Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Uranyl ion‐specific DNAzyme : A DNAzyme (lower strand) cleaves the substrate (upper strand) in the presence of the uranyl ion. The enzyme folds into a bulged three‐way‐junction structure with catalytically important nucleotides residing in the bulge. A highly conserved G?A mismatch is also crucial for the enzyme's activity.

     

The Biosynthesis of the Aroma Volatile 2‐Methyltetrahydrothiophen‐3‐one in the Bacterium Chitinophaga Fx7914

2‐Methyltetrahydrothiophen‐3‐one ( 3 ) is a volatile compound that plays an important role especially in food and flavour chemistry because it contributes to the aroma of several foodstuffs including wine. Although 3 can be formed by chemical reactions during food preparation, it is also produced by microorganisms. Recent studies with yeasts showed that methionine ( 1 ) is a potential precursor of 3 , but the mechanism of the transformation is unknown. The biosynthetic pathway leading to 3 in the bacterium Chitinophaga Fx7914 was probed. Extensive feeding experiments with differently labelled precursors by using liquid cultures of Chitinophaga Fx7914 were performed. The volatiles released by the bacterium were collected by using a closed loop stripping apparatus (CLSA) and analysed by GC–MS. The observed incorporation pattern of the precursors into 3 led to the elucidation of the biosynthetic pathway. One part of the compound 2 originates from homocysteine ( 15 ), which is transformed into 3‐mercaptopropanal ( 17 ). The second biosynthetic building block is pyruvate ( 14 ). An acyloin‐forming reaction furnishes the key intermediate 21 , which cyclises intramolecularly to a diol. Dehydration followed by tautomerisation lead to the cyclic ketone 3 , which is produced by the bacterium in racemic form.     

High‐performance liquid chromatography‐mass spectrometry of epoxy resins

The application of liquid chromatography coupled to mass spectrometry (LC‐MS) for the analysis of epoxy resins is shown in two examples. Electro spray (ESI) and atmospheric pressure chemical ionization (APCI) are compared with respect to the ionization of diglycidylether of bisphenol A‐based (DGEBA) epoxy resins. By‐products in a typical modified solid DGEBA‐based epoxy resin and in a new weatherable crosslinker for powder coating applications are characterized and discussed. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 72: 913–925, 1999     

A High‐Throughput Mass‐Spectrometry‐Based Assay for Identifying the Biochemical Functions of Putative Glycosidases

The most commonly employed glycosidase assays rely on bulky ultraviolet or fluorescent tags at the anomeric position in potential carbohydrate substrates, thereby limiting the utility of these assays for broad substrate characterization. Here we report a qualitative mass spectrometry–based glycosidase assay amenable to high‐throughput screening for the identification of the biochemical functions of putative glycosidases. The assay utilizes a library of methyl glycosides and is demonstrated on a high‐throughput robotic liquid handling system for enzyme substrate screening. Identification of glycosidase biochemical function is achieved through the observation of an appropriate decrease in mass between a potential sugar substrate and its corresponding product by electrospray ionization mass spectrometry (ESI‐MS). In addition to screening known glycosidases, the assay was demonstrated to characterize the biochemical function and enzyme substrate competency of the recombinantly expressed product of a putative glycosidase gene from the thermophilic bacterium Thermus thermophilus.     

Position‐Specific Mass Shift Analysis: A Systematic Method for Investigating the EI‐MS Fragmentation Mechanism of epi‐Isozizaene

The EI‐MS fragmentation mechanism of the bacterial sesquiterpene epi‐isozizaene was investigated through enzymatic conversion of all 15 synthetic (¹³C₁)FPP isotopomers with the epi‐isozizaene synthase from Streptomyces albus and GC‐MS and GC‐QTOF analysis including MS‐MS. A systematic method, which we wish to call position‐specific mass shift analysis, for the identification of the full set of fragmentation reactions was developed.     

