Field-tuned quantum effects in a triangular-lattice Ising magnet.

We report thermodynamic and neutron scattering measurements of the triangular-lattice quantum Ising magnet TmMgGaO4 in longitudinal magnetic fields. Our experiments reveal a quasi-plateau state induced by quantum fluctuations. This state exhibits an unconventional non-monotonic field and temperature dependence of the magnetic order and excitation gap. In the high field regime where the quantum fluctuations are largely suppressed, we observed a disordered state with coherent magnon-like excitations despite the suppression of the spin excitation intensity. Through detailed semi-classical calculations, we are able to understand these behaviors quantitatively from the subtle competition between quantum fluctuations and frustrated Ising interactions.

Erythropoietin-driven dynamic proteome adaptations during erythropoiesis prevent iron overload in the developing embryo.

Erythropoietin (Epo) ensures survival and proliferation of colony-forming unit erythroid (CFU-E) progenitor cells and their differentiation to hemoglobin-containing mature erythrocytes. A lack of Epo-induced responses causes embryonic lethality, but mechanisms regulating the dynamic communication of cellular alterations to the organismal level remain unresolved. By time-resolved transcriptomics and proteomics, we show that Epo induces in CFU-E cells a gradual transition from proliferation signature proteins to proteins indicative for differentiation, including heme-synthesis enzymes. In the absence of the Epo receptor (EpoR) in embryos, we observe a lack of hemoglobin in CFU-E cells and massive iron overload of the fetal liver pointing to a miscommunication between liver and placenta. A reduction of iron-sulfur cluster-containing proteins involved in oxidative phosphorylation in these embryos leads to a metabolic shift toward glycolysis. This link connecting erythropoiesis with the regulation of iron homeostasis and metabolic reprogramming suggests that balancing these interactions is crucial for protection from iron intoxication and for survival.

Magnetic Bloch oscillations and domain wall dynamics in a near-Ising ferromagnetic chain.

When charged particles in periodic lattices are subjected to a constant electric field, they respond by oscillating. Here we demonstrate that the magnetic analogue of these Bloch oscillations are realised in a ferromagnetic easy axis chain. In this case, the "particles" undergoing oscillatory motion in the presence of a magnetic field are domain walls. Inelastic neutron scattering reveals three distinct components of the low energy spin-dynamics including a signature Bloch oscillation mode. Using parameter-free theoretical calculations, we are able to account for all features in the excitation spectrum, thus providing detailed insights into the complex dynamics in spin-anisotropic chains.

Structural characterization and magnetic properties of chromium jarosite KCr3(OD)6(SO4)2.

Potassium chromium jarosite, KCr3(OH)6(SO4)2 (Cr-jarosite), is considered a promising candidate to display spin liquid behavior due to the strong magnetic frustration imposed by the crystal structure. However, the ground state magnetic properties have been debated, since Cr-jarosite is notoriously non-stoichiometric. Our study reports the magnetic properties for deuterated KCr3(OD)6(SO4)2 on chemically well-defined samples, which have been characteried by a combination of powder X-ray diffraction, neutron diffraction, solid state NMR spectroscopy, and scanning electron microscopy with energy dispersive spectroscopy. Eight polycrystalline samples, which all contained only 1-3% Cr vacancies were obtained. However, significant substitution (2-27%) of potassium with H2O and/or H3O+ was observed and resulted in pronounced stacking disorder along the c-axis. A clear second-order transition to an antiferromagnetically ordered phase at TN = 3.8(1) K with a small net moment of 0.03 µB per Cr3+-ion was obtained from vibrating sample magnetometry and temperature dependent neutron diffraction. The moment is attributed to spin canting caused by the Dzyaloshinskii-Moriya interaction. Thus, our experimental results imply that even ideal potassium chromium jarosite will exhibit magnetic order below 4 K and therefore it does not qualify as a true spin liquid material.

Fractional antiferromagnetic skyrmion lattice induced by anisotropic couplings.

Magnetic skyrmions are topological solitons with a nanoscale winding spin texture that hold promise for spintronics applications1-4. Skyrmions have so far been observed in a variety of magnets that exhibit nearly parallel alignment for neighbouring spins, but theoretically skyrmions with anti-parallel neighbouring spins are also possible. Such antiferromagnetic skyrmions may allow more flexible control than conventional ferromagnetic skyrmions5-10. Here, by combining neutron scattering measurements and Monte Carlo simulations, we show that a fractional antiferromagnetic skyrmion lattice is stabilized in MnSc2S4 through anisotropic couplings. The observed lattice is composed of three antiferromagnetically coupled sublattices, and each sublattice is a triangular skyrmion lattice that is fractionalized into two parts with an incipient meron (half-skyrmion) character11,12. Our work demonstrates that the theoretically proposed antiferromagnetic skyrmions can be stabilized in real materials and represents an important step towards their implementation in spintronic devices.

