Structural Significance of the C-terminal Amphiphilic Helix of Interleukin-2

A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation

Background

The temporal coordination of biological processes by the circadian clock is an important mechanism, and its disruption has negative health outcomes, including cancer. Experimental and theoretical evidence suggests that the oscillators driving the circadian clock and the cell cycle are coupled through phase locking.

Results

We present a detailed and documented map of known mechanisms related to the regulation of the circadian clock, and its coupling with an existing cell cycle map which includes main interactions of the mammalian cell cycle. The coherence of the merged map has been validated with a qualitative dynamics analysis. We verified that the coupled circadian clock and cell cycle maps reproduce the observed sequence of phase markers. Moreover, we predicted mutations that contribute to regulating checkpoints of the two oscillators.

Conclusions

Our approach underlined the potential key role of the core clock protein NR1D1 in regulating cell cycle progression. We predicted that its activity influences negatively the progression of the cell cycle from phase G2 to M. This is consistent with the earlier experimental finding that pharmacological activation of NR1D1 inhibits tumour cell proliferation and shows that our approach can identify biologically relevant species in the context of large and complex networks.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04158-9.

Increased endosomal sorting of ligand to recycling enhances potency of an interleukin-2 analog

An interleukin-2 (IL-2) variant containing adjacent point mutations (L18M/L19S, termed 2D1) displaying binding affinity to the heterotrimeric IL-2 receptor similar to that of wild-type IL-2 (WT) had been previously found to surprisingly exhibit increased bioactivity in a peripheral blood lymphocyte proliferation assay. In order to provide an explanatory mechanism for this unexpected potency enhancement, we hypothesize that altered endocytic trafficking of the 2D1 variant might be responsible by increasing the number of ligand-receptor complexes. We demonstrate here that the internalization kinetics of 2D1 via the high affinity IL-2 receptor are equivalent to those of WT but that a significantly increased fraction of internalized 2D1 is sorted to recycling instead of to lysosomal degradation. We further find a reduced pH sensitivity of binding to IL-2 receptor alpha relative to IL-2 receptor beta compared with WT, which could be responsible for the altered sorting behavior of 2D1 in the acidic endosomal compartment. Accordingly, the 2D1 variant displays a half-life 36 h longer than that of IL-2 in T-lymphocyte culture at concentrations equal to the K(D) of the IL-2 receptor. The extended half-life of intact 2D1 provides enhanced mitogenesis as compared with IL-2. In addition, 2D1 stimulates natural killer cells to a lesser degree than IL-2 at equal concentrations. We conclude that this IL-2 variant provides increased mitogenic stimulation that could not be easily predicted from its cell surface receptor binding affinity while minimizing undesired stimulation of natural killer cells. This concept of altering trafficking dynamics may offer a generalizable approach to generating improvements in the pharmacological efficacy of therapeutic cytokines.

Structural modifications of interleukin-2 at positions 47 and 65

Interleukin-2 (IL-2) is a cytokine essential for the growth and proliferation of T-cells. The purpose of this research was to study the effects of altering the "kink" caused by Pro in an alpha-helix of the protein. The Pro-47 residue was chosen because it was originally, but mistakenly, traced to the kink of an alpha-helix [1]. Pro-65 is now recognized to be situated in the middle of helix B [2]. To study the significance of this Pro for the bioactivity and overall conformation of IL-2 it was mutated to Gly and Ala. We successfully obtained 17 different mutants at position 47 and two mutants at position 65. Certain amino acid substitutions representing different categories of amino acids, namely, acidic, neutral and helix stabilizing, were chosen for more thorough investigation. The results showed that Asn-47 and Asp-47 decreased the bioactivity of these mutants by 50- and 700-fold respectively, while the Kd to its high affinity receptors was increased 180- and 90-fold respectively, compared to IL-2. The intermediate binding affinity of Asn-47 and Asp-47 was decreased 8- and 37-fold, respectively. On the other hand, Gly-47, Gly-65 and Ala-65 showed less dramatic decreases in bioactivity and high affinity binding. The intermediate binding affinity of these mutants decreased from 5- to 3-fold and low affinity binding decreased approximately 4-fold suggesting some structural and conformational changes. From these observations, we conclude that Asn-47 or Asp-47 disrupt the hydrophobic packing of the core and thus changed the overall conformation of the protein, thereby giving rise to partial agonists. Although Pro-65 lies within the helix, it may be near the surface of the protein but may not be the actual binding site and thus any conservative mutation can be better tolerated.

Modification of Escherichia coli B glutathione synthetase with polyethylene glycol for clinical application to enzyme replacement therapy for glutathione deficiency

Glutathione synthetase of Escherichia coli B was modified with polyethylene glycol, and the properties of the resultant modified enzyme were investigated. The thermal stability of the modified enzyme and its resistance against several proteases increased compared with those of the native enzyme. The modified enzyme was injected intravenously via the rat tail vein, and the circulating life of the enzyme in plasma was monitored. The half-life of the native enzyme was 50 min, whereas that of the modified enzyme was approximately 24 h. The systemic anaphylaxis reaction was tested by using rats intravenously injected with the native and modified enzymes. For the native enzyme, strong reactions such as dyspnea and tumble were observed; however, no symptom or only a very weak reaction, such as scratching, was observed with the modified enzyme.

