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Chemical Probes (chemical + probe)

Distribution by Scientific Domains

Chemistry	66%
Life Sciences	33%

Selected Abstracts

Synthesis and Evaluation of New Thiodigalactoside-Based Chemical Probes to Label Galectin-3

CHEMBIOCHEM, Issue 10 2009
Monique van Scherpenzeel
Abstract Light up galectin: Photoprobes based on thiodigalactoside were prepared for galectin-3, a lectin linked to cancer. The probes contained either benzophenone or acetophenone moieties as the photolabel for covalent attachment to the protein. One particular probe labeled galectin-3 selectively, even in the presence of cell lysate. New chemical probes were synthesized to label galectin-3. They are based on the high affinity thiodigalactoside ligand. The probes were synthesized with benzophenone or acetophenone moieties as the photolabel for covalent attachment to the protein. Besides labeling the protein, these aromatic photolabels also greatly enhance the affinity of the probes towards galectin-3, due to the interaction of the photolabel with two arginine guanidinium groups of the protein. The linkage between the sugar and the photolabel was varied as an ester, an amide, and a triazole. For the amide and triazole derivatives, a versatile synthetic route towards a symmetrical 3-azido-3-deoxy-thiodigalactoside was developed. The new probes were evaluated for their binding affinity of human galectin-3. They were subsequently tested for their labeling efficiency, as well as specificity in the presence of a protein mixture and a human cancer cell lysate. [source]

Rapid and selective isolation of ,-xylosidase through an activity-based chemical approach

BIOTECHNOLOGY JOURNAL, Issue 2 2006
Lee-Chiang Lo Dr.
Abstract ,-Xylosidase is a key enzyme in the xylanolytic system with a great potential in many biotechnological applications, especially in the food as well as the pulp and paper industries. We have developed a chemical approach for the rapid screening and isolation of ,-xylosidase. Activity probe LCL-6X targeting ,-xylosidase was utilized in this study. It carries a ,-xylopyranosyl recognition head, a latent trapping device consisting of a 2-fluoromethylphenoxyl group, and a biotin reporter group. The biotin reporter group serves both as a readout device and as a tool for enriching the labeled proteins. LCL-6X could selectively label a model ,-xylosidase from Trichoderma koningii. All other bystander proteins used in this study, including phosphorylase b, BSA, ovalbumin, carbonic anhydrase, and trypsin inhibitor, gave negligible cross-labeling effect. With the assistance of streptavidin agarose beads and mass spectrophotometry for the recovery and identification of the biotinylated proteins, we demonstrated that LCL-6X could be successfully applied to identify a bi-functional enzyme with ,- L -arabinofuranosidase/,-xylosidase activity from the total protein extract of a Pichia expressing system and a prospective ,-xylosidase in the culture medium of Aspergillus fumigatus. The ,-xylosidase activities from numerous microbes were also screened using the LCL-6X probe. Preliminary results showed significant differences among these microbial sources and some distinct protein bands were observed. Thus, we have successfully developed a novel chemical probe that has potential applications in xylan-related research. [source]

Synthesis and Characterization of the D5h Isomer of the Endohedral Dimetallofullerene Ce2@C80: Two-Dimensional Circulation of Encapsulated Metal Atoms Inside a Fullerene Cage

CHEMISTRY - A EUROPEAN JOURNAL, Issue 37 2009
Michio Yamada Dr.
Abstract Herein we show the synthesis and characterization of the second known Ce2@C80 isomer. A 13C,NMR spectroscopic study revealed that the structure of the second isomer has D5h symmetry. Paramagnetic NMR spectral analysis and theoretical calculation display that the encapsulated Ce atoms circulate two-dimensionally along a band of ten contiguous hexagons inside a D5h -C80 cage, which is in sharp contrast to the three-dimensional circulation of two Ce atoms in an Ih -C80 cage. The electronic properties were revealed by means of electrochemical measurements. The D5h isomer of Ce2@C80 has a much smaller HOMO,LUMO gap than cluster fullerenes (M3N@C80, M=Sc, Tm, and Lu) with the same D5h -C80 cages. The chemical reactivity was investigated by using disilirane as a chemical probe. The high thermal reactivity toward 1,1,2,2-tetramesityl-1,2-disilirane is consistent with the trends of the redox potentials and the lower LUMO level of the D5h isomer of Ce2@C80 compared with that of C60. [source]

Orthogonal Chemical Genetic Approaches for Unraveling Signaling Pathways

IUBMB LIFE, Issue 6 2005
Kavita Shah
Abstract While chemical genetic approach uses small molecules to probe protein functions in cells or organisms, orthogonal chemical genetics refers to strategies that utilize reengineered protein-small molecule interfaces, to alter specificities, in order to probe their functions. The advantage of orthogonal chemical genetics is that the changes at the interfaces are generally so minute that it goes undetected by natural processes, and thus depicts a true physiological picture of biological phenomenon. This review highlights the recent advances in the area of orthogonal chemical genetics, especially those designed to probe signaling processes. Dynamic protein-protein and enzyme-substrate interactions following stimuli form the foundation of signal transduction. These processes not only break spatial and temporal boundaries between interacting proteins, but also impart distinct regulatory properties by creating functional diversity at the interfaces. Functional and temporal modulation of these dynamic interactions by specific chemical probes provides extremely powerful tools to initiate, ablate, decouple and deconvolute different components of a signaling pathway at multiple stages. Not surprisingly, multiple receptor-ligand reengineering approaches have been developed in the last decade to selectively manipulate these transient interactions with the aim of unraveling signaling events. However, given the diversity of protein-protein interactions and novel chemical genetic probes developed to perturb these processes, a short review cannot do adequate justice to all aspects of signaling. For this reason, this review focuses on some orthogonal chemical-genetic strategies that are developed to study signaling processes involving enzyme-substrate interactions. IUBMB Life, 57: 397-405, 2005 [source]

Lipolytic and esterolytic activity-based profiling of murine liver

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2008
Ruth Birner-Gruenberger
Abstract In lipid metabolism, the liver acts as a buffer for transient energy fluctuations. It temporarily stores fatty acids as triacylglycerol and secretes them as very low density lipoprotein into the circulation when the period of maximum lipid load has passed. The lipolytic enzymes responsible for mobilization of internal lipid stores in the liver have not been identified yet. We introduced active site-directed chemical probes for lipolytic activity profiling in complex mixtures, known as activity-based proteomics, and employed it for global analysis and functional annotation of lipolytic proteins in mouse adipose tissue. Here we report the combined application of two approaches using fluorescent and biotinylated probes for discovery and discrimination of lipolytic and esterolytic enzymes in mouse liver subproteomes. Proteomes labeled with the fluorescent probes were analyzed by 2-DE while proteomes labeled with the biotinylated probe were subjected to avidin-affinity isolation. Of 37 totally identified proteins, 15 were detected using both approaches while 14 and 8 were solely identified by 2-DE and avidin-affinity isolation, respectively. Moreover, 12 enzymes were classified as potential lipases and/or cholesteryl esterases by their reaction with probes specific for the respective activities directly in their proteomes. [source]