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Chembiochem: a European Journal of Chemical Biology

Youngmi Kim, Jihee Park
We report a fluorescent probe that is highly sensitive and selective for serum albumins. Signal transduction results from the disassembly of fluorescence-quenched aggregates upon binding to human serum albumin (HSA). The probe offers a rapid (≤ 2 s) fluorimetric assay of HSA in either PBS buffer, urine or blood serum with a high signal-to-noise ratio. It is also useful as a wash-free prestaining reagent for detecting HSA on electrophoresis gels.
November 9, 2018: Chembiochem: a European Journal of Chemical Biology
Santosh Kumar Padhi, D H Sreenivasa Rao
Hydroxynitrile lyase (HNL) catalysed stereoselective synthesis of β-nitro alcohols is considered as an efficient biocatalytic approach. However, there exist only one (S)-selective HNL i.e. Hevea brasiliensis (HbHNL) to synthesize (S)-β-nitro alcohols from corresponding aldehydes. Further, HbHNL synthesis is limited by long reaction time (48 h) and moderate yield. We prepared a number of (S)-β-nitro alcohols using a (R)-selective HNL from Arabidopsis thaliana (AtHNL). Optimization of the reaction conditions of AtHNL catalyzed stereoselective C-C bond cleavage of racemic 2-ntro-1-phenylethanol (NPE) produced (S)-NPE up to 99% ee and 47% conversion...
November 8, 2018: Chembiochem: a European Journal of Chemical Biology
Carlos G Acevedo-Rocha, Zhoutong Sun, Manfred T Reetz
Oil and water, apples and pears: Mixing things that should not be mixed can result in scientifically unsound conclusions. A recent directed-evolution study compared iterative saturation mutagenesis (ISM) with the OmniChange version of saturation mutagenesis (SM). ISM is a semirational strategy in directed evolution that is independent of the particular type of SM, thus the two should not be compared.
November 8, 2018: Chembiochem: a European Journal of Chemical Biology
Borja Mateos, Robert Konrat, Roberta Pierattelli, Isabella Caterina Felli
Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable 3D structure and are able to adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. A widely used NMR experimental approach to study long-range contacts in IDPs exploits paramagnetic effects and 1H detected experiments are generally used to determine paramagnetic relaxation enhancement (PRE) for amide protons. However, under physiological conditions exchange broadening hampers the detection of solvent exposed amide protons reducing the content of information available...
November 8, 2018: Chembiochem: a European Journal of Chemical Biology
Sunayana Kapil, Cecile Petit, Victoria N Drago, Donald R Ronning, Steven J Sucheck
α,α'-Trehalose plays roles in the synthesis of several cell wall components involved in pathogenic mycobacteria virulence. Its absence in mammalian biochemistry makes trehalose-related biochemical processes potential targets for chemotherapy. The trehalose-6-phosphate synthase (TPS)/trehalose-6-phosphate phosphatase (TPP) pathway, also referred to as the OtsA/OtsB2 pathway, is the major pathway involved in the production of trehalose in Mycobacterium tuberculosis (Mtb). In addition, TPP is essential for Mtb survival...
November 6, 2018: Chembiochem: a European Journal of Chemical Biology
Yanping He, Yibo Zhou, Da Chen, Juewen Liu
Recently a few RNA-cleaving DNAzymes have been isolated with excellent specificity for Na+, and some of them contain a Na+ binding aptamer. This metal recognition mechanism is different from most previously reported DNAzymes. Previous studies using 2-aminopurine (2AP) as a probe have indicated interesting local folding by Na+. In this work, fluorescence resonance energy transfer (FRET) was used to probe the global folding of the Ce13d DNAzyme, one of the Na+-specific DNAzymes. FRET pairs were at different locations yielding a total of five constructs to probe its three-way junc-tion structure with a large loop...
November 6, 2018: Chembiochem: a European Journal of Chemical Biology
Natalia Putkaradze, Martin Litzenburger, Michael Christopher Hutter, Rita Bernhardt
In this study, the ability of CYP109E1 from Bacillus megaterium DSM319 to metabolize cholesterol was investigated. This steroid was identified as a new substrate to be converted by CYP109E1 using adrenodoxin and adrenodoxin reductase as redox partners in vitro. The biotransformation was successfully reproduced in vivo using Bacillus megaterium cells overexpressing CYP109E1. To enhance the production of cholesterol derivatives, an Escherichia coli based whole-cell system harbouring CYP109E1 was established. This novel system showed a 3...