A point mutation in interleukin-2 that alters ligand internalization

In previous studies, we have identified an interleukin-2 (IL-2) analog containing a point mutation at position 51 (T51P) that expresses nearly wild-type bioactivity, yet has approximately 10-fold lower receptor binding affinity. Since ligand-dependent receptor internalization may be the rate-limiting step controlling the duration of IL-2 receptor signaling, a reduction in the receptor internalization rate could contribute to the observed response enhancement for this analog. To evaluate this possibility, we compared the internalization of IL-2 and T51P in three separate assays. While the internalization rate for IL-2 agreed with values determined by others, the internalization of T51P was markedly reduced. The receptor binding rate constants for this analog were only slightly different; thus, altered binding kinetics could not explain the decreased internalization rate. The effects of reduced internalization were also observable in bioassays, where T51P maintained T-cell proliferation for a longer period compared with IL-2. These results indicate that the T51P point mutation reduces the receptor internalization rate compared with IL-2 in a fashion that is independent of the dissociation rate. This analog may represent a new approach to the preparation of cytokine analogs with potentiated agonist and antagonist properties.

Sarcoplasmic reticulum Ca2+ uptake is not decreased in aorta from deoxycorticosterone acetate hypertensive rats: functional assessment with cyclopiazonic acid

Ca2+ plays a major role in vascular contraction, and a defect in intracellular Ca2+ regulation has been associated with increased vascular reactivity in hypertension. To test the hypothesis that the sarcoplasmic reticulum does not adequately buffer Ca2+ in deoxycorticosterone acetate (DOCA) hypertension, contractile experiments were performed with a specific inhibitor of the sarcoplasmic reticulum Ca2+ ATPase, cyclopiazonic acid (CPA). Contractile force in aortic strips from DOCA and control rats was measured, using standard muscle bath procedures, to evaluate (i) Ca2+ handling, assessing caffeine and serotonin (5HT) induced contractions in Ca(2+)-free buffer and (ii) relaxation rate after 5HT washout. Contractile responses elicited with 5HT (3 x 10(-6) mol/L) and caffeine (20 mmol/L) were greater in DOCA than in control arteries. CPA (1 x 10(-7) to 3 x 10(-5) mol/L) reduced phasic contractions to 5HT and caffeine in DOCA and control aorta, and no differences in the IC50 values were observed. Aortae from DOCA rats contracted when placed in normal buffer, subsequent to treatment with Ca(2+)-free buffer, but control aortae did not. CPA potentiated these responses in DOCA aorta and only caused a modest contraction in control aorta. CPA-induced contraction did not occur in Ca(2+)-free buffer, and it was inhibited by nifedipine (IC50 = 4 x 10(-9) mol/L). The relaxation rate, after 5HT washout (3 x 10(-6) mol/L), was increased in DOCA aorta (2.6 +/- 0.3 min) compared with control (1.7 +/- 0.2 min), and CPA (10(-5) mol/L) increased the relaxation rate in both groups. The results support the hypothesis of defective Ca2+ handling in DOCA hypertension. However, an increased Ca2+ influx, and not a decreased buffering ability of the sarcoplasmic reticulum, contributes to the enhanced vascular reactivity observed in DOCA hypertension.

Substitutions at the Glu62 residue of human interleukin-2 differentially affect its binding to the alpha chain and the beta gamma complex of the interleukin-2 receptor

Human interleukin-2 (IL-2) alpha helix B is more conserved than the whole molecule, but has been less studied than other alpha helices of IL-2. Using site-directed mutagenesis, several IL-2 mutants in this helix were obtained. We found that the IL-2 mutant containing Leu at position 62 (Leu62-IL-2) loses its ability to bind IL-2 receptor subunit alpha (IL-2R alpha), but retains binding affinity to IL-2R subunit beta gamma as well as some bioactivity; nevertheless, another substitution at the same residue, Arg62IL-2, loses its binding ability to both IL-2R alpha and IL-2R beta gamma, and can no longer stimulate IL-2-dependent cell growth, showing that Glu62 not only takes part in IL-2R alpha binding, but can also affect IL-2 binding to IL-2R beta gamma. In this regard, Glu62 may be a key site in the IL-2/IL-2R alpha interaction, and can facilitate IL-2R ternary-complex formation, leading to IL-2R alpha-mediated, IL-2-stimulated signal transduction.