Low-energy spin dynamics of orthoferrites AFeO3 (A = Y, La, Bi).

YFeO3 and LaFeO3 are members of the rare-earth orthoferrites family with Pbnm space group. Using inelastic neutron scattering, the low-energy spin excitations have been measured around the magnetic Brillouin zone center. Splitting of magnon branches and finite magnon gaps (∼2 meV) are observed for both compounds, where the Dzyaloshinsky-Moriya interactions account for most of this gap with some additional contribution from single-ion anisotropy. We also make comparisons with multiferroic BiFeO3 (R3c space group), in which similar behavior was observed. By taking into account all relevant local Dzyaloshinsky-Moriya interactions, our analysis allows for the precise determination of all experimentally observed parameters in the spin-Hamiltonian. We find that different properties of the Pbnm and R3c space group lead to the stabilization of a spin cycloid structure in the latter case but not in the former, which explains the difference in the levels of complexity of magnon band structures for the respective compounds.

Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression.

Upon stimulation of cells with transforming growth factor ß (TGF-ß), Smad proteins form trimeric complexes and activate a broad spectrum of target genes. It remains unresolved which of the possible Smad complexes are formed in cellular contexts and how these contribute to gene expression. By combining quantitative mass spectrometry with a computational selection strategy, we predict and provide experimental evidence for the three most relevant Smad complexes in the mouse hepatoma cell line Hepa1-6. Utilizing dynamic pathway modeling, we specify the contribution of each Smad complex to the expression of representative Smad target genes, and show that these contributions are conserved in human hepatoma cell lines and primary hepatocytes. We predict, based on gene expression data of patient samples, increased amounts of Smad2/3/4 proteins and Smad2 phosphorylation as hallmarks of hepatocellular carcinoma and experimentally verify this prediction. Our findings demonstrate that modeling approaches can disentangle the complexity of transcription factor complex formation and its impact on gene expression.

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib.

IL-6 is a central mediator of the immediate induction of hepatic acute phase proteins (APP) in the liver during infection and after injury, but increased IL-6 activity has been associated with multiple pathological conditions. In hepatocytes, IL-6 activates JAK1-STAT3 signaling that induces the negative feedback regulator SOCS3 and expression of APPs. While different inhibitors of IL-6-induced JAK1-STAT3-signaling have been developed, understanding their precise impact on signaling dynamics requires a systems biology approach. Here we present a mathematical model of IL-6-induced JAK1-STAT3 signaling that quantitatively links physiological IL-6 concentrations to the dynamics of IL-6-induced signal transduction and expression of target genes in hepatocytes. The mathematical model consists of coupled ordinary differential equations (ODE) and the model parameters were estimated by a maximum likelihood approach, whereas identifiability of the dynamic model parameters was ensured by the Profile Likelihood. Using model simulations coupled with experimental validation we could optimize the long-term impact of the JAK-inhibitor Ruxolitinib, a therapeutic compound that is quickly metabolized. Model-predicted doses and timing of treatments helps to improve the reduction of inflammatory APP gene expression in primary mouse hepatocytes close to levels observed during regenerative conditions. The concept of improved efficacy of the inhibitor through multiple treatments at optimized time intervals was confirmed in primary human hepatocytes. Thus, combining quantitative data generation with mathematical modeling suggests that repetitive treatment with Ruxolitinib is required to effectively target excessive inflammatory responses without exceeding doses recommended by the clinical guidelines.

Magnetic Structure and Excitations in CeCuxAl4-x System.

