A homology model of human interferon a-2 (original) (raw)
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A homology model of human interferon α-2
Proteins: Structure, Function, and Genetics, 1993
An atomic coordinate five a-helix three-dimensional model is presented for human interferon 01-2 (HuIFNa2). The HuIFNa2 structure was constructed from murine interferon p (MuIFNp) by homology modeling using the STEREO and IMPACT programs. The HuIFNor2 model is consistent with its known biochemical and biophysical properties including epitope mapping. Lysine residues predicted to be buried in the model were primarily unreactive with succinimidyl-7-amino-4methylcoumarin-3-acetic acid (AMCA-NHS), a lysine modification agent, as shown by mass spectrometric analysis of tryptic digests. N-terminal sequence analysis of polypeptides generated by limited digestion of HuIFNor2 with endoproteinase Lys-C demonstrated rapid cleavage at K31, which is consistent with the presence of this residue in a loop in the proposed H u I F N d model. Based on this model structure potential receptor binding sites are identified. o 1993 wiley-Liss, hc.
Homology model of human interferon-α8 and its receptor complex
Protein Science, 2008
Human interferond (HuIFNa8), a type I interferon (IFN), is a cytokine belonging to the hematopoietic superfamily that includes human growth hormone (HGH). Recent data identified two human type I IFN receptor components. One component (p40) was purified from human urine by its ability to bind to immobilized type I IFN. A second receptor component (IFNAR), consisting of two cytokine receptor-like domains (D200 and D200'), was identified by expression cloning. Murine cells transfected with a gene encoding this protein were able to produce an antiviral response to human IFNa8. Both of these receptor proteins have been identified as members of the immunoglobulin superfamily of which H G H receptor is a member. The cytokine receptor-like structural motifs present in p40 and IFNAR were modeled based on the HGH receptor X-ray structure. Models of the complexes of HuIFNa8 with the receptor subunits were built by superpositioning the conserved C a backbone of the HuIFNa8 and receptor subunit models with HGH and its receptor complex. The HuIFNa8 model was constructed from the Ca coordinates of murine interferon-p crystal structure. Electrostatic potentials and hydrophobic interactions appear to favor the model of HuIFNa8 interacting with p40 at site 1 and the D200' domain of IFNAR at site 2 because there are regions of complementary electrostatic potential and hydrophobic interactions at both of the proposed binding interfaces. Some of the predicted receptor binding residues within HuIFNa8 correspond to functionally important residues determined previously for human IFNal, IFNa2, and IFNa4 subtypes by site-directed mutagenesis studies. The models predict regions of interaction between HuIFNa8 and each of the receptor proteins, and provide insights into interactions between other type I IFNs (IFN-a subtypes and IFN-p) and their respective receptor components.
Type I interferon structures: Possible scaffolds for the interferon-α receptor complex
Canadian Journal of Chemistry
The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN-cell receptor complexes. However, the structure of the IFN -cell receptor -IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-a 2b dimer as the ligand. Both the structures of recombinant human IFN-a 2b and IFN-b were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-a 2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-b and IFN-g to contrast similarities and differences. The mutual binding sites of human IFN-a 2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.
Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex
Canadian Journal of Chemistry, 2002
The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN-cell receptor complexes. However, the structure of the IFN -cell receptor -IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-a 2b dimer as the ligand. Both the structures of recombinant human IFN-a 2b and IFN-b were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-a 2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-b and IFN-g to contrast similarities and differences. The mutual binding sites of human IFN-a 2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.
Protein Science, 2006
Type I interferons (IFNs) are a family of homologous helical cytokines that exhibit pleiotropic effects on a wide variety of cell types, including antiviral activity and antibacterial, antiprozoal, immunomodulatory, and cell growth regulatory functions. Consequently, IFNs are the human proteins most widely used in the treatment of several kinds of cancer, hepatitis C, and multiple sclerosis. All type I IFNs bind to a cell surface receptor consisting of two subunits, IFNAR1 and IFNAR2, associating upon binding of interferon. The structure of the extracellular domain of IFNAR2 (R2-EC) was solved recently. Here we study the complex and the binding interface of IFNα2 with R2-EC using multidimensional NMR techniques. NMR shows that IFNα2 does not undergo significant structural changes upon binding to its receptor, suggesting a lock-and-key mechanism for binding. Cross saturation experiments were used to determine the receptor binding site upon IFNα2. The NMR data and previously published mutagenesis data were used to derive a docking model of the complex with an RMSD of 1 Å, and its well-defined orientation between IFNα2 and R2-EC and the structural quality greatly improve upon previously suggested models. The relative ligand–receptor orientation is believed to be important for interferon signaling and possibly one of the parameters that distinguish the different IFN I subtypes. This structural information provides important insight into interferon signaling processes and may allow improvement in the development of therapeutically used IFNs and IFN-like molecules.
