Conformations of JNK3α splice variants analyzed by hydrogen/deuterium exchange mass spectrometry.

c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed. Here, we analyzed the conformation of the elongated C-terminal tail and investigated conformational differences between long and short splice variants of JNKs using JNK3α2 and JNK3α1 as models. We adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to analyze the conformation. HDX-MS revealed that the C-terminal tail is mostly intrinsically disordered, and that the conformation of the kinase domain of JNK3α2 is more dynamic than that of JNK3α1. The different conformation dynamics between long and short splice variants of JNK3α might affect the cellular functions of JNK3.

Biophysical characterization of Ca2+-binding of S100A5 and Ca2+-induced interaction with RAGE.

S100A5 is a calcium-binding protein of S100 family, which represents a major ligand to the receptor for advanced glycation end product (RAGE), a pattern recognition receptor engaged in diverse pathological processes. Here we have characterized calcium binding of S100A5 and the complex formation between S100A5 and RAGE using calorimetry and NMR spectroscopy. S100A5 binds to calcium ions in a sequential manner with the equilibrium dissociation constants (KD) of 1.3 µM and 3.5 µM, which corresponds to the calcium-binding at the C-terminal and N-terminal EF-hands. Upon calcium binding, S100A5 interacts with the V domain of RAGE (RAGE-v) to form a heterotrimer (KD ∼5.9 µM) that is distinct among the S100 family proteins. Chemical shift perturbation data from NMR titration experiments indicates that S100A5 employs the periphery of the dimer interface to interact with RAGE-v. Distinct binding mode and stoichiometry of RAGE against different S100 family proteins could be important to modulate diverse RAGE signaling.

Different conformational dynamics of various active states of ß-arrestin1 analyzed by hydrogen/deuterium exchange mass spectrometry.

Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. Two major intra-molecular interactions, the polar core and the three-element region, maintain arrestins in the basal conformation by connecting the N- and C-domains. Mutations in these regions that disrupt the polar core (R169E or p44) or the three-element (3A) have been reported to interact with GPCRs in a phosphorylation-independent manner, and thus these mutants are referred to as pre-activated arrestins. On the other hand, deletion of 7 residues in the linker region between N- and C-domains (Δ7) freezes arrestins in the inactive state, which has a much lower binding affinity to GPCRs compared to the wild type form. Although these mutants are widely used for functional studies of arrestins, the conformations of these mutants have not yet been fully elucidated. Here, we analyzed the conformational dynamics of ß-arrestin1 with various mutants (R169E, p44, 3A, and Δ7) by hydrogen/deuterium exchange mass spectrometry (HDX-MS). HDX-MS data revealed that pre-activated mutants have more deuterium uptake than the basal state, and also that the regions and degree of increased deuterium uptake differ between pre-activated mutants. Unexpectedly, the inactive mutant also showed increased deuterium uptake in a few regions.

Different conformational dynamics of ß-arrestin1 and ß-arrestin2 analyzed by hydrogen/deuterium exchange mass spectrometry.

Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. There have been four arrestins identified: arrestin1, arrestin2 (e.g. ß-arrestin1), arrestin3 (e.g. ß-arrestin2), and arrestin4. ß-Arrestin1 and ß-arrestin2 are ubiquitously expressed and regulate a broad range of GPCRs, while arrestin1 and arrestin4 are expressed in the visual system. Although the functions of ß-arrestin1 and ß-arrestin2 widely overlap, ß-arrestin2 has broader receptor selectivity, and a few studies have suggested that ß-arrestin1 and ß-arrestin2 have distinct cellular functions. Here, we compared the conformational dynamics of ß-arrestin1 and ß-arrestin2 by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We also used the R169E mutant as a pre-activation model system. HDX-MS data revealed that ß-strands II through IV were more dynamic in ß-arrestin2 in the basal state, while the middle loop was more dynamic in ß-arrestin1. With pre-activation, both ß-arrestin1 and ß-arrestin2 became more flexible, but broader regions of ß-arrestin1 became flexible compared to ß-arrestin2. The conformational differences between ß-arrestin1 and ß-arrestin2 in both the basal and pre-activated states might determine their different receptor selectivities and different cellular functions.

Survivin mediates prostate cell protection by HIF-1alpha against zinc toxicity.