Immunochemical characterization of antigenic domains on human IL-2: Spatially distinct epitopes are associated with binding to the p55 and p70 subunits of IL-2 receptor

We have isolated and characterized 8 mAb against human rIL-2. All recognize nonglycosylated rIL-2 in liquid phase with similar affinities (Kd approximately 1 nM). Based on the epitopes of the IL-2 molecule that they recognize and their pattern of reactivity against glycosylated and non-glycosylated IL-2, they have been classified into four groups. The first group of anti-IL-2 mAb (2C4, 19B11 and 12C2) inhibits IL-2 binding to p70 IL-2R, while the second one (16F11, 18E1 and 2A4) prevents its binding to p55 IL-2R. These two groups neutralize IL-2 activity in a T cell proliferation assay equally well, due to their similar inhibition of IL-2 binding to high affinity IL-2R. Two mAb, 3H9 and 17F4, recognize separate epitopes on IL-2 molecule, are poor inhibitors of IL-2 binding, and they are inefficient in the neutralization of its biological activity; they have been assigned to the third and fourth groups, respectively. These results show that mAb from the first and second group recognize two epitopes of the human IL-2 molecule which probably overlap the p70 IL-2R and p55 IL-2R binding sites, respectively. In addition, these areas together form the high affinity IL-2R binding site. The two mAb from the third and fourth group recognized epitopes of IL-2 not directly involved in IL-2 binding to its receptor. All eight mAb anti-human IL-2 recognize murine IL-2 and with the exception of one, 17F4 mAb are also able to neutralize it in a T cell proliferation assay. The relationship between the structure and the function of the IL-2 molecule is discussed.

Intermolecular cystine-bonding of murine interleukin 2 indicates that ligand dimerization is important for the formation of the high-affinity receptor complex

Interleukin 2 is thought to be active as a monomeric protein. As the nonessential Cys-140 of murine interleukin 2 (mIL2) is located in the hydrophobic interface of the amphiphilic F domain it was successfully used to stabilize hydrophobic amino acid contacts between two mIL2 cores yielding biologically active cystine-bonded dimeric mIL2. (3H) thymidine incorporation assays with intermolecular cystine-bonded or monomeric mIL2 revealed almost identical median effective concentrations (EC50) and high-affinity dissociation constants (Kdh), respectively. Comparative binding and internalization assays suggest that one cystine-bonded dimeric or two monomeric mIL2 molecules bind to the high-affinity receptor complex. Furthermore, DSS concentration-dependent crosslinking studies using monomeric mIL2 revealed four membrane-derived protein-complexes with apparent molecular weights of about 70 kDa, 85 kDa, 95 kDa and 100 kDa, respectively, showing that both mIL2 receptor chains may be crosslinked to a monomeric or dimeric ligand molecule, respectively. We therefore propose that dimerization of murine interleukin 2 occurring either in solution at concentrations above the low-affinity dissociation constant or at the low-affinity receptor is important for regulation of high-affinity complex formation and signal transduction.

Experimental and theoretical studies of the three-dimensional structure of human interleukin-4

The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all alpha-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly alpha-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.

Conformational perturbation of interleukin-2: a strategy for the design of cytokine analogs

Interleukin-2 (IL-2) is a representative of a growing family of small proteins termed lymphokines which are responsible for mediating cell differentiation, growth and function in the immune system. Many of these proteins are being evaluated for their clinical potential. From the perspective of drug development, structure-function analysis of these molecules and their receptors require the use methodologies different than those traditionally employed for small peptides and other natural products. However, similar pharmacologic principles apply and an understanding of ligand-receptor interactions and the associated responses is required in order to efficiently pursue agonist and antagonist design. Although IL-2 is a protein of only 133 amino acid residues for which a low resolution X-ray structure does exist, the complexity of its receptor system has provided an added challenge to structure-function studies. Consequently, little is known concerning the receptor contact residues for this protein. We have attempted to utilize established principles of protein and peptide structure to manipulate the conformation of IL-2 in a manner which has provided analogs helpful for receptor interaction studies. These proteins have not only providing useful information on the nature of the IL-2 receptor but have also revealed potential strategies for the design of IL-2 agonists and antagonists.

Haemopoietic receptors and helical cytokines

A bewitching interplay of proteins, variously clothed as chemical messengers and cellular receptors, control the pace of growth and the course of progressive differentiation in blood cell types. The messengers are lymphokines, interleukins, colony-stimulating factors, growth hormones and interferons: generically, the cytokines. The second components of the regulatory pairs are membrane-spanning receptor proteins: these molecules transduce the specific binding of cognate cytokines into a mitogenic cellular response. In this article, Fernando Bazan discusses a provocative structural model for cytokine-receptor interactions which, if correct, will alter perceptions of the evolutionary design of the haemopoietic system.

Interleukin 2: prototype for a new generation of immunoactive pharmaceuticals

Molecular biological techniques have revealed the interleukin-2 receptor to be a dimer composed of one alpha-subunit and one beta-subunit which interact noncovalently in a cooperative manner. Site-directed mutagenesis, in conjunction with structural analysis, is beginning to clarify the relationship between structural components of the receptor and their function, and Thomas Ciardelli and Kendall Smith explain why this is bringing drug developers closer to the design of IL-2 agonists and antagonists.