The solution structure of the cytokine-binding domain of the common beta-chain of the receptors for granulocyte-macrophage colony-stimulating factor, interleukin-3 and interleukin-5

A Photoprotective Effect by Cation-π-Interaction? Quenching of Singlet Oxygen by an Indole Cation-π Model System

We investigated the effect of the cation-π interaction on the susceptibility of a tryptophan model system toward interaction with singlet oxygen, that is, type II photooxidation. The model system consists of two indole units linked to a lariat crown ether to measure the total rate of removal of singlet oxygen by the indole units in the presence of sodium cations (i.e. indole units subject to a cation-π interaction) and in the absence of this interaction. We found that the cation-π interaction significantly decreases the total rate of removal of singlet oxygen (k_T ) for the model system, that is, (k_T  = 2.4 ± 0.2) × 10⁸  m^-1  s^-1 without sodium cation vs (k_T  = 6.9 ± 0.9) × 10⁷  m^-1  s^-1 upon complexation of sodium cation to the crown ether. Furthermore, we found that the indole moieties undergo type I photooxidation processes with triplet excited methylene blue; this effect is also inhibited by the cation-π interaction. The chemical rate of reaction of the indole groups with singlet oxygen is also slower upon complexation of sodium cation in our model system, although we were unable to obtain an exact ratio due to differences of the chemical reaction rates of the two indole moieties.

Investigations on the role of π-π interactions and π-π networks in eNOS and nNOS proteins

π-π Interactions play an important role in the stability of protein structures. In the present study, we have analyzed the influence of π-π interactions in eNOS and nNOS proteins. The contribution of these π-π interacting residues in sequential separation, secondary structure involvement, solvent accessibility and stabilization centers has been evaluated. π-π interactions stabilize the core regions within eNOS and nNOS proteins. π-π interacting residues are evolutionary conserved. There is a significant number of π-π interactions in spite of the lesser natural occurrences of π-residues in eNOS and nNOS proteins. In addition to π-π interactions, π residues also form π-π networks in both eNOS and nNOS proteins which might play an important role in the structural stability of these protein structures.

Arginine and Lysine interactions with π residues in metalloproteins

Metalloproteins have many different functions in cells such as enzymes; signal transduction, transport and storage proteins. About one third of all proteins require metals to carry out their functions. In the present study we have analyzed the roles played by Arg and Lys (cationic side chains) interactions with π (Phe, Tyr or Trp) residues and their role in the structural stability of metalloproteins. These interactions might play an important role in the global conformational stability in metalloproteins. In spite of its lower natural occurrence (1.76%) the number of Trp residues involved in energetically significant interactions is higher in metalloproteins.

The WSXWS motif in cytokine receptors is a molecular switch involved in receptor activation: insight from structures of the prolactin receptor

The prolactin receptor (PRLR) is activated by binding of prolactin in a 2:1 complex, but the activation mechanism is poorly understood. PRLR has a conserved WSXWS motif generic to cytokine class I receptors. We have determined the nuclear magnetic resonance solution structure of the membrane proximal domain of the human PRLR and find that the tryptophans of the motif adopt a T-stack conformation in the unbound state. By contrast, in the hormone bound state, a Trp/Arg-ladder is formed. The conformational change is hormone-dependent and influences the receptor-receptor dimerization site 3. In the constitutively active, breast cancer-related receptor mutant PRLR(I146L), we observed a stabilization of the dimeric state and a change in the dynamics of the motif. Here we demonstrate a structural link between the WSXWS motif, hormone binding, and receptor dimerization and propose it as a general mechanism for class 1 receptor activation.

Structural stability studies in adhesion molecules--role of cation-π interactions

Cell adhesion molecules are important for their various roles in many cellular events and responses. In the present study, we have analyzed the roles played by cation-π interactions in the structural stability of adhesion molecules. These interactions are mainly formed by long-range contacts. The occurrence of arginine is higher than lysine to form cation-π interactions. The secondary structure preferences of interacting residues are independent of amino acid class. Cation-π interactions might stabilize the interface between the terminus and core in this class of proteins. The results obtained in the present study will be useful in understanding the contribution of cation-π interactions to the overall stability of adhesion proteins.