BACKGROUND: The prostate contains extremely high concentrations of zinc, but survives and grows without apparent injury. This begs the question as to how prostate cells avoid the toxic effects of zinc. In a previous study, the authors found that; HIF-1alpha is expressed concomitantly with the accumulation of zinc in the epithelial cells of normal rat prostates, the zinc ion stabilizes HIF-1alpha in prostate cells, and that HIF-1alpha protects prostate cells from zinc toxicity. In the present study, the authors addressed the mechanism responsible for the protective effect of HIF-1alpha in a high zinc environment. METHODS: Immunofluorescent staining, immunoblotting, reverse transcription-polymerase chain reaction, reporter assay, and cell cycle analysis. RESULTS: Survivin was induced by ZnCl(2) in a HIF-1 dependent manner in both DU-145 and PNT2 prostate cells. Furthermore, HIF-1 induced survivin expression at the transcriptional level and the induction of survivin was abolished by HIF-1alpha knock-down. In addition, HIF-1-dependent survivin overexpression promoted prostrate cell survival and prevented cell arrest in the presence of high zinc concentrations, and si-survivin transfected cells under zinc rich conditions contained markedly higher levels of cleaved caspase-9 and PARP than si-con transfected cells. Finally, survivin expression patterns well matched rat prostate proliferation statuses. CONCLUSION: Under zinc rich conditions, prostate epithelial cells HIF-1-dependently express survivin, which promotes prostate cell proliferation, and prevents apoptosis and cell cycle arrest. Accordingly, the HIF-1alpha-survivin pathway appears to facilitate prostate cell survival and growth in zinc rich environments, and this pathway could be a therapeutic target for the treatment of prostate hyperplasia.

Structural Mechanism of the Arrestin-3/JNK3 Interaction.

Arrestins, in addition to desensitizing GPCR-induced G protein activation, also mediate G protein-independent signaling by interacting with various signaling proteins. Among these, arrestins regulate MAPK signal transduction by scaffolding mitogen-activated protein kinase (MAPK) signaling components such as MAPKKK, MAPKK, and MAPK. In this study, we investigated the binding mode and interfaces between arrestin-3 and JNK3 using hydrogen/deuterium exchange mass spectrometry, 19F-NMR, and tryptophan-induced Atto 655 fluorescence-quenching techniques. Results suggested that the ß1 strand of arrestin-3 is the major and potentially only interaction site with JNK3. The results also suggested that C-lobe regions near the activation loop of JNK3 form the potential binding interface, which is variable depending on the ATP binding status. Because the ß1 strand of arrestin-3 is buried by the C-terminal strand in its basal state, C-terminal truncation (i.e., pre-activation) of arrestin-3 facilitates the arrestin-3/JNK3 interaction.

Astrometrically registered maps of H2O and SiO masers toward VX Sagittarii.

The supergiant VX Sagittarii is a strong emitter of both H2O and SiO masers. However, previous VLBI observations have been performed separately, which makes it difficult to spatially trace the outward transfer of the material consecutively. Here we present the astrometrically registered, simultaneous maps of 22.2 GHz H2O and 43.1/42.8/86.2/129.3 GHz SiO masers toward VX Sagittarii. The H2O masers detected above the dust-forming layers have an asymmetric distribution. The multi-transition SiO masers are nearly circular ring, suggesting spherically symmetric wind within a few stellar radii. These results provide the clear evidence that the asymmetry in the outflow is enhanced after the smaller molecular gas clump transform into the inhomogeneous dust layers. The 129.3 GHz maser arises from the outermost region compared to that of 43.1/42.8/86.2 GHz SiO masers. The ring size of the 129.3 GHz maser is maximized around the optical maximum, suggesting that radiative pumping is dominant.

Dimerization facilitates the conformational transitions for bacterial phosphotransferase enzyme I autophosphorylation in an allosteric manner.

The bacterial phosphotransferase system is central to sugar uptake and phosphorylation. Enzyme I (EI), the first enzyme of the system, autophosphorylates as a dimer using phosphoenolpyruvate (PEP), but it is not clearly understood how dimerization activates the enzyme activity. Here, we show that EI dimerization is important for proper conformational transitions and the domain association required for the autophosphorylation. EI(G356S) with reduced dimerization affinity and lower autophosphorylation activity revealed that significantly hindered conformational transitions are required for the phosphoryl transfer reaction. The G356S mutation does not change the binding affinity for PEP, but perturbs the domain association accompanying large interdomain motions that bring the active site His189 close to PEP. The interface for the domain association is separate from the dimerization interface, demonstrating that dimerization can prime the conformational change in an allosteric manner.

Thermodynamic dissection of large-scale domain motions coupled with ligand binding of enzyme I.