Synthesis of C‐H‐O Symbiosis Networks

The concept of synthesizing carbon, hydrogen, and oxygen (C‐H‐O) SYmbiosis Networks (CHOSYNs) for the design of eco‐industrial parks is introduced. Within a CHOSYN, compounds containing C‐H‐O are exchanged, converted, separated, mixed, and allocated. The use of C‐H‐O as the basis for integration creates numerous opportunities for synergism because C, H, and O are the primary building blocks for many industrial compounds that can be exchanged and integrated. A particularly attractive feature of the CHOSYN framework is its ability to use atomic‐based targets to establish benchmarks for the design of macroscopic systems involving multiple processes. Several structural representations, benchmarking, and optimization formulations are developed to embed potential CHOSYN configurations of interest and to synthesize cost‐effective networks. A case study with several scenarios is solved to demonstrate the new concept and tools. © 2015 American Institute of Chemical Engineers AIChE J, 61: 1242–1262, 2015     

Multi‐phosphorylation of the Intrinsically Disordered Unique Domain of c‐Src Studied by In‐Cell and Real‐Time NMR Spectroscopy

Intrinsically disordered regions (IDRs) are preferred sites for post‐translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase–phosphatase networks. Here we used real‐time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the “unique domain” of c‐Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin‐dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP‐dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK‐dependent sites, thus suggesting indirect effects of kinase–phosphatase networks. This study provides a proof‐of‐concept of the use of real‐time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains.     

Dual Maleimide Tagging for Relative and Absolute Quantitation of Cysteine‐Containing Peptides by MALDI‐TOF MS

A dual maleimide (DuMal) tagging method has been developed for both relative and absolute quantitation of cysteine‐containing peptides (CCPs) in combination with MALDI‐TOF mass spectrometry. A pair of maleimides with minimal differences in their chemical structures, N‐methylmaleimide and Nethylmaleimide, have been chosen to allow for the rapid (≈minutes) tagging of CCPs in the Michael addition reaction with high efficiency. It has been validated that the DuMal tagging technique is sensitive and reliable in the quantitative analysis of CCPs. Absolute quantitation of CCPs can be achieved with a detection limit as low as 7.3 nm . Relative quantitation of CCPs can be performed in various sample mixtures with consistent results (coefficient of variation <5 %). The DuMal tagging technique provides a sensitive and accurate approach for the quantitation of biomolecules containing thiol reactive sites; thus it is promising for protein detection, disease diagnosis, and biomarker discovery associated with post‐translational modifications of cysteines.     

Characterisation of Photoaffinity‐Based Chemical Probes by Fluorescence Imaging and Native‐State Mass Spectrometry

Chemical probes are small‐molecule reagents used by researchers for labelling and detection of biomolecules. We present the design, synthesis, and characterisation of a panel of 11 structurally diverse photoaffinity labelling (PAL) probes as research tools for labelling the model enzyme carbonic anhydrase (CA) in challenging environments, including in protein mixtures and cell lysates. We targeted the ubiquitous CA II as well as the two cancer‐associated CAs (CA IX and CA XII) that are of high priority as potential biomarkers of aggressive and/or multidrug‐resistant cancer. We utilise an atypical biophysical approach, native state mass spectrometry, to monitor the initial protein–probe binding and subsequent UV crosslinking efficiency of the protein:probe complex. This mass spectrometry methodology represents a new approach for chemical probe optimisation and development that might have broader applications to chemical probe characterisation beyond this study. This also represents one of the first studies, to the best of our knowledge, in which a comprehensive set of PAL probes has been used to establish the relationship between probe structure, noncovalent protein–probe binding, and covalent protein–probe crosslinking efficiency. Our results demonstrate the benefits of a comprehensive analysis of chemical probe structure–activity relationships to support the development of optimum chemical probes.     

Molecular Insights into the Thermal Stability of mAbs with Variable‐Temperature Ion‐Mobility Mass Spectrometry

The aggregation of protein‐based therapeutics such as monoclonal antibodies (mAbs) can affect the efficacy of the treatment and can even induce effects that are adverse to the patient. Protein engineering is used to shift the mAb away from an aggregation‐prone state by increasing the thermodynamic stability of the native fold, which might in turn alter conformational flexibility. We have probed the thermal stability of three types of intact IgG molecules and two Fc‐hinge fragments by using variable‐temperature ion‐mobility mass spectrometry (VT‐IM‐MS). We observed changes in the conformations of isolated proteins as a function of temperature (300–550 K). The observed differences in thermal stability between IgG subclasses can be rationalized in terms of changes to higher‐order structural organization mitigated by the hinge region. VT‐IM‐MS provides insights into mAbs structural thermodynamics and is presented as a promising tool for thermal‐stability studies for proteins of therapeutic interest.     

