A homology model of human interferon alpha-2

Diversity of folding pathways and folding models of disulfide proteins

Comprehensive understanding of the mechanism of protein folding requires the elucidation of both a folding pathway and a folding model. This entails characterization of the properties and structures of folding intermediates populated along the folding pathway, as well as the formation and interplay of secondary structures and tertiary structures along the course of folding. Using the conventional unfolding-refolding technique, there are limitations of acquiring these data in detail because of the inherent difficulty of trapping and analysis of folding intermediates. The technique of oxidative folding, in contrast, permits trapping, isolation, and further structural characterization of folding intermediates at any stage of the folding process. In this brief review, we present the potential of the technique of oxidative folding for concurrent analysis of both folding pathways and folding models.

Pathway of Oxidative Folding of Bovine α-Interferon: Predominance of Native Disulfide-Bonded Folding Intermediates

Bovine alpha-interferon (BoINF-alpha) is a single polypeptide protein containing 166 amino acids, two disulfide bonds (Cys1-Cys99 and Cys29-Cys138), and five stretches of alpha-helical structure. The pathway of oxidative folding of BoINF-alpha has been investigated here. Of the eight possible one- and two-disulfide isomers, only two nativelike one-disulfide isomers, BoINF-alpha (Cys1-Cys99) and BoINF-alpha (Cys29-Cys138), predominate as intermediates along the folding pathway. More strikingly, alpha-helical structures formed almost quantitatively before any detectable formation of a disulfide bond. This is demonstrated by the observation that fully reduced BoINF-alpha (starting material of oxidative folding) and reduced carboxymethylated BoINF-alpha both exhibit alpha-helical structure content indistinguishable form that of native BoINF-alpha. The folding mechanism of BoINF-alpha appears to be compatible with the framework model, in which secondary structures fold first, followed by docking (compaction) of preformed secondary structural elements yielding the native structure.

Divergence of Binding, Signaling, and Biological Responses to Recombinant Human Hybrid IFN

Three human IFN-α hybrids, HY-1 [IFN-α21a(1-75)/α2c(76-165)], HY-2 [IFN-α21a(1-95)/α2c(96-165)], and HY-3 [IFN-α2c(1-95)/α21a(96-166)], were constructed, cloned, and expressed. The hybrids had comparable specific antiviral activities on Madin-Darby bovine kidney (MDBK)3 cells but exhibited very different antiproliferative and binding properties on human Daudi and WISH cells and primary human lymphocytes. Our data suggest that a portion of the N-terminal region of the molecule is important for interaction with components involved in binding of IFN-α2b while the C-terminal portion of IFN is critical for antiproliferative activity. A domain affecting the antiproliferative activity was found within the C-terminal region from amino acid residues 75–166. The signal transduction properties of HY-2 and HY-3 were evaluated by EMSA and RNase protection assays. Both HY-2 and HY-3 induced activation of STAT1 and 2. However, HY-2 exhibited essentially no antiproliferative effects at concentrations that activated STAT1 and 2. Additionally, at concentrations where no antiproliferative activity was seen, HY-2 induced a variety of IFN-responsive genes to the same degree as HY-3. RNase protection assays also indicate that, at concentrations where no antiproliferative activity was seen for HY-2, this construct retained the ability to induce a variety of IFN-inducible genes. These data suggest that the antiproliferative response may not be solely directed by the activation of the STAT1 and STAT2 pathway in the cells tested.

IFN-tau: a novel subtype I IFN1. Structural characteristics, non-ubiquitous expression, structure-function relationships, a pregnancy hormonal embryonic signal and cross-species therapeutic potentialities

IFN-tau (IFN-tau) constitutes a new class of type I IFN which is not virus-inducible, unlike IFN-alpha and IFN-beta, but is constitutively produced by the trophectoderm of the ruminant conceptus during a very short period in early pregnancy. It plays a pivotal role in the mechanisms of maternal recognition of pregnancy in ruminants and it displays high antiviral and antiproliferative activities across species with a prominent lack of cytotoxicity at high concentrations in vitro in cell culture and possibly in vivo. It exhibits high antiretroviral activity against HIV and exhibits immunosuppressive activity in a multiple sclerosis model and reduces embryo and fetal mortality by stimulation of IL-10 production. In this review all the biochemical and para-hormonal properties of this novel IFN-tau are described in detail: structural characteristics of proteins and genes, trophoblast expression, regulation of its expression, structure of its gene promoter, its absence in human species and in non-ruminant animals, the evolution of the IFN-tau genes, its structure-function relationships with its three-dimensional structure, structural localization of biological activities, its lack of cytotoxicity and its receptor. Surprisingly, for an IFN, IFN-tau is also a pregnancy-embryonic signal with paracrine antiluteolytic activity. In order to maintain luteal progesterone secretion, IFN-tau inhibits PGF-2alpha pulsatile secretion and oxytocin uterine receptivity in early pregnancy. It is believed to suppress pulsatile release of endometrial PGF-2alpha by preventing oxytocin and estrogen receptor expression. Additionally, it directly regulates prostaglandin metabolism and possibly the PGE:PGF-2alpha ratio.