CeCuAl3 crystallizing in the tetragonal BaNiSn3-type structure and CeCuxAl4-x solid solutions were investigated by means of elastic and inelastic neutron scattering. Powder neutron diffraction brought information on both temperature evolution of crystallographic parameters and magnetic order at low temperatures. No structural change was observed in the investigated temperature range from 1.5 to 300 K. Weak magnetic peaks outside nuclear Bragg positions observed in solid solutions with 0.90 ≤ x ≤ 1.10 were described by the propagation vector k = (0.40 + δx, 0.60 + δy, 0), where δx ≈ 0.02 and δy ≈ 0.01. The magnetic structure of CeCu0.75Al3.25 consists of two components: an anti-ferromagnetic one described by the same k and a ferromagnetic one with k0 = (0, 0, 0) and magnetic moments lying within the tetragonal basal plane. The evolution of magnetic excitations as a function of Cu-Al concentration in CeCuxAl4-x was studied by inelastic neutron scattering. The measured spectra of CeCuAl3 and the solution with x = 0.95 point to a three-magnetic-peak energy scheme, while only two excitations are expected from the local symmetry conditions on Ce atoms. The standard two-peak spectrum of crystal electric field excitations was observed for Cu-Al substitutions further from the 1:1:3 stoichiometry (x = 0.75 and 1.10). The intermediate concentrations (x = 0.90 and 1.05) exhibit spectra on the border between the former cases with a less clear pronounced first inelastic magnetic peak. The observed behavior is discussed considering the evolution of structural parameters in the CeCuxAl4-x system and the coupling between the lattice vibrations and the crystal electric field excitations.

Immunosuppression and Aberrant T Cell Development in the Absence of N-Myristoylation.

N-myristoylation refers to the attachment of myristic acid to the N-terminal glycine of proteins and substantially affects their intracellular targeting and functions. The thymus represents an organ with a prominent N-myristoylation activity. To elucidate the role of protein N-myristoylation for thymocyte development, we generated mice with a T cell lineage-specific deficiency in N-myristoyl transferase (Nmt)1 and 2. Depletion of Nmt activity in T cells led to a defective transmission of TCR signals, a developmental blockage of thymocytes at the transition from double-negative 3 to 4 stages, and a reduction of all the following stages. We could demonstrate that Lck and myristoylated alanine-rich C kinase substrate, two main myristoylated kinases in T cells, were mislocalized in the absence of Nmt activity. N-myristoylation was also indispensable for early and distal TCR signaling events such as CD3ζ, Zap70, and Erk activation and for release of cytokines such as IFN-γ and IL-2. As a consequence, the initiation and propagation of the TCR signaling cascade was severely impaired. Furthermore, we showed that the absence of myristoylation had an immunosuppressive effect on T cells in vivo after treatment with CpG and stimulation of the TCR with the staphylococcal enterotoxin B superantigen. Therefore, protein myristoylation is indispensable in T cell development and activation and its inhibition might offer a novel strategy to achieve immunosuppression.

Identification of isoform-specific dynamics in phosphorylation-dependent STAT5 dimerization by quantitative mass spectrometry and mathematical modeling.

STAT5A and STAT5B are important transcription factors that dimerize and transduce activation signals of cytokine receptors directly to the nucleus. A typical cytokine that mediates STAT5 activation is erythropoietin (Epo). Differential functions of STAT5A and STAT5B have been reported. However, the extent to which phosphorylated STAT5A and STAT5B (pSTAT5A, pSTAT5B) form homo- or heterodimers is not understood, nor is how this might influence the signal transmission to the nucleus. To study this, we designed a concept to investigate the isoform-specific dimerization behavior of pSTAT5A and pSTAT5B that comprises isoform-specific immunoprecipitation (IP), measurement of the degree of phosphorylation, and isoform ratio determination between STAT5A and STAT5B. For the main analytical method, we employed quantitative label-free and -based mass spectrometry. For the cellular model system, we used Epo receptor (EpoR)-expressing BaF3 cells (BaF3-EpoR) stimulated with Epo. Three hypotheses of dimer formation between pSTAT5A and pSTAT5B were used to explain the analytical results by a static mathematical model: formation of (i) homodimers only, (ii) heterodimers only, and (iii) random formation of homo- and heterodimers. The best agreement between experimental data and model simulations was found for the last case. Dynamics of cytoplasmic STAT5 dimerization could be explained by distinct nuclear import rates and individual nuclear retention for homo- and heterodimers of phosphorylated STAT5.

One-source peptide/phosphopeptide ratio standards for accurate and site-specific determination of the degree of phosphorylation.