Nature of cation-pi interactions and their role in structural stability of immunoglobulin proteins

Cation-pi interactions are known to be important contributors to protein stability and ligand-protein interactions. In this study, we have analyzed the influence of cation-pi interactions in single chain immunoglobulin proteins. We observed 87 cation-pi interactions in a data set of 33 proteins. These interactions are mainly formed by long-range contacts, and there is preference of Arg over Lys in these interactions. Arg-Tyr interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp-cation interactions is quite high. This information suggests that the cation-pi interactions involving Trp might be of high relevance to the proteins. Secondary structure analysis reveals that cation-pi interactions are formed preferably between residues in which at least one is in beta-strand. Proteins having beta-strand regions have the highest number of cation-pi interaction-forming residues.

The granulocyte-macrophage colony-stimulating factor receptor: linking its structure to cell signaling and its role in disease

Already 20 years have passed since the cloning of the granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor alpha-chain, the first member of the GM-CSF/interleukin (IL)-3/IL-5 family of hemopoietic cytokine receptors to be molecularly characterized. The intervening 2 decades have uncovered a plethora of biologic functions transduced by the GM-CSF receptor (pleiotropy) and revealed distinct signaling networks that couple the receptor to biologic outcomes. Unlike other hemopoietin receptors, the GM-CSF receptor has a significant nonredundant role in myeloid hematologic malignancies, macrophage-mediated acute and chronic inflammation, pulmonary homeostasis, and allergic disease. The molecular mechanisms underlying GM-CSF receptor activation have recently been revealed by the crystal structure of the GM-CSF receptor complexed to GM-CSF, which shows an unexpected higher order assembly. Emerging evidence also suggests the existence of intracellular signosomes that are recruited in a concentration-dependent fashion to selectively control cell survival, proliferation, and differentiation by GM-CSF. These findings begin to unravel the mystery of cytokine receptor pleiotropy and are likely to also apply to the related IL-3 and IL-5 receptors as well as other heterodimeric cytokine receptors. The new insights in GM-CSF receptor activation have clinical significance as the structural and signaling nuances can be harnessed for the development of new treatments for malignant and inflammatory diseases.

Clarification of the role of N-glycans on the common beta-subunit of the human IL-3, IL-5 and GM-CSF receptors and the murine IL-3 beta-receptor in ligand-binding and receptor activation

Granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-3 and IL-5 are related cytokines that play key roles in regulating the differentiation, proliferation, survival and activation of myeloid blood cells. The cell surface receptors for these cytokines are composed of cytokine-specific alpha-subunits and a common beta-receptor (betac), a shared subunit that is essential for receptor signaling in response to GM-CSF, IL-3 and IL-5. Previous studies have reached conflicting conclusions as to whether N-glycosylation of the betac-subunit is necessary for functional GM-CSF, IL-3 and IL-5 receptors. We sought to clarify whether betac N-glycosylation plays a role in receptor function, since all structural studies of human betac to date have utilized recombinant protein lacking N-glycosylation at Asn(328). Here, by eliminating individual N-glycans in human betac and the related murine homolog, beta(IL-3), we demonstrate unequivocally that ligand-binding and receptor activation are not critically dependent on individual N-glycosylation sites within the beta-subunit although the data do not preclude the possibility that N-glycans may exert some sort of fine control. These studies support the biological relevance of the X-ray crystal structures of the human betac domain 4 and the complete ectodomain, both of which lack N-glycosylation at Asn(328).