November 6, 2018: Chembiochem: a European Journal of Chemical Biology
Matthias Christen, Cassandra Kamischke, Hemantha D Kulasekara, Kathleen C Olivas, Bridget R Kulasekara, Beat Christen, Toni Kline, Samuel I Miller
The bacterial second messenger cyclic diguanosine monophos-phate (c-di-GMP) is a key regulator of cellular motility, the cell cycle, and biofilm formation with its resultant antibiotic tolerance, which may make chronic infections difficult to treat. Therefore, diguanylate cyclases, which regulate the spatiotemporal production of c-di-GMP, may be attractive drug targets to control biofilm formation that is part of chronic infections. In this paper, we present a FRET-based biochemical high-throughput screening approach coupled with detailed structure-activity studies to identify synthetic small molecule modulators of the diguanylate cyclase, DgcA, from Caulobacter crescentus...
November 5, 2018: Chembiochem: a European Journal of Chemical Biology
Kui Zeng, Thomas Groth, Kai Zhang
Polysaccharide sulfates as the mimetics of native heparin and heparan sulfate are important bioactive compounds, since they show great potential for tuning crucial biological activities within living organisms. In this Mini-Review, we summarize the progress of polysaccharide sulfates, such as cellulose sulfate, chitosan sulfate, other sulfated polysaccharides, in particular in the fields of biomedical and bioengineering applications in the past ten years with emphasis on their effects on cell growth and differentiation, but also as building blocks for drug carriers and medical implants...
November 5, 2018: Chembiochem: a European Journal of Chemical Biology
Taisuke Kojima, Chu-Chi Lin, Shuichi Takayama, Shih-Kang Fan
Handling aqueous two phase systems (ATPSs) formed by liquid-liquid phase separation (LLPS) relies on the accurate construction of binodal curves and tie-lines, which delineate polymer concentrations required for phase separation and depict the properties of the resulting phases, respectively. Various techniques to determine binodal curves and tie-lines of ATPSs exist, but most rely on manual pipetting of relatively large volumes of fluids in a slow and tedious manner. To overcome these disadvantages, this paper describes microscale droplet manipulation by electrowetting-on-dielectric (EWOD) for determination of ATPS binodals and tie-lines...
November 5, 2018: Chembiochem: a European Journal of Chemical Biology
Kevin Neumann, Alessia Gambardella, Mark Bradley
Traditionally, prodrug activation has been limited to enzymatic triggers or gross physiological aberrations, such as pH, that offer low selectivity and control over dosage. In recent years, the field of prodrug activation chemistries has been transformed by the use of bioorthogonal reactions - chemistries that can be carried out under biological conditions at sub-millimolar concentrations with the tetrazine-mediated inverse electron demand Diels Alder reaction amongst the most recognized. Its high reaction rates, chemoselectivity and excellent biocompatibility make tetrazines an ideal small molecule for activating prodrugs...
November 5, 2018: Chembiochem: a European Journal of Chemical Biology
Le Wang, Wenfu Zheng, Shaoqin Liu, Bing Li, Xingyu Jiang
The precise editing of the genome of a living body is a goal pursued by the scientists of many fields. In recent years, CRISPR (clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome editing systems have become a revolutionary toolbox for gene editing across various species. However, the low transfection efficiency of CRISPR/Cas9 system to mammalian cells in vitro and in vivo is a big obstacle hindering the wide and deep application. In this review, we briefly summarized the recently developed delivery strategies for various CRISPR/Cas9 formulations and their applications in treating gene-related diseases...
November 4, 2018: Chembiochem: a European Journal of Chemical Biology
Kyle A Pelot, David M Hagelthorn, Young J Hong, Dean J Tantillo, Philipp Zerbe
The diterpene synthase CLERODIENYL DIPHOSPHATE SYNTHASE 1 (PvCPS1) from the crop plant switchgrass (Panicum virgatum) stereoselectively converts (E,E,E)-geranylgeranyl diphosphate (GGPP) into the clerodane natural product, cis-trans-clerodienyl diphosphate (CLPP, 1). Structure-guided point mutations of PvCPS1 redirected product stereoselectivity toward the formation of a rare cis-clerodane diastereomer, cis-cis-CLPP (2). Additionally, an alternate cis-clerodane diastereomer, (5S,8S,9R,10R)-13Z-CLPP (3), was produced when reacting PvCPS1 and select variants thereof with the cis-prenyl substrate (Z,Z,Z)-nerylneryl diphosphate (NNPP)...
November 4, 2018: Chembiochem: a European Journal of Chemical Biology
Jiaqing Wang, Jie Zhou, Hongjian He, Difei Wu, Xuewen Du, Bing Xu
Phosphatases play an important role in cell biology, but there are few suitable probes for selectively imaging phosphatase activity of live cells because the current probes require cell fixation or exhibit considerable cytotoxicity. Here we show that conjugating a D-peptide to a quinazolinone derivative generates cell-compatible, biostable probes for imaging phosphatase activities inside live cells. Moreover, our results show that inhibiting ectophosphatases is a critical factor for imaging intracellular phosphatases...