Ligand‐Induced Dimerization of a Truncated Parallel MYC G‐Quadruplex

Binding of an indoloquinoline derivative with an aminoalkyl side chain to a truncated sequence from the MYC promoter region was studied through isothermal titration calorimetry (ITC). The targeted MYC3 sequence lacks 3′‐flanking nucleotides and forms a monomeric parallel quadruplex (G4) with a blunt‐ended 3′‐outer tetrad under the solution conditions employed. Analysis of ITC isotherms reveals multiple binding equilibria with the initial formation of a 1:2 ligand/quadruplex complex. Evaluation of electrophoretic mobilities as well as NMR spectral data confirm ligand‐induced dimerization of MYC3 quadruplexes with the ligand sandwiched between the two 3′‐outer tetrads. Additional ligand molecules in excess bind to the 5′‐outer tetrads of the sandwich complex. Such a ligand‐promoted G4 dimerization may be exploited for the controlled assembly or disassembly of G4 aggregates to expand on present quadruplex‐based technologies.     

Identification,Quantification, and Determination of the Absolute Configuration of the Bacterial Quorum‐Sensing Signal Autoinducer‐2 by Gas Chromatography–Mass Spectrometry

Sensing the signal : A gas chromatography–mass spectrometry (GC–MS) method for the analysis of the quorum‐sensing autoinducer‐2 is described. It allows, for the first time, the direct analysis and accurate determination of this highly water soluble signaling compound, which exists in complex equilibria. The application on the caries‐causing bacterium Streptococcus mutans is described.

     

K‐BILDS: A Kinase Substrate Discovery Tool

Kinases catalyze protein phosphorylation to regulate cell signaling events. However, identifying kinase substrates is challenging due to the often low abundance and dynamic nature of protein phosphorylation. Development of novel techniques to identify kinase substrates is necessary. Here, we report kinase‐catalyzed biotinylation with inactivated lysates for discovery of substrates (K‐BILDS) as a tool to identify direct substrates of a kinase. As a proof of concept, K‐BILDS was applied to cAMP‐dependent protein kinase A (PKA) with HeLa cell lysates. Subsequent enrichment and MS/MS analysis identified 279 candidate PKA substrates, including 56 previously known PKA substrates. Of the candidate substrates, nuclear autoantigenic sperm protein (NASP), BCL2‐associated athanogene 3 (BAG3), and 14‐3‐3 protein Tau (YWHAQ) were validated as novel PKA substrates. K‐BILDS provides a valuable tool to identify direct substrates of any protein kinase.     

Profiling and Imaging of Phospholipids in Brains of Abcd1‐Deficient Mice

ABCD1 is a gene responsible for X‐linked adrenoleukodystrophy (X‐ALD), and is critical for the transport of very long‐chain fatty acids (VLCFA) into peroxisomes and subsequent β‐oxidation. VLCFA‐containing lipids accumulate in X‐ALD patients, although the effect of ABCD1‐deficiency on each lipid species in the central nervous system has not been fully characterized. In this study, each phospholipid and lysophospholipid species in Abcd1‐deficient mice brains were profiled by liquid chromatography‐mass spectrometry. Among the phospholipid and lysophospholipid species that are significantly more enriched in Abcd1‐deficient mice brains, VLCFA were present in 75, 15, 5, 4, and 1 species of phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, lysophosphatidylcholine, and lysophosphatidylethanolamine, respectively. Most VLCFA were incorporated at the sn‐1 position of phosphatidylcholine and phosphatidylethanolamine. Among the phospholipid species that are significantly less enriched in Abcd1‐deficient mice brains, odd‐numbered saturated or mono‐unsaturated fatty acyl moieties are contained in all phosphatidylcholine species. In addition, a number of phosphatidylglycerol, phosphatidylinositol, and phosphatidylserine species contained highly unsaturated fatty acyl moieties. Intriguingly, 44:1 phosphatidylcholine with VLCFA was mainly distributed in the gray matter, such as the cortex, but not in the white matter in the cerebrum and cerebellum. These results show that ABCD1‐deficiency causes metabolic alternation of long‐chain fatty acids and VLCFA. Moreover, our results imply a molecular mechanism for the incorporation of saturated or monounsaturated VLCFA into the sn‐1 position of phospholipids, and also indicate that the distribution of phospholipids with VLCFA may correlate with the development of X‐ALD.