Exploring the role of cation–π interactions in glycoproteins lipid-binding proteins and RNA-binding proteins

We have analyzed and compared the influence of cation-pi interactions in glycoproteins (GPs), lipid-binding proteins (LBPs) and RNA-binding proteins (RBPs) in this study. We observed that all the proteins included in the study had profound cation-pi interactions. There is an average of one energetically significant cation-pi interaction for every 71 residues in GPs, for every 58 residues in LBPs and for every 64 residues in RBPs. Long-range contacts are predominant in all the three types of proteins studied. The pair-wise cation-pi interaction energy between the positively charged and aromatic residues shows that Arg-Trp pair energy was the strongest among all six possible pairs in all the three types of proteins studied. There were considerable differences in the preference of cation-pi interacting residues to different secondary structure elements and ASA and these might contribute to differences in biochemical functions of GPs, LBPs and RBPs. It was interesting to note that all the five residues involved in cation-pi interactions were found to have stabilization centers in GPs, LBPs and RBPs. Majority of the cation-pi interacting residues investigated in the present study had a conservation score of 6, the cutoff value used to identify the stabilizing residues. A small percentage of cation-pi interacting residues were also present as stabilizing residues. The cation-pi interaction-forming residues play an important role in the structural stability of in GPs, LBPs and RBPs. The results obtained in this study will be helpful in further understanding the stability, specificity and differences in the biochemical functions of GPs, LBPs and RBPs.

Influence of cation-π interactions on RNA-binding proteins

The energy contribution due to cation-pi interactions has been computed for 37 RNA binding proteins. The contribution of these cation-pi interacting residues in sequential separation, secondary structure involvement, solvent accessibility, and stabilization centers has been evaluated. Sequential separation of the cation-pi involving residues show that, long range contacts predominates in all the proteins studied. Lys and Arg prefers to be in helical structures. Of the cation-pi interacting residues, Arg and Lys were in the exposed regions and the aromatic residues (Phe, Tyr and Trp) were in the buried and partially buried regions in the protein structures. Stabilization centers for these proteins showed that all the five residues found in cation-pi interactions are important in locating one or more of such centers. On the whole, the results presented in this work will be very useful for further investigations on the specificity and selectivity of RNA binding proteins and also for their structural studies.

Exploring the environmental preference of weak interactions in (α/β)8 barrel proteins

The environmental preference for the occurrence of noncanonical hydrogen bonding and cation-pi interactions, in a data set containing 71 nonredundant (alpha/beta)(8) barrel proteins, with respect to amino acid type, secondary structure, solvent accessibility, and stabilizing residues has been performed. Our analysis reveals some important findings, which include (a) higher contribution of weak interactions mediated by main-chain atoms irrespective of the amino acids involved; (b) domination of the aromatic amino acids among interactions involving side-chain atoms; (c) involvement of strands as the principal secondary structural unit, accommodating cross strand ion pair interaction and clustering of aromatic amino acid residues; (d) significant contribution to weak interactions occur in the solvent exposed areas of the protein; (e) majority of the interactions involve long-range contacts; (f) the preference of Arg is higher than Lys to form cation-pi interaction; and (g) probability of theoretically predicted stabilizing amino acid residues involved in weak interaction is higher for polar amino acids such as Trp, Glu, and Gln. On the whole, the present study reveals that the weak interactions contribute to the global stability of (alpha/beta)(8) TIM-barrel proteins in an environment-specific manner, which can possibly be exploited for protein engineering applications.

IL-3, IL-5, and GM-CSF signaling: crystal structure of the human beta-common receptor

The cytokines, interleukin-3 (IL-3), interleukin-5 (IL-5), and granulocyte-macrophage colony stimulating factor (GM-CSF), are polypeptide growth factors that exhibit overlapping activities in the regulation of hematopoietic cells. They appear to be primarily involved in inducible hematopoiesis in response to infections and are involved in the pathogenesis of allergic and inflammatory diseases and possibly in leukemia. The X-ray structure of the beta common (betac) receptor ectodomain has given new insights into the structural biology of signaling by IL-3, IL-5, and GM-CSF. This receptor is shared between the three ligands and functions together with three ligand-specific alpha-subunits. The structure shows betac is an intertwined homodimer in which each chain contains four domains with approximate fibronectin type-III topology. The two betac-subunits that compose the homodimer are interlocked by virtue of the swapping of beta-strands between domain 1 of one subunit and domain 3 of the other subunit. Site-directed mutagenesis has shown that the interface between domains 1 and 4 in this unique structure forms the functional epitope. This epitope is similar to those of other members of the cytokine class I receptor family but is novel in that it is formed by two different receptor chains. The chapter also reviews knowledge on the closely related mouse beta(IL-3) receptor and on the alpha-subunit-ligand interactions. The knowledge on the two beta receptors is placed in context with advances in understanding of the structural biology of other members of the cytokine class I receptor family.

