Structural comparisons among the short-chain helical cytokines

Abstract

Background: Cytokines and growth factors are soluble proteins that regulate the development and activities of many cell types. One group of these proteins have structures based on a four-helix bundle, though this similarity is not apparent from amino acid sequence comparisons. An understanding of how diverse sequences can adopt the same fold would be useful for recognizing and aligning distant homologs and for applying structural information gained from one protein to other sequences. Results: We have approached this problem by comparing the five known structures which adopt a granulocytemacrophage colony-stimulating factor (GM-CSF)-like, or short-chain fold: interleukin (IL)-4, GM-CSF, IL-2, IL-5, and macrophage colony-stimulating factor. The comparison reveals a common structural framework of five segments including 31 inner-core and 30 largely exposed residues. Buried polar interactions found in each protein illustrate how complementary substitutions maintain protein stability and may help specify unique core packing. A profile based on the known structures is not sufficient to guarantee accurate amino acid sequence alignments with other family members. Comparisons of the conserved short-chain framework with growth hormone define the optimal structural alignment. Conclusions: Our results are useful for extrapolating functional results among the short-chain cytokines and growth hormone, and provide a foundation for similar characterization of other subfamilies. These results also show that the placement of polar residues at different buried positions in each protein complicates sequence comparisons, and they document a challenging test case for methods aimed at recognizing and aligning distant homologs. 1994, 2:159-173 Structure 15 March

Threading analysis suggests that the obese gene product may be a helical cytokine

“…The helical cytokines are a diverse family in which there is no detectable sequence similarity between its members, but where all possess a common 'core' substructure containing a 4-helix bundle with a distinctive 'up-up-down-down' topology [18]. Proteins in this family for which 3-dimensional structures are available include interleukin-2 [19] (IL2), interleukin-4 [20] (IL-4), granulocyte-macrophage colony-stimulating factor [21] (GMCSF), macrophage colony-stimulating factor [22] (M-CSF), granulocyte colony-stimulating factor [23] (G-CSF), growth hormone [24] (GH), and interferon-fl [25] (IFN-fl).…”

“…Proteins in this family for which 3-dimensional structures are available include interleukin-2 [19] (IL2), interleukin-4 [20] (IL-4), granulocyte-macrophage colony-stimulating factor [21] (GMCSF), macrophage colony-stimulating factor [22] (M-CSF), granulocyte colony-stimulating factor [23] (G-CSF), growth hormone [24] (GH), and interferon-fl [25] (IFN-fl). Division into subclasses based on structural similarities beyond the 4-helix bundle places IL-2, IL4, GM-CSF and M-CSF into the 'short-chain' subclass, G-CSF and GH in the 'long-chain' subclass, and IFN-fl in the 'interferon-like' subclass [18]. The finding that the ob protein sequence is compatible with the IL-2 structure suggests that it should to some extent be compatible with the structures of the other helical cytokines.…”

“…All rights reserved. SSDI 0014-5793(95)00977-9 ture similar to the helical cytokines, proteins which function as mediators of cell-to-cell communication [18]. We present a threading-derived alignment of the ob gene product and the common structural core of the helical cytokines, and discuss the implications of this putative structural model with respect to the biological function of oh.…”

“…For threading experiments we omit the putative N-terminal signal sequence of 21 residues [4]. The structural alignment of helical cytokines shown in Table 2 is based on that presented by Rozwarski et al [18], with extension to the long-chain and interferon-like subclasses by manual superposition using the program Insight, from Biosym Technologies Inc. Root mean square superposition residuals for all models with complete backbone coordinates are under 3 A. Coordinates for known cytokines were taken from the Protein Data Bank [17], with accession codes as indicated in the header to Table 1. Residue numbering for known cytokines as shown in Table 2 corresponds to that in the Protein Data Bank file.…”

Small-Molecule Inhibitors of IL-2/IL-2R: Lessons Learned and Applied

“…3) determined in 1987 (Brandhuber et al 1987). IL-2 is a compact globular protein, composed of four tightly packed a-helices adopting a down-down-up-up configuration (cytokine fold) common to many interleukins and (Bazan 1990;Rozwarski et al 1994). A single disulfide bond establishes a covalent link between helix A and the middle of a 13 residue stretch of extended peptide preceding helix D. Site-specific mutagenesis identified a set of surface residues (Lys 35, Arg 38, Phe 42, Lys 43) critical for receptor binding; these residues lie on a concave face of IL-2 whose character (hydrophobic and basic) and location were consistent with a ligand-receptor hotspot for the PPI (Sauve et al 1991).…”