Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples

Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS3 ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions. �� 2013 Elsevier B.V.

Phosphorus catalysis in the pyrolysis behaviour of biomass

Phosphorus is a key plant nutrient and as such, is incorporated into growing biomass in small amounts. This paper examines the influence of phosphorus, present in either acid (HPO) or salt ((NH)PO) form, on the pyrolysis behaviour of both Miscanthus �� giganteus, and its cell wall components, cellulose, hemicellulose (xylan) and lignin (Organosolv). Pyrolysis-gas chromatography-mass spectrometry (PY-GC-MS) is used to examine the pyrolysis products during thermal degradation, and thermogravimetric analysis (TGA) is used to examine the distribution of char and volatiles. Phosphorus salts are seen to catalyse the pyrolysis and modify the yields of products, resulting in a large increase in char yield for all samples, but particularly for cellulose and Miscanthus. The thermal degradation processes of cellulose, xylan and Miscanthus samples occur in one step and the main pyrolysis step is shifted to lower temperature in the presence of phosphorus. A small impact of phosphorus was observed in the case of lignin char yields and the types of pyrolysis decomposition products produced. Levoglucosan is a major component produced in fast pyrolysis of cellulose. Furfural and levoglucosenone become more dominant products upon P-impregnation pointing to new rearrangement and dehydration routes. The P-catalysed xylan decomposition route leads to a much simpler mixture of products, which are dominated by furfural, 3-methyl-2-cyclopenten-1-one and one other unconfirmed product, possibly 3,4-dihydro-2-methoxy-2H-pyran or 4-hydroxy-5,6-dihydro-(2H)-pyran-2-one. Phosphorus-catalysed lignin decomposition also leads to a modified mixture of tar components and desaspidinol as well as other higher molecular weight component become more dominant relative to the methoxyphenyl phenols, dimethoxy phenols and triethoxy benzene. Comparison of the results for Miscanthus lead to the conclusion that the understanding of the fast pyrolysis of biomass can, for the most part, be gained through the study of the individual cell wall components, provided consideration is given to the presence of catalytic components such as phosphorus.

Potassium catalysis in the pyrolysis behaviour of short rotation willow coppice

Short rotation willow coppice (SRC) and a synthetic biomass, a mixture of the basic biomass components (cellulose, hemicellulose and lignin), have been investigated for the influence of potassium on their pyrolysis behaviours. The willow sample was pre-treated to remove salts and metals by hydrochloric acid, and this demineralised sample was impregnated with potassium. The same type of pre-treatment was applied to components of the synthetic biomass. Characterisation was performed using thermogravimetric analysis with measurement of products by means of Fourier transform infrared spectroscopy (TGA-FTIR) and pyrolysis-gas chromatography-mass spectrometry (PY-GC-MS). A comparison of product distributions and kinetics are reported. While the general features of decomposition of SRC are described well by an additive behaviour of the individual components, there are some differences in the magnitude of the influence of potassium, and on the products produced. For both SRC and the synthetic biomass, TGA traces indicate catalytic promotion of both of the two-stages of biomass decomposition, and potassium can lower the average apparent first-order activation energy for pyrolysis by up to 50 kJ/mol. For both SRC and synthetic biomass the yields and distribution of pyrolysis products have been influenced by the presence of the catalyst. Potassium catalysed pyrolysis increases the char yields markedly and this is more pronounced for synthetic biomass than SRC. Gas evolution profiles during pyrolysis show the same general features for both SRC and synthetic biomass. Relative methane yields increase during the char formation stage of pyrolysis of the potassium doped samples. The evolution profiles of acetic acid and formaldehyde change, and these products are seen in lower relative amounts for both the demineralised samples. A greater variation in pyrolysis products is observed from the treated SRC samples compared to the different synthetic biomass samples. Furthermore, substituted phenols from lignin pyrolysis are more dominant in the pyrolysis profiles of the synthetic biomass than of the SRC, implying that the extracted lignins used in the synthetic biomass yield a greater fraction of monomeric type species than the lignocellulosic cell wall material of SRC. For both types of samples, PY-GS-MS analyses show that potassium has a significant influence on cellulose decomposition markers, not just on the formation of levoglucosan, but also other species from the non-catalysed mechanism, such as 3,4-dihydroxy-3-cyclobutene-1,2-dione. �� 2007 Elsevier Ltd. All rights reserved.

