Conformational Changes of the Troponin—Tropomyosin Complex on F-Actin Observed by Fluorescence Resonance Energy Transfer Measurements

Contraction of vertebrate striated muscle is regulated by the strong Ca²⁺-dependent interaction among troponin (Tn), tropomyosin (Tm), and actin on the thin filament. Using fluorescence resonance energy transfer (FRET), the interactions between Tm and the Tn complex or between Tm and the Tn subunit, TnI or TnC, with or without other troponin subunits, were characterized in the presence or absence of F-actin and Ca²⁺ ions. Cys-190 of Tm was selectively labeled with the acceptor probe, 4-dimethylaminophenylazophenyl 4-maleimide. Troponin was selectively labeled at position 9 or 133 of TnI and position 98 of TnC with a donor probe, 5-(2-iodoacetylaminoethyl)aminonaphtha lene 1-sulfonic acid. FRET measurements indicate that the interaction between TnI and Tm alone is very weak, but that in the presence of F-actin, TnI binds to the proper binding site on Tm even in the absence of TnT. The distances between Cys-190 of Tm on F-actin and Cys-9 or Cys-133 of Tnl or Cys-98 of TnC in the reconstituted Tn were determined to be 52.8, 53.7, Å and 56.5 Å, respectively, in the absence of Ca²⁺, indicating that the Tnl—TnC complex, the globular portion of Tn, is located near Cys-190 of Tm on the reconstituted thin filaments. Upon binding of Ca²⁺ to TnC, these distances increased by 5.6 and 1.4 Å or decreased by 5.4 Å, respectively. These Ca²⁺-induced changes in Tn—Tm seem to occur only when F-actin is present, suggesting that the stable complex formation of TnI with the outer domain of F-actin upon removal of Ca²⁺ is a very important event during inhibition.     

Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis

We have developed a metabolic flux analysis method that is based on (13)C-labeling patterns of the intracellular metabolites directly measured by capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The flux distribution of the central carbon metabolism in Escherichia coli was determined by this new approach and the results were compared with findings obtained by conventional GC-MS analysis based on isotopomer of the proteinogenic amino acids. There were some differences in estimation results between new approach using CE-TOFMS and conventional approach using GC-MS. These were thought to be attributable to variations in measured mass distributions between amino acids and the corresponding precursors and to differences in the sensitivity of the exchange coefficients to mass distributions. However, our CE-TOFMS method facilitates high-throughput flux analysis without requiring complicated sample preparation such as hydrolysis of proteins and derivatization of amino acids.     

P-BOSS: a new filtering method for treasure hunting in metabolomics

Metabolomics is expected to boost data driven research. In biomarker discovery, powerful filtering methods to remove noise and outliers are essential for screening significant candidates from the huge volume of omic data. Here we propose a post-measurement peak filtering method (named P-BOSS) for CE electrospray ionization-time-of-flight MS (CE-TOFMS) data. Combining outlier detection method functions in parallel, we applied P-BOSS to the data using Escherichia coli knockout mutants of the tryptophan and purine biosynthesis pathways. As the result, P-BOSS showed remarkably superior performance, reducing 65% of all peaks, while leaving significant peaks.     

Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separation

We have fabricated a coaxial sheath liquid flow microelectrospray ionization (microESI) interface for capillary electrophoresis coupled with mass spectrometry (CE/MS). The ESI interface, which features a reduced probe diameter (130 microm i.d. x 174 microm o.d.) with a nebulizer-free format, can relatively easily electrospray a large amount of make-up sheath liquid (5-10 microL/min) over the long term (more than 80 runs) with a high degree of stability. The interface also provides higher separation qualities and improved detection sensitivities compared with a conventional ion spray (IS) interface.     

Three-dimensional distribution function theory for the prediction of protein-ligand binding sites and affinities: application to the binding of noble gases to hen egg-white lysozyme in aqueous solution

The three-dimensional distribution function theory of molecular liquids is applied to lysozyme in mixtures of water and noble gases. The results indicate that the theory has the capability of predicting the protein-ligand binding sites and affinities. First, it is shown that the theory successfully reproduces the binding sites of xenon found by X-ray crystallography. Then, the ability of the theory to predict the size selectivity of noble gases is demonstrated. The effect of water on the selectivity is clarified by a theoretical analysis. Finally, it is demonstrated that the dose-response curve, which is employed in experiments for examining the binding affinity, is realized by the theory.     

Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy

Capillary electrophoresis coupled with time-of-flight mass spectrometry was used to explore new serum biomarkers with high sensitivity and specificity for diabetic nephropathy (DN) diagnosis, through comprehensive analysis of serum metabolites with 78 diabetic patients. Multivariate analyses were used for identification of marker candidates and development of discriminative models. Of the 289 profiled metabolites, orthogonal partial least-squares discriminant analysis identified 19 metabolites that could distinguish between DN with macroalbuminuria and diabetic patients without albuminuria. These identified metabolites included creatinine, aspartic acid, γ-butyrobetaine, citrulline, symmetric dimethylarginine (SDMA), kynurenine, azelaic acid, and galactaric acid. Significant correlations between all these metabolites and urinary albumin-to-creatinine ratios (p?<?0.009, Spearman’s rank test) were observed. When five metabolites (including γ-butyrobetaine, SDMA, azelaic acid and two unknowns) were selected from 19 metabolites and applied for multiple logistic regression model, AUC value for diagnosing DN was 0.927 using the whole dataset, and 0.880 in a cross-validation test. In addition, when four known metabolites (aspartic acid, SDMA, azelaic acid and galactaric acid) were applied, the resulting AUC was still high at 0.844 with the whole dataset and 0.792 with cross-validation. Combination of serum metabolomics with multivariate analyses enabled accurate discrimination of DN patients. The results suggest that capillary electrophoresis-mass spectrometry based metabolome analysis could be used for DN diagnosis.     

Jacobi forms that characterize paramodular forms

The Fourier Jacobi expansions of paramodular forms are characterized from among all sequences of Jacobi forms by two conditions on the Fourier coefficients of the Jacobi forms: a growth condition and a set of linear relations. Examples, both theoretical and computational, indicate that the growth condition may be superfluous.     

Direct assembly synthesis of metal complex-semiconductor hybrid photocatalysts anchored by phosphonate for highly efficient CO2 reduction

Hybrid photocatalysts consisting of a ruthenium complex and p-type photoactive N-doped Ta(2)O(5) anchored with an organic group were successfully synthesized by a direct assembly method. The photocatalyst anchored by phosphonate exhibited excellent photoconversion activity of CO(2) to formic acid under visible-light irradiation with respect to the reaction rate and stability.     

Photocatalytic generation of a non-heme oxoiron(IV) complex with water as an oxygen source

The photocatalytic formation of a non-heme oxoiron(IV) complex, [(N4Py)Fe(IV)(O)](2+) [N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine], efficiently proceeds via electron transfer from the excited state of a ruthenium complex, [Ru(II)(bpy)(3)](2+)* (bpy = 2,2'-bipyridine) to [Co(III)(NH(3))(5)Cl](2+) and stepwise electron-transfer oxidation of [(N4Py)Fe(II)](2+) with 2 equiv of [Ru(III)(bpy)(3)](3+) and H(2)O as an oxygen source. The oxoiron(IV) complex was independently generated by both chemical oxidation of [(N4Py)Fe(II)](2+) with [Ru(III)(bpy)(3)](3+) and electrochemical oxidation of [(N4Py)Fe(II)](2+).