Structural analysis of cation-pi interactions in DNA binding proteins

Cation-pi interactions play an important role in the stability of protein structures. In this work, we have analyzed the influence of cation-pi interactions in DNA binding proteins. We observed cation-pi interactions in 45 out of 62 DNA binding proteins and there is no significant correlation between the number of amino acid residues and number of cation-pi interactions. These interactions are mainly formed by long-range contacts, and the role of short and medium-range contacts is minimal. The preference of Arg is higher than Lys to form cation-pi interactions. The pair-wise cation-pi interaction energy between aromatic and positively charged residues shows that Arg-Tyr energy is the strongest among the possible six pairs. The structural analysis of cation-pi interaction forming residues shows that Lys, Trp, and Tyr prefer to be in the binding site of protein-DNA complexes. Further, the accessible surface areas of cation-pi interaction forming cationic residues are significantly less than that of other residues. The preference of cation-pi interaction forming residues in different secondary structures shows that Lys prefers to be in strand and Phe prefers to be in turn regions. The results obtained in the present study will be useful in understanding the contribution of cation-pi interactions to the stability and specificity of protein-DNA complexes.

Structural analysis of residues involving cation-π interactions in different folding types of membrane proteins

Cation-pi interactions play an important role to the stability of protein structures. In our earlier work, we have analyzed the influence and energetic contribution of cation-pi interactions in three-dimensional structures of membrane proteins. In this work, we investigate the characteristic features of residues that are involved in cation-pi interactions. We have computed several parameters, such as surrounding hydrophobicity, number of long-range contacts, conservation score and normalized B-factor for all these residues and identified their location, whether in the membrane or at surface. We found that the cation-pi interactions are mainly formed by long-range interactions. The cationic residues involved in cation-pi interactions have higher surrounding hydrophobicity than their average values in the whole dataset and an opposite trend is observed for aromatic residues. In transmembrane helical proteins, except Phe, all other residues that are responsible for cation-pi interactions are highly conserved with other related protein sequences whereas in transmembrane strand proteins, an appreciable conservation is observed only for Arg. The analysis on the flexibility of residues reveals that the cation-pi interaction forming residues are more stable than other residues. The results obtained in the present study would be helpful to understand the role of cation-pi interactions in the structure and folding of membrane proteins.

Molecular mechanisms of cytokine receptor activation

Cytokine receptors are transmembrane proteins that transmit a signal into the cell upon ligand binding. Commonly, these molecules have one hydrophobic segment of about 20-26 amino acids that is believed to span the membrane as a helix and this divides these receptors into extra- and intracellular components. By utilizing two different epitopes, the cytokines bridge two receptor chains, resulting in a close proximity of the intracellular component and thereby initiating the intracellular signalling cascade. The dimerization event is believed to be the mechanism by which the signal is transmitted across a membrane. In the light of new results obtained for the erythropoietin receptor, James A. Wells questioned whether any dimer would be sufficient. This review will expand upon the above question by discussing the more complex signal-transducing receptor subunits of the Interleukin-6 type family of cytokines. Based on the recently solved quaternary structure of the Insulin receptor, possible analogies will be confronted.