Recent developments in heterogeneous catalysis for the sustainable production of biodiesel

The quest for energy security and widespread acceptance of the anthropogenic origin of rising CO2 emissions and associated climate change from combusting fossil derived carbon sources, is driving academic and commercial research into new routes to sustainable fuels to meet the demands of a rapidly rising global population. Biodiesel is one of the most readily implemented and low cost, alternative source of transportation fuels to meet future societal demands. However, current practises to produce biodiesel via transesterification employing homogeneous acids and bases result in costly fuel purification processes and undesired pollution. Life-cycle calculations on biodiesel synthesis from soybean feedstock show that the single most energy intensive step is the catalytic conversion of TAGs into biodiesel, accounting for 87% of the total primary energy input, which largely arises from the quench and separation steps. The development of solid acid and base catalysts that respectively remove undesired free fatty acid (FFA) impurities, and transform naturally occurring triglycerides found within plant oils into clean biodiesel would be desirable to improve process efficiency. However, the microporous nature of many conventional catalysts limits their ability to convert bulky and viscous feeds typical of plant or algal oils. Here we describe how improved catalyst performance, and overall process efficiency can result from a combination of new synthetic materials based upon templated solid acids and bases with hierarchical structures, tailored surface properties and use of intensified process allowing continuous operation.

Heterogeneous catalysis in an oscillatory baffled flow reactor

The first demonstration of heterogeneous catalysis within an oscillatory baffled flow reactor (OBR) is reported, exemplified by the solid acid catalysed esterification of organic acids, an important prototypical reaction for fine chemicals and biofuel synthesis. Suspension of a PrSOH-SBA-15 catalyst powder is readily achieved within the OBR under an oscillatory flow, facilitating the continuous esterification of hexanoic acid. Excellent semi-quantitative agreement is obtained between OBR and conventional stirred batch reaction kinetics, demonstrating efficient mixing, and highlighting the potential of OBRs for continuous, heterogeneously catalysed liquid phase transformations. Kinetic analysis highlights acid chain length (i.e. steric factors) as a key predictor of activity. Continuous esterification offers improved ester yields compared with batch operation, due to the removal of water by-product from the catalyst, evidencing the versatility of the OBR for heterogeneous flow chemistry and potential role as a new clean catalytic technology. �� The Royal Society of Chemistry 2013.

Heterogeneous catalysis for sustainable biodiesel production via esterification and transesterification

Concern over the economics of accessing fossil fuel reserves, and widespread acceptance of the anthropogenic origin of rising CO2 emissions and associated climate change from combusting such carbon sources, is driving academic and commercial research into new routes to sustainable fuels to meet the demands of a rapidly rising global population. Here we discuss catalytic esterification and transesterification solutions to the clean synthesis of biodiesel, the most readily implemented and low cost, alternative source of transportation fuels to meet future societal demands.

Fundamental investigations of enantioselective heterogeneous catalysis

Enantioselective catalysis is an increasingly important method of providing enantiomeric compounds for the pharmaceutical and agrochemical industries. To date, heterogeneous catalysts have failed to match the industrial impact achieved by homogeneous systems. One successful approach to the creation of heterogeneous enantioselective catalysts has involved the modification of conventional metal particle catalysts by the adsorption of chiral molecules. This article examines the contribution of effects such as chiral recognition and amplification to these types of system and how insight provided by surface science model studies may be exploited in the design of more effective catalysts.

Nanoengineering the active site in heterogeneous catalysis

Here we demonstrate the first application of time-resolved synchrotron X-ray absorption spectroscopy to simultaneously follow dynamic nanoparticle surface restructuring and the evolution of surface and gas-phase products during an organic reaction. Surface palladium oxide, and not metal, is identified as the catalytic species responsible for the selective oxidation (selox) of crotyl alcohol to crotonaldehyde. Elevated reaction temperatures facilitate reversible nanoparticle redox processes, and concomitant catalytic selectivity loss, in response to reaction conditions. These discoveries highlight the importance of stabilizing surface palladium oxide and minimizing catalyst reducibility in order to achieve high selox yields, and will aid the future design of Pd-derived selox catalysts. This discovery has important implications for the design of future liquid and vapor phase selox catalysts, and the thermochemical behavior of Pd nanostructures in general.

R. A. Sheldon, I. Arends and U. Hanefeld. Green chemistry and catalysis. Wiley-VCH, 2007, 448 pp; ISBN 978-3-527-30715-9 (Hardcover)

Book review

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition

Funded by United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel Israel Science Foundation (ISF). Grant Number: 1349 Israel Science Foundation Israel Strategic Alternative Energy Foundation (I-SAEF) BBSRC. Grant Number: BB/L009951/1 Scottish Government Food, Land and People program Society for Applied Microbiology

Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition

Funded by United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel Israel Science Foundation (ISF). Grant Number: 1349 Israel Science Foundation Israel Strategic Alternative Energy Foundation (I-SAEF) BBSRC. Grant Number: BB/L009951/1 Scottish Government Food, Land and People program Society for Applied Microbiology

Enzymatic transhalogenation of dendritic RGD peptide constructs with the fluorinase

We thank EPSRC and the Scottish Imaging Network (SINAPSE) for grants. DO���H thanks the Royal Society for a Wolfson Research Merit Award and ST is grateful to the John and Kathleen Watson Scholarship for financial support. We are grateful to Dr Catherine Botting and Dr Sally Shirran of the St Andrews Mass Spectrometry Service for MALDI-MS acquisitions. We also thank Dr Sally Pimlott of the University of Glasgow for the use of radiochemistry facilities.