Reversible protein phosphorylation is a key mediator for intracellular signal transduction. Here we describe an innovative method for the production of pairs of peptide standards designed for quantitative mass spectrometry. These standard pairs can be used for site-specific analysis of the degree of phosphorylation of proteins in a bottom-up approach. The method starts from an isotopically labeled phosphopeptide analogue of the analyte phosphopeptide and ends up with a labeled peptide/phosphopeptide ratio standard in which the molar ratio between the phosphorylated and the unphosphorylated form is exactly defined. The signals of the ratio standard are used to standardize the corresponding analyte signals. This compensates for differences in LC recovery or ionization efficiency between the phosphorylated and unphosphorylated forms. The method can also be extended to quantitative analysis of multisite phosphorylation in a single peptide, which is exemplified for the presence of two phosphorylation sites. Peptide/phosphopeptide ratio standards exhibit high ratio accuracy, since ratio adjustment is performed by volumetric operations only.

Anisotropic propagating excitations and quadrupolar effects in Tb2Ti2O7.

The dynamical magnetic correlations in Tb2Ti2O7 have been investigated using polarized inelastic neutron scattering. Dispersive excitations are observed, emerging from pinch points in reciprocal space and characterized by an anisotropic spectral weight. Anomalies in the crystal field and phonon excitation spectrum at Brillouin zone centers are also reported. These findings suggest that Coulomb phases, although they present a disordered ground state with dipolar correlations, allow the propagation of collective excitations. They also point out a strong spin-lattice coupling, which likely drives effective interactions between the 4f quadrupolar moments.

Cellular ERK phospho-form profiles with conserved preference for a switch-like pattern.

ERK is a member of the MAPK pathway with essential functions in cell proliferation, differentiation, and survival. Complete ERK activation by the kinase MEK requires dual phosphorylation at T and Y within the activation motif TEY. We show that exposure of primary mouse hepatocytes to hepatocyte growth factor (HGF) results in phosphorylation at the activation motif, but not of other residues nearby. To determine the relative abundances of unphosphorylated ERK and the three ERK phospho-forms pT, pY, and pTpY, we employed an extended one-source peptide/phosphopeptide standard method in combination with nanoUPLC-MS. This method enabled us to determine the abundances of phospho-forms with a relative variability of ≤5% (SD). We observed a switch-like preference of ERK phospho-form abundances toward the active, doubly phosphorylated and the inactive, unphosphorylated form. Interestingly, ERK phospho-form profiles were similar upon growth factor and cytokine stimulation. A screening of several murine and human cell systems revealed that the balance between TY- and pTpY-ERK is conserved while the abundances of pT- and pY-ERK are more variable within cell types. We show that the phospho-form profiles do not change by blocking MEK activity suggesting that cellular phosphatases determine the ERK phospho-form distribution. This study provides novel quantitative insights into multisite phosphorylation.

Site-specific degree of phosphorylation in proteins measured by liquid chromatography-electrospray mass spectrometry.

This review focuses on quantitative protein phosphorylation analysis based on coverage of both the phosphorylated and nonphosphorylated forms. In this way, site-specific data on the degree of phosphorylation can be measured, generating the most detailed level of phosphorylation status analysis of proteins. To highlight the experimental challenges in this type of quantitative protein phosphorylation analysis, we discuss the typical workflows for mass spectrometry-based proteomics with a focus on the quantitative analysis of peptide/phosphopeptide ratios. We review workflows for measuring site-specific degrees of phosphorylation including the label-free approach, differential stable isotope labeling of analytes, and methods based on the addition of stable isotope labeled peptide/phosphopeptide pairs as internal standards. The discussion also includes the determination of phosphopeptide isoform abundance data for multiply phosphorylated motifs that contain information about the connectivity of phosphorylation events. The review closes with a prospective on the use of intact stable isotope labeled proteins as internal standards and a summarizing discussion of the typical accuracies of the individual methods.

Improving the precision of quantitative bottom-up proteomics based on stable isotope-labeled proteins.

Stable isotope dilution-based quantitative proteomics with intact labeled proteins as internal standards in combination with a bottom-up approach, i.e., with quantification on the peptide level, is an established method. To explore the technical precision of this approach, calmodulin-like protein 3 was prepared in non-labeled (light) and SILAC-type labeled (heavy) form by cell-free synthesis, mixed, digested with trypsin, and analyzed by UPLC-ESI-MS. In total, 16 light/heavy peptide pair ratios were determined. Pair-wise comparison of ratios of 12 peptides selected according to S/N ratios >50 revealed that the majority exhibited ratios, which were different at a high level of statistical significance (p < 0.001). HPLC-MALDI-MS ratio data confirmed this observation, thus excluding the ionization method as a source of the observed ratio differences. Variation of the digestion time from 0.25 to 4 h showed that the light/heavy ratios of most peptides decrease with time, indicating a kinetic isotope effect leading to preferred cleavage of light calmodulin-like protein 3. The subset of peptides with statistically identical ratios resulted in an average ratio with a RSD of 1.0 %. The light/heavy ratio calculated on the basis of these peptides probably provides the most accurate molar protein ratio.