Structural and functional differences between glycosylated and non-glycosylated forms of human interferon-beta (IFN-beta)

PURPOSE

Two recombinant IFN-beta products have been approved for the treatment of multiple sclerosis, a glycosylated form with the predicted natural amino acid sequence (IFN-beta-1a) and a non-glycosylated form that has a Met-1 deletion and a Cys-17 to Ser mutation (IFN-beta-1b). The structural basis for activity differences between IFN-beta-1a and IFN-beta-1b, is determined.

METHODS

In vitro antiviral, antiproliferative and immunomodulatory assays were used to directly compare the two IFN-beta products. Size exclusion chromatography (SEC), SDS-PAGE, thermal denaturation, and X-ray crystallography were used to examine structural differences.

RESULTS

IFN-beta-1a was 10 times more active than IFN-beta-1b with specific activities in a standard antiviral assay of 20 x 10(7) IU/mg for IFN-beta-1a and 2 x 10(7) IU/mg for IFN-beta-1b. Of the known structural differences between IFN-beta-1a and IFN-beta-1b, only glycosylation affected in vitro activity. Deglycosylation of IFN-beta-1a produced a decrease in total activity that was primarily caused by the formation of an insoluble disulfide-linked IFN precipitate. Deglycosylation also resulted in an increased sensitivity to thermal denaturation. SEC data for IFN-beta-1b revealed large, soluble aggregates that had reduced antiviral activity (approximated at 0.7 x 10(7) IU/mg). Crystallographic data for IFN-beta-1a revealed that the glycan formed H-bonds with the peptide backbone and shielded an uncharged surface from solvent exposure.

CONCLUSIONS

Together these results suggest that the greater biological activity of IFN-beta-1a is due to a stabilizing effect of the carbohydrate on structure.

Identification of an adenine-nucleotide-binding site on interferon alpha2

Using 32P-labeled 2-azidoadenosine 5'-triphosphate (2N3ATP) and 8-azidoadenosine 5'-triphosphate (8N3ATP), we have identified a site on human interferon alpha2 (IFN-alpha2) that binds adenine nucleotides. The results from saturation and competition experiments demonstrated the specificity of the nucleotide interaction. Half-maximal saturation of IFN-alpha2 was observed at 10 microM 2N3ATP or 35 microM 8N3ATP. ATP effectively decreased photoinsertion of both photoaffinity analogs of ATP. Photoinsertion of 8N3ATP was enhanced by MgCl2, independent of the ionic strength, and exhibited an optimum pH between 7.0 and 7.5. Immobilized-Al3+ affinity chromatography and HPLC were used to purify the modified peptides from IFN-alpha2 that had been photolabeled with 8N3ATP and digested with trypsin or chymotrypsin. Overlapping-sequence analysis localized the sites of photoinsertion to the region corresponding to Lys121-Tyr135 in the amino acid sequence of IFN-alpha2, which almost perfectly overlaps a nuclear-localization signal (R120KYFQRITLYLKEKKY135).

Modelling of the 3-D structure of IFN-alpha-k and characterization of its surface molecular properties

The 3-D structure of IFN-alpha-k (one of the alpha-interferon family) was constructed and optimized by molecular modelling starting from the X-ray structure of IFN-beta. The molecular surface of the optimized 3-D structure of IFN-alpha-k was then evaluated and characterized for its hydrophobicity/hydrophilicity. The structure of IFN-alpha-k was completed with its first segment (23 amino acid residues) called signal peptide. The 3-D structure of this segment was predicted to be in helical form bonded to the core by one loop. It was found that the complete structure of IFN-alpha-k can exist in at least two main conformations as far as the orientation of the signal peptide is concerned, i.e. in the open form (in which the signal peptide is directed outward of the 'body' of the molecule) and the closed form (where the signal peptide is aligned with the body). The relative stability of these forms strongly depends on the stabilization by the environment (e.g. by solvation) due to the prevailing hydrophilicity of the body and hydrophobic character of the signal peptide.