The solution structure and intramolecular associations of the Tec kinase SRC homology 3 domain

Tec is the prototypic member of a family of intracellular tyrosine kinases that includes Txk, Bmx, Itk, and Btk. Tec family kinases share similarities in domain structure with Src family kinases, but one of the features that differentiates them is a proline-rich region (PRR) preceding their Src homology (SH) 3 domain. Evidence that the PRR of Itk can bind in an intramolecular fashion to its SH3 domain and the lack of a regulatory tyrosine in the C terminus indicates that Tec kinases must be regulated by a different set of intramolecular interactions to the Src kinases. We have determined the solution structure of the Tec SH3 domain and have investigated interactions with its PRR, which contains two SH3-binding sites. We demonstrate that in vitro, the Tec PRR can bind in an intramolecular fashion to the SH3. However, the affinity is lower than that for dimerization via reciprocal PRR-SH3 association. Using site-directed mutagenesis we show that both sites can bind the Tec SH3 domain; site 1 (155KTLPPAP161) binds intramolecularly, while site 2 (165KRRPPPPIPP174) cannot and binds in an intermolecular fashion. These distinct roles for the SH3 binding sites in Tec family kinases could be important for protein targeting and enzyme activation.

Peptide insertions in domain 4 of hbeta(c), the shared signalling receptor subunit for GM-CSF, IL3 and IL5, induce ligand-independent activation

A mutant form of the common beta-subunit of the GM-CSF, interleukin-3 (IL3) and IL5 receptors is activated by a 37 residue duplicated segment which includes the WSXWS motif and an adjacent, highly conserved, aliphatic/basic element. Haemopoietic expression of this mutant, hbeta(c)FIDelta, in mice leads to myeloproliferative disease. To examine the mechanism of activation of this mutant we targetted the two conserved motifs in each repeat for mutagenesis. Here we show that this mutant exhibits constitutive activity in BaF-B03 cells in the presence of mouse or human GM-CSF receptor alpha-subunit (GMRalpha) and this activity is disrupted by mutations of the conserved motifs in the first repeat. In the presence of these mutations the receptor reverts to an alternative conformation which retains responsiveness to human IL3 in a CTLL cell line co-expressing the human IL3 receptor alpha-subunit (hIL3Ralpha). Remarkably, the activated conformation is maintained in the presence of substitutions, deletions or replacement of the second repeat. This suggests that activation occurs due to insertion of extra sequence after the WSXWS motif and is not dependent on the length or specific sequence of the insertion. Thus hbeta(c) displays an ability to fold into functional receptor conformations given insertion of up to 37 residues in the membrane-proximal region. Constitutive activation most likely results from a specific conformational change which alters a dormant, inactive receptor complex, permitting functional association with GMRalpha and ligand-independent mitogenic signalling.

Structural and functional hot spots in cytokine receptors

The activation of cytokine receptors is a stepwise process that depends on their specific interaction with cognate cytokines, the formation of oligomeric receptor complexes, and the initiation of cytoplasmic phosphorylation events. The recent determination of the structure of extracellular domains of several cytokine receptors allows comparison of their cytokine-binding surfaces. This comparison reveals a common structural framework that supports considerable diversity and adaptability of the binding surfaces that determine both the specificity and the orientation of subunits in the active receptor complex. These regions of the cytokine receptors have been targeted for the development of specific agonists and antagonists. The physical coupling of signaling intermediates to the intracellular domains of their receptors plays a major role in determining biological responses to cytokines. In this review, we focus principally on the receptors for cytokines of the granulocyte-macrophage colony-stimulating factor (GM-CSF) family and, where appropriate, compare them with related cytokine receptors. Several paradigms are beginning to emerge that focus on the ability of the extracellular portion of the cytokine receptor to recognize the appropriate cytokine and on a phosphorylated motif in the intracellular region of the GM-CSF receptor that couples to a specific signaling pathway.

Structure of the complete extracellular domain of the common beta subunit of the human GM-CSF, IL-3, and IL-5 receptors reveals a novel dimer configuration

The receptor systems for the hemopoietic cytokines GM-CSF, IL-3, and IL-5 consist of ligand-specific alpha receptor subunits that play an essential role in the activation of the shared betac subunit, the major signaling entity. Here, we report the structure of the complete betac extracellular domain. It has a structure unlike any class I cytokine receptor described thus far, forming a stable interlocking dimer in the absence of ligand in which the G strand of domain 1 hydrogen bonds into the corresponding beta sheet of domain 3 of the dimer-related molecule. The G strand of domain 3 similarly partners with the dimer-related domain 1. The structure provides new insights into receptor activation by the respective alpha receptor:ligand complexes.