Domain motions are central to the biological functions of many proteins. The energetics of the motions, however, is often difficult to characterize when motions are coupled with the ligand binding. Here, we determined the thermodynamic parameters of individual domain motions and ligand binding of enzyme I (EI) using strategic domain-deletion mutants that selectively removed particular motions. Upon ligand binding, EI employs two large-scale domain motions, the hinge motion and the swivel motion, to switch between conformational states of distinct domain-domain orientations. Calorimetric analysis of the EI mutants separated the free energy changes of the binding and motions, demonstrating that the unfavorable hinge motion (ΔG = 1.5 kcal mol(-1)) was driven by the favorable swivel motion (ΔG = -5.2 kcal mol(-1)). The large free energy differences could be explained by the physicochemical nature of the domain interfaces associated with the motions; the hinge motion employed much narrower interface than the swivel motion without any hydrogen bonds or salt bridges. The small heat capacity further suggested that the packing of the domain interfaces associated with the hinge motion was less compact than that commonly observed in proteins. Lastly, thermodynamic analysis of phosphorylated EI suggests that the domain motions are regulated by the ligand binding and the phosphorylation states. Taken together, the thermodynamic dissection approach illustrates how multiple motions and ligand binding are energetically connected during the functional cycle of EI.

Calorimetric and spectroscopic investigation of the interaction between the C-terminal domain of Enzyme I and its ligands.

Enzyme I initiates a series of phosphotransfer reactions during sugar uptake in the bacterial phosphotransferase system. Here, we have isolated a stable recombinant C-terminal domain of Enzyme I (EIC) of Escherichia coli and characterized its interaction with the N-terminal domain of Enzyme I (EIN) and also with various ligands. EIC can phosphorylate EIN, but their binding is transient regardless of the presence of phosphoenolpyruvate (PEP). Circular dichroism and NMR indicate that ligand binding to EIC induces changes near aromatic groups but not in the secondary structure of EIC. Binding of PEP to EIC is an endothermic reaction with the equilibrium dissociation constant (K(D) ) of 0.28 mM, whereas binding of the inhibitor oxalate is an exothermic reaction with K(D) of 0.66 mM from calorimetry. The binding thermodynamics of EIC and PEP compared to that of Enzyme I (EI) and PEP reveals that domain-domain motion in EI can contribute as large as ∼-3.2 kcal/mol toward PEP binding.

Active site phosphoryl groups in the biphosphorylated phosphotransferase complex reveal dynamics in a millisecond time scale.

The N-terminal domain of Enzyme I (EIN) and phosphocarrier HPr can form a biphosphorylated complex when they are both phosphorylated by excess cellular phosphoenolpyruvate. Here we show that the electrostatic repulsion between the phosphoryl groups in the biphosphorylated complex results in characteristic dynamics at the active site in a millisecond time scale. The dynamics is localized to phospho-His15 and the stabilizing backbone amide groups of HPr, and does not impact on the phospho-His189 of EIN. The dynamics occurs with the k(ex) of ~500 s(-1) which compares to the phosphoryl transfer rate of ~850 s(-1) between EIN and HPr. The conformational dynamics in HPr may be important for its phosphotransfer reactions with multiple partner proteins.

Activation of NMDA receptors increases proliferation and differentiation of hippocampal neural progenitor cells.

The prolonged effects of N-methyl-D-aspartate (NMDA) receptor activation on the proliferation and differentiation of hippocampal neural progenitor cells (NPCs) were studied. Under conditions of mitogen-mediated proliferation, a single NMDA pulse (5 microM) increased the fraction of 5-bromo-2-deoxyuridine (BrdU)-positive (BrdU(+)) cells after a delay of 72 hours. Similarly, a single systemic injection of NMDA (100 mg/kg) increased the number of BrdU(+) cells in the dentate gyrus (DG) after 28 days, but not after 3 days. NMDA receptor activation induced an immediate influx of Ca(2+) into the NPCs and the NPCs expressed and released vascular endothelial growth factor (VEGF) in an NMDA receptor-dependent manner within 72 hours. With repetitive stimulation at the same dose, NMDA stimulated the acquisition of a neuronal phenotype accompanied by an increase in the expression of proneural basic helix-loop-helix (bHLH) factors. Together these findings suggest that neurogenesis in the developing brain is likely to be both directly and indirectly regulated by complex interactions between Ca(2+) influx and excitation-releasable cytokines, even at mild levels of excitation. In addition, our results are the first to show that stimulation of NPCs may lead to either proliferation or neuronal differentiation, depending on the level of NMDA receptor activation.