Interferons alpha/beta and their receptors: place in the hierarchy of cytokines

Interferons alpha/beta (IFNs-alpha/beta) are the first cytokines to be produced by recombinant DNA technology. They regulate growth and differentiation, affecting cellular communication, signal transduction pathways and immunological control. This review focuses on the relationships between the structure and biological activities of IFNs-alpha/beta induced as a result of specific interactions with different types of polypeptide receptors as well as on the role of glycolipids in the modulation of these activities. The discovery of the primary structure homology of HuIFNs-alpha and thymus hormone-thymosin alpha 1 (TM alpha 1), the experimental finding of the competition between IFN-alpha and TM alpha 1 for common receptors and the reproduction by reHuIFN-alpha 2 of TM alpha 1 immunomodulating activities create the basis of reHuIFN-alpha therapeutics instead of TM alpha 1, and potentiation of vaccines by reHuIFN-alpha. The first successful attempt at grafting of the HuIFN-alpha 2s TM alpha 1-like immunomodulating site to the designed de novo protein albeferon is described. This article also aims at reviewing recent data concerning the structure of other cytokines and their receptors. Their reciprocal structure-function taxonomy is proposed. The place of IFNs-alpha/beta and their receptors in the hierarchy of cytokines is determined.

Structure-activity of type I interferons

Type I IFNs constitute a family of proteins exhibiting high homology in primary, secondary, and tertiary structures. They interact with the same receptor and transmit signals to cellular nucleus through a similar mechanism, eliciting roughly homogeneous biological activity. Nevertheless, the members of that family, IFN alpha species, IFN beta and IFN omega, due to local differences in the structure sometime show distinct properties. From the reported data it results that even minute changes or differences in the primary sequences could be responsible for a significant variety of biological actions, thus inducing to the hypothesis that Type I IFNs, rather than to be the result of a redundant replication during the evolution play definite roles in the defense of living organisms to foreign agents.

Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography

BACKGROUND

The human alpha-interferon (huIFN-alpha) family displays broad spectrum antiviral, antiproliferative and immunomodulatory activities on a variety of cell types. The diverse biological activities of the IFN-alpha's are conveyed to cells through specific interactions with cell-surface receptors. Despite considerable effort, no crystal structure of a member of this family has yet been reported, because the quality of the protein crystals have been unsuitable for crystallographic studies. Until now, structural models of the IFN-alpha's have been based on the structure of murine IFN-beta (muIFN-beta). These models are likely to be inaccurate, as the amino acid sequence of muIFN-beta differs significantly from the IFN-alpha's at proposed receptor-binding sites. Structural information on a huIFN-alpha subtype would provide an improved basis for modeling the structures of the entire IFN-alpha family.

RESULTS

The crystal structure of recombinant human interferon-alpha 2b (huIFN-alpha 2b) has been determined at 2.9 A resolution. HuIFN-alpha 2b exists in the crystal as a noncovalent dimer, which associates in a novel manner. Unlike other structurally characterized cytokines, extensive interactions in the dimer interface are mediated by a zinc ion (Zn2+). The overall fold of huIFN-alpha 2b is most similar to the structure of muIFN-beta. Unique to huIFN-alpha 2b is a 3(10) helix in the AB loop which is held to the core of the molecule by a disulfide bond.

CONCLUSIONS

The structure of huIFN-alpha 2b provides an accurate model for analysis of the > 15 related type 1 interferon molecules. HuIFN-alpha 2b displays considerable structural similarity with muIFN-beta, interleukin-10 and interferon-gamma, which also bind related class 2 cytokine receptors. From these structural comparisons and numerous studies on the effects of mutations on biological activity, we have identified protein surfaces that appear to be important in receptor activation. This study also reveals the potential biological importance of the huIFN-alpha 2b dimer.

Refolding, isolation and characterization of crystallizable human interferon-alpha 8 expression in Saccharomyces cerevisiae

Human interferon-alpha 8 was expressed in Saccharomyces cerevisiae and found to accumulate intracellularly in an insoluble form. The protein could be solubilized and converted to a biologically active form with high yield by a denaturation-refolding procedure. The interferon-alpha 8 was further purified to apparent homogeneity by copper-chelate affinity chromatography and anion-exchange chromatography and fully characterized by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE), N-terminal sequence analysis, mass spectrometry, circular-dichroism (CD) spectroscopy and specific activity. Secondary-structure predictions from CD spectroscopy indicate that the molecule is correctly folded. Peptide mapping supported the correct sequence and the expected disulfide-bridge connectivity. The purified protein elutes on reversed-phase high-pressure liquid chromatography (RP-HPLC) as two peaks. Electrospray mass spectrometry and N-terminal sequence analysis of the minor component indicated the existence of an N-terminal acetyl group for the later eluting HPLC-component. In anti-viral assays, the two IFN forms were equally active. Hexagonal crystals of this interferon preparation could be obtained. On the basis of the electrophoretic mobility, HPLC profile, and biological activity assay, the crystalline material was judged to be identical to the uncrystallized interferon. Interferon in crystallized form was found to be stable for up to 24 months and, therefore, could be used for long-term storage, particularly for material intended for clinical use.