Journal of Molecular Biology, 1997
The solution structure of recombinant human interferon a-2a (Roferon-A) has been determined by multidimensional heteronuclear NMR spectroscopy. The calculations using simulated annealing produced a family of 24 convergent structures which satisfy the experimental restraints comprising 1541 NOE-derived inter-proton distances, 187 dihedral restraints, 66 pairs of hydrogen bond restraints, and six upper and lower limits for two disul®de bridges. The fractional labeling of methyl groups allowed their direct and unambiguous stereospeci®c assignment which proved to be essential for obtaining a high resolution of the structures. A best ®t superposition of residues 10 to 47, 50 to 101 and 111 to 157 gives an rms deviation of 0.62 A Ê for the backbone heavy atoms and 1.39 A Ê for all heavy atoms of these segments. The dominant feature of the structure is a cluster of ®ve a-helices, four of which are arranged to form a lefthanded helix bundle with an up-up-down-down topology and two overhand connections. The interpretation of heteronuclear 15 N-{ 1 H} NOE data shows the co-existence of¯exible regions within an otherwise rigid framework of the protein. Four stretches of pronounced¯exibility can be located: Cys1-Ser8, Gly44-Ala50, Ile100-Lys112, and Ser160-Glu165. Among the structurally related four-helical bundle cytokines, the structure of IFN a-2a is most similar to that of human interferon a-2b and murine interferon-b. From this structural information and mutagenesis data, areas on the surface of the protein are identi®ed which seem to be important in receptor interactions.
Preparative Biochemistry & Biotechnology, 2019
Type I interferons (IFNs) are homologous cytokines that bind to a cell surface receptor and establish signaling pathways that motivate immune responses. The purpose of the current study is to assess the activity of a novel-engineered IFN-a2b. The crystallographic structure of IFN-a2b and its receptors was acquired from Protein Data Bank. Various amino acid substitutions were designed based on structural properties and other biological characteristics of residues to find the most effective amino acid on IFN affinity to advanced activities. The IFN-a2b mutants and receptors have been modeled and the interactions between two proteins have been studied as in silico by protein-protein docking for both mutants and native forms. The proper nucleic acid sequence IFN-a2 (T79Q) has been prepared based on the selected mutant. The modified IFN gene was cloned in pcDNA 3.1(À) and introduced to Chinese Hamster Ovary (CHO) cell line. Antiviral and antiproliferative assays of native and IFN-a2 (T79Q) proteins were performed in vitro. The results showed twofold increasing in IFN-a2 (T79Q) activity (antiviral and antiproliferative activity) in comparison to native IFN-a2b. This engineered IFN-a2b may have significant novel therapeutic applications and in silico studies can be an influential method for practical research function and structure of these molecules.
Structure-function studies of human interferons-[alpha]: Enhanced activity on human and murine cells
Antiviral research, 1991
To identify functionally important regions of the human interferon (IFN)-a molecule, mutagenesis in vitro of human IFN-a genes was used to create analogs with deletions or specific amino acid replacements. These analogs were expressed in vitro using SP6 RNA polymerase and a rabbit reticulocyte lysate protein synthesis system. Deletion of 7 highly conserved hydrophilic amino acids from the Cterminus of human IFN-a4 reduced, but did not abolish, antiviral activity on human cells. However, analogs with deletions of 15 or 25 amino acids from the C-terminus, or 28 amino acids from the N-terminus, had no measurable antiviral activity. The antiviral activity of human IFN-a4 was increased by substitution of cysteine for serine at position 86, and lysine for arginine at position 121. However, other amino acid substitutions at positions 121, 122 or 123 reduced antiviral activity. The size of the side chain of the amino acid residue at position 130 was shown to be important. Replacement of the absolutely conserved leucine residue at position 13 l with glutamine had little effect on antiviral activity. However, the introduction of a proline residue at this position abolished antiviral activity, probably due to the formation of a fl turn in the polypeptide chain. The antiviral activity of human IFN-a4 on murine cells was increased by substitutions at positions 86, 121 and 133. This study illustrates the utility of the in vitro mutagenesis and rabbit reticulocyte lysate systems for the investigation of structure-function relationships, and extends our knowledge of the biologically active regions and species specificity of the human IFN-a molecule.
The crystal structure of human interferon β at 2.2-Å resolution
Proceedings of the National Academy of Sciences, 1997
Type I interferons (IFNs) are helical cytokines that have diverse biological activities despite the fact that they appear to interact with the same receptor system. To achieve a better understanding of the structural basis for the different activities of ␣ and  IFNs, we have determined the crystal structure of glycosylated human IFN- at 2.2-Å resolution by molecular replacement. The molecule adopts a fold similar to that of the previously determined structures of murine IFN- and human IFN-␣ 2b but displays several distinct structural features. Like human IFN-␣ 2b , human IFN- contains a zinc-binding site at the interface of the two molecules in the asymmetric unit, raising the question of functional relevance for IFN- dimers. However, unlike the human IFN-␣ 2b dimer, in which homologous surfaces form the interface, human IFN- dimerizes with contact surfaces from opposite sides of the molecule. The relevance of the structure to the effects of point mutations in IFN- at specific exposed residues is discussed. A potential role of ligand-ligand interactions in the conformational assembly of IFN receptor components is discussed.