Cdc14-dependent dephosphorylation of Inn1 contributes to Inn1-Cyk3 complex formation.

In Saccharomyces cerevisiae the Cdc14 phosphatase plays a well-established role in reverting phosphorylation events on substrates of the mitotic cyclin-dependent kinase (M-Cdk1), thereby promoting mitotic exit and downregulation of M-Cdk1 activity. Cdc14 localizes at the site of cell cleavage after M-Cdk1 inactivation, suggesting that Cdc14 may perform a crucial, yet ill-defined, role during cytokinesis. Here, we identified Inn1, as a novel direct substrate of both M-Cdk1 and Cdc14. Cdc14 colocalizes with Inn1 at the cell division site and interacts with the C-terminal proline-rich domain of Inn1 that mediates its binding to the SH3-domain-containing proteins Hof1 and Cyk3. We show that phosphorylation of Inn1 by Cdk1 partially perturbs the interaction of Inn1 with Cyk3 thereby reducing the levels of Cyk3 at the cell division site. We propose that Cdc14 counteracts Cdk1 phosphorylation of Inn1 to facilitate Inn1-Cyk3 complex formation and so promote cytokinesis.

Phosphorylation-dependent regulation of the F-BAR protein Hof1 during cytokinesis.

Spatial and timely coordination of cytokinesis is crucial for the maintenance of organelle inheritance and genome integrity. The mitotic exit network (MEN) pathway controls both the timely initiation of mitotic exit and cytokinesis in budding yeast. Here we identified the conserved F-BAR protein Hof1 as a substrate of the MEN kinase complex Dbf2-Mob1 during cytokinesis. We show that polo-like kinase Cdc5 first phosphorylates Hof1 to allow subsequent phosphorylation by Dbf2-Mob1. This releases Hof1 from the septin ring and facilitates Hof1 binding to the medial actomyosin ring (AMR), where Hof1 promotes AMR contraction and membrane ingression. Domain structure analysis established that the central, unstructured, region of Hof1, named the ring localization sequence (RLS), is sufficient to mediate Hof1's binding to the medial ring in a cell cycle-dependent manner. Genetic and functional data support a model in which Dbf2-Mob1 regulates Hof1 by inducing domain rearrangements, leading to the exposure of the Hof1 RLS domain during telophase.

Metal ion-mobilizing additives for comprehensive detection of femtomole amounts of phosphopeptides by reversed phase LC-MS.

It is hypothesized that metal ion-mediated adsorption of phosphorylated peptides on stationary phases of LC-columns is the major cause for their frequently observed poor detection efficiency in LC-MS. To study this phenomenon in more detail, sample solutions spiked with metal ion-mobilizing additives were analyzed by reversed phase µLC-ICP-MS or nanoLC-ESI-MS. Using µLC-ICP-MS, metal ions were analyzed directly as atomic ions. Using electrospray ionization, either metal ion chelates or phosphopeptide standard mixtures injected in subpicomole amounts were analyzed. Deferoxamine, imidazole, ascorbate, citrate, EDTA, and the tetrapeptide pSpSpSpS were tested as sample additives for the interlinked purposes of metal ion-mobilization and improvement of phosphopeptide recovery. Iron probably represents the major metal ion contamination of reversed phase columns. Based on the certified iron level in LC-grade solvents, a daily metal ion load of >10 pmol was estimated for typical nanoLC flow rates. In addition, phosphopeptide fractions from IMAC columns were identified as source for metal ion contamination of the LC column, as demonstrated for Ga(3+)-IMAC. The three metal ion-chelating additives, EDTA, citrate and pSpSpSpS, were found to perform best for improving the LC recovery of multiply phosphorylated peptides injected at subpicomole amounts. The benefits of metal ion-mobilizing LC (mimLC) characterized by metal ion complexing sample additives is demonstrated for three different instrumental setups comprising (a) a nanoUPLC-system with direct injection on the analytical column, (b) a nanoLC system with inclusion of a trapping column, and (c) the use of a HPLC-Chip system with integrated trapping and analytical column.

De novo sequencing of peptides by MS/MS.

The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.