolecular salt bridge</scene> with Glu149(IFN), but <scene name='User:David_Canner/Workbench2/Ifnw_ifnar2_no_interact/1'>does not contact Glu77 of the receptor</scene>.

Because of the lower resolution of the IFNa ternary complex, we focused on the <scene name='User:David_Canner/Workbench2/Ifnw_ifnar21_structure/3'>IFNw complex</scene> in our analysis of the IFN-IFNAR1 interface. In the <scene name='User:David_Canner/Workbench2/Ifnw_ifnar21_structure/3'>IFNw-IFNAR1 complex</scene>, the <scene name='User:David_Canner/Workbench2/Ifnw_ifnar21_zoomed/1'>ligand-binding site of IFNAR1</scene> only contains two hotspot residues we could experimentally confirm, <scene name='User:David_Canner/Workbench2/W-1-tyr_70/1'>Tyr70(IFNAR1)</scene> 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. [[Image:IFNw_IFNAR1_interaction_map.png|300px||left|]]

<scene name='User:David_Canner/Workbench2/Ifnbeta/1'>IFNb exhibits</scene> 30% and 33% sequence identity with <scene name='User:David_Canner/Workbench2/Ifnbeta/2'>IFNw </scene>and IFNa2, respectively.<scene name='User:David_Canner/Workbench2/Ifnbeta_gamma_overlay/3'> Superimposing human IFNb onto IFNw</scene>  in our ternary complex structure leads <scene name='User:David_Canner/Workbench2/Ifnbeta_gamma_clashing_out/1'>to only two clashes</scene> of side chains (Tyr92 and <scene name='User:David_Canner/Workbench2/Ifnbeta_gamma_clashing_155/3'>Tyr155</scene>) 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 <scene name='User:David_Canner/Workbench2/Superimosed_beta_alpha/6'>superposition of IFNb onto IFNa2 in complex with IFNAR2</scene> shows that <scene name='User:David_Canner/Workbench2/Superimosed_1922/1'>Trp22 in IFNb and Ala19 in IFNa2 overlay onto each other</scene>. As a result, Ala19(IFN), when mutated to tryptophan, promotes an increased binding affinity to IFNAR2, which is a result of the <scene name='User:David_Canner/Workbench2/Superimosed_1922100/2'>contact made to Trp100 in IFNAR2</scene> (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. <scene name='User:David_Canner/Workbench3/Morph_1/6'>A comparison</scene> 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 <scene name='User:David_Canner/Workbench3/Morph_2/10'>clear outwards movement of the D2 domain</scene> 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 <scene name='User:David_Canner/Workbench3/Morph3/7'>reveals an additional domain movement</scene> 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 <scene name='User:David_Canner/Workbench3/Morph_4/4'>undergoes major conformational changes</scene> 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.

==See Also==

*[[Interferon receptor|Interferon receptor]]

*[[Interferon regulatory factor]]

*[[Multiple sclerosis|Multiple sclerosis]]

*[[Journal:Cell:1|Structural linkage between ligand discrimination and receptor activation by type I interferons]]