November 2, 2018: Chembiochem: a European Journal of Chemical Biology
Ridvan Nepravishta, Samuel Walpole, Louise Tailford, Nathalie Juge, Jesus Angulo
DEEP-STD NMR is a recently developed powerful approach for structure and pharmacophore elucidation of weak protein-ligand interactions, reporting key information on the orientation of the ligand and the architecture of the binding pocket. The method relies on selective saturation of protein residues in the binding site and the generation of a differential epitope map by observing the ligand, which depicts the nature of the protein residues contacting the ligand in the bound state. Selective saturation requires knowledge of the chemical shift assignment of the protein residues, which can be obtained either experimentally by NMR or predicted from 3D structures...
October 31, 2018: Chembiochem: a European Journal of Chemical Biology
Wei-Cheng Huang, Jiahn-Haur Liao, Tzu-Chun Hsiao, Tong-You Wade Wei, Manuel Maestre-Reyna, Yoshitaka Bessho, Ming-Daw Tsai
Human tumor-necrosis-factor-receptor-associated factor (TRAF)-interacting protein with a forkhead-associated domain (TIFA) is a key regulator of NF-κB activation. It also plays a key role in the activation of innate immunity in response to bacterial infection, through heptose 1,7-bisphosphate (HBP), a metabolite of lipopolysaccharide (LPS). However, the mechanism of TIFA function is largely unexplored, except the suggestion for interacting with TRAF6. Here we provide evidence for direct binding, albeit weak, between TIFA and the TRAF domain of TRAF6, and show that the binding is enhanced for a rationally designed double mutant TIFA S174Q/M179D...
October 31, 2018: Chembiochem: a European Journal of Chemical Biology
Werner Hoffmann, René Stürmer, Sönke Harder, Hartmut Schlüter
Mucous gels (mucus) cover internal body surfaces. The secretory mucins MUC5AC, MUC6 and the protective peptide TFF2 are characteristic constituents of gastric mucus, TFF2 being co-secreted with MUC6. Here, we investigate two commercial mucin preparations via FPLC and proteomics because they are model systems for studying the rheology of gastric mucins. One preparation is also used as a saliva substitute, e.g. after radiation therapy. We show that both preparations contain TFF2 (about 0.6 to 1.1% w/w). The majority of TFF2 is strongly bound non-covalently to mucin in a manner, which is resistant to boiling in SDS...
October 29, 2018: Chembiochem: a European Journal of Chemical Biology
Hongchang Bu, Dinggeng He, Xiaoxiao He, Kemin Wang
Exosomes are cell-derived small extracellular vesicles that are naturally secreted by all types of cells and widely distributed in various biofluids. They carry a variety of key bioactive molecules (e.g., nucleic acids, proteins, growth factors, cytokines) of their parental cells and convey them to the neighboring or even distant cells through circulation. In recent years, tumor-derived exosomes have attracted great interests of investigators because they actively participate in nearly all aspects of tumor development and facilitate both tumor growth and metastasis by exosome-mediated intercellular communication...
October 29, 2018: Chembiochem: a European Journal of Chemical Biology
Hoyoung Jung, Son Hye Shin, Jung-Min Kee
In contrast to the well-recognized protein phosphorylation on the side chain oxygen of Ser, Thr, or Tyr residues, the analogous phosphoramidates on the nitrogen of His, Lys, and Arg side chains remain much less investigated, mainly due to the instability of the post-translational modifications (PTMs) and the technical difficulties involved in their analysis. For example, reports of the enzyme activities responsible for the formation and hydrolysis of these phosphoramidates date back to as early as the 1950s, but some of these enzymes have only recently been identified and functionally characterized, aided by the development of novel research tools...
October 29, 2018: Chembiochem: a European Journal of Chemical Biology
Liraz Chai, Razan Abbasi, Reem Mousa, Noa Dekel, Hadar Amartely, Tsafi Danieli, Mario Lebendiker, Yael Levi-Kalisman, Deborah E Shalev, Norman Metanis
Biofilms are aggregates of microbial cells that form on surfaces and at interfaces and are encased in an extracellular matrix. In biofilms made by the soil bacterium Bacillus subtilis, the protein TapA mediates the assembly of the functional amyloid protein TasA into extracellular fibers and it also anchors these fibers to the cell surface. Here we used circular dichroism and NMR to show that, unlike the structured TasA, TapA is disordered. In addition, TapA is composed of two weakly interacting domains, a disordered C-terminal domain and a more structured N-terminal domain...
October 29, 2018: Chembiochem: a European Journal of Chemical Biology
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