A three-dimensional model of interferon-tau

The interferon-tau (IFN-tau) are type I IFN whose expression is restricted to the embryonic trophectoderm of the developing placenta of ruminant ungulate species, where they act as hormones of pregnancy. Here computer modeling has been used to generate homology models of bovine and ovine IFN-tau based on the refined crystal structure of murine IFN-beta. The IFN-tau structure, like that of MuIFN-beta, is based on five long alpha helices (A-E), one short helix in the middle of the loop connecting helices C and D and a long loop between helices A and B. BoIFN-tau differs from MuIFN-beta in three important respects. First, as in all IFN-tau, there is a carboxyl tail of nine amino acids that cannot be accurately modeled but that would have a length of approximately 30 A when fully extended. Second, like the IFN-alpha subtype, all IFN-tau have a three-amino acid insertion in loop AB and a likely disulfide bridge between Cys29 and Cys139 that lead to marked conformational differences between them and MuIFN-beta in a region (Leu22 to Arg33 in IFN-tau) believed to interact with the receptor. Third, all IFN-tau, as well as the related IFN-omega, possess a Gly at position 126 (rather than the equivalent Arg on MuIFN-beta and IFN-alpha) that will impair an extensive hydrogen bonding interaction between helix D and loop AB. As a result, the polypeptide segment around this region (Phe36 to Gln40) of loop AB is likely to be considerably more flexible than in other type I IFN.

Interferon-alpha hybrids

The alpha-interferons (IFN-alpha) belong to a family of polypeptides comprising several subtypes. Using recombinant DNA technology, it has been possible to create IFN hybrids that provide novel combinations of the amino acid residues from the parental protein sequences. They have been used to study structure-activity relationships of IFN-alpha and interactions with the IFN-alpha receptor, and to create analogs of natural IFNs with novel properties for potential therapeutic application. The biological data obtained with these hybrids are now evaluated in terms of the published structural and homology models of IFN-beta and -alpha.

Interferon receptor recognition peptides enhance the biological potency of interferon alphas

Based on our earlier studies that defined three strategic regions in the Type 1 interferon (IFN) molecule associated with receptor interactions and biological activity, three IFN receptor recognition peptides (IRRP) were synthesized, with amino acid sequences CLKDRHD (IRRP1), ESLLEKFYTELYQQLND (IRRP2) and YFQRITLYLTEKKYSPCA (IRRP3) and examined for biological effectiveness. In cell surface receptor binding studies, the binding capacity of cells for IFN-alpha s was increased in the presence of the IRRPs. Increased receptor occupancy resulted in increased phosphorylation-activation of the transcription factor ISGF3 and enhanced antiviral activity. The potentiating effect on IFN-induced growth inhibition was less marked. These data suggest that the IRRPs may influence the biological potency of IFN-alpha by facilitating accessibility to cell surface receptor components. The IRRPs may function to increase the number of low affinity receptor-ligand interactions necessary to initiate receptor oligomerization, thereby catalysing the formation of high affinity IFN-receptor complexes.

Homology model of human interferon-alpha 8 and its receptor complex

Human interferon-alpha 8 (HuIFN alpha 8), a type I interferon (IFN), is a cytokine belonging to the hematopoietic super-family 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 IFN alpha 8. Both of these receptor proteins have been identified as members of the immunoglobulin superfamily of which HGH 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 HuIFN alpha 8 with the receptor subunits were built by superpositioning the conserved C alpha backbone of the HuIFN alpha 8 and receptor subunit models with HGH and its receptor complex. The HuIFN alpha 8 model was constructed from the C alpha coordinates of murine interferon-beta crystal structure. Electrostatic potentials and hydrophobic interactions appear to favor the model of HuIFN alpha 8 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 HuIFN alpha 8 correspond to functionally important residues determined previously for human IFN alpha 1, IFN alpha 2, and IFN alpha 4 subtypes by site-directed mutagenesis studies. The models predict regions of interaction between HuIFN alpha 8 and each of the receptor proteins, and provide insights into interactions between other type I IFNs (IFN-alpha subtypes and IFN-beta) and their respective receptor components.