Last-step enzymatic [18F]-fluorination of cysteine-tethered RGD peptides using modified Barbas linkers

Acknowledgements We thank the Engineering and Physical Sciences Research Council, UK, for a research grant. Funded by Engineering and Physical Sciences Research Council, UK

Highly stable PEGylated gold nanoparticles in water: applications in biology and catalysis

Gold nanoparticles (Au NPs) with diameters ranging between 5-60 nm have been synthesised in water, and further stabilized with polyethylene glycol-based thiol polymers (mPEG-SH). Successful PEGylation of the Au NPs was confirmed by Dynamic Light scattering (DLS) and Zeta potential measurements. PEG coating of the Au NPs is the key of their colloidal stabilty, and its successful applications. Catalytic efficiency testing of the PEG-AuNPs were carried out on homocoupling of boronic acid. PEG-Au NPs with AuNps diameter < 30 nm were useful as catalyst in water. Finally, the PEG-Au NPs were also shown to be stable in biological fluid and not cytotoxic on B16.F10 cell line, making them attractive for further studies.

Structural and Biochemical Dissection of the Trehalose Biosynthetic Complex in Pathogenic Fungi

<p>Trehalose is a non-reducing disaccharide essential for pathogenic fungal survival and virulence. The biosynthesis of trehalose requires the trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. More importantly, the trehalose biosynthetic pathway is absent in mammals, conferring this pathway as an ideal target for antifungal drug design. However, lack of germane biochemical and structural information hinders antifungal drug design against these targets. </p><p>In this dissertation, macromolecular X-ray crystallography and biochemical assays were employed to understand the structures and functions of proteins involved in the trehalose biosynthetic pathway. I report here the first eukaryotic Tps1 structures from Candida albicans (C. albicans) and Aspergillus fumigatus (A. fumigatus) with substrates or substrate analogs. These structures reveal the key residues involved in substrate binding and catalysis. Subsequent enzymatic assays and cellular assays highlight the significance of these key Tps1 residues in enzyme function and fungal stress response. The Tps1 structure captured in its transition-state with a non-hydrolysable inhibitor demonstrates that Tps1 adopts an ���internal return like��� mechanism for catalysis. Furthermore, disruption of the trehalose biosynthetic complex formation through abolishing Tps1 dimerization reveals that complex formation has regulatory function in addition to trehalose production, providing additional targets for antifungal drug intervention. </p><p>I also present here the structure of the Tps2 N-terminal domain (Tps2NTD) from C. albicans, which may be involved in the proper formation of the trehalose biosynthetic complex. Deletion of the Tps2NTD results in a temperature sensitive phenotype. Further, I describe in this dissertation the structures of the Tps2 phosphatase domain (Tps2PD) from C. albicans, A. fumigatus and Cryptococcus neoformans (C. neoformans) in multiple conformational states. The structures of the C. albicans Tps2PD -BeF3-trehalose complex and C. neoformans Tps2PD(D24N)-T6P complex reveal extensive interactions between both glucose moieties of the trehalose involving all eight hydroxyl groups and multiple residues of both the cap and core domains of Tps2PD. These structures also reveal that steric hindrance is a key underlying factor for the exquisite substrate specificity of Tps2PD. In addition, the structures of Tps2PD in the open conformation provide direct visualization of the conformational changes of this domain that are effected by substrate binding and product release. </p><p>Last, I present the structure of the C. albicans trehalose synthase regulatory protein (Tps3) pseudo-phosphatase domain (Tps3PPD) structure. Tps3PPD adopts a haloacid dehydrogenase superfamily (HADSF) phosphatase fold with a core Rossmann-fold domain and a ��/�� fold cap domain. Despite lack of phosphatase activity, the cleft between the Tps3PPD core domain and cap domain presents a binding pocket for a yet uncharacterized ligand. Identification of this ligand could reveal the cellular function of Tps3 and any interconnection of the trehalose biosynthetic pathway with other cellular metabolic pathways. </p><p>Combined, these structures together with significant biochemical analyses advance our understanding of the proteins responsible for trehalose biosynthesis. These structures are ready to be exploited to rationally design or optimize inhibitors of the trehalose biosynthetic pathway enzymes. Hence, the work described in this thesis has laid the groundwork for the design of Tps1 and Tps2 specific inhibitors, which ultimately could lead to novel therapeutics to treat fungal infections.</p>