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Chembiochem: a European Journal of Chemical Biology

Monique Mertens, Malte Hilsch, Ivan Haralampiev, Rudolf Volkmer, Pablo Wessig, Peter Mueller
The present study describes the synthesis and characterization of an amphiphilic construct which is aimed to recruit SH-containing molecules to membranes. The construct consists of (i) an aliphatic chain to enable the anchoring within membranes, (ii) a maleimide moiety to react with the sulfhydryl group of a soluble (bio)molecule, and (iii) a fluorescence moiety to follow the construct by fluorescence spectroscopy and microscopy. It is shown, that the construct can be incorporated into preformed membranes allowing the application of the approach with biological membranes...
May 22, 2018: Chembiochem: a European Journal of Chemical Biology
Erwan Galardon, Jean-Chrstophe Lec
A synthesis of the sulfur metabolic compound 3-mercaptopyruvic acid (3-MPH) is reported and allowed its isolation and characterization for the first time. Detailed kinetic, thermodynamic and spectroscopic studies of its complex behaviour in solution are discussed.
May 20, 2018: Chembiochem: a European Journal of Chemical Biology
Yumin Dai, Hannah R Valentino, Pablo Sobrado
The redox-neutral reaction catalyzed by 2-haloacrylate hydratase (2-HAH) leads to the conversion of 2-chloroacrylate to pyruvate. Previous mechanistic studies demonstrated formation of a flavin-iminium ion as an important intermediate in the 2-HAH catalytic cycle. Time-resolved flavin absorbance studies were performed in this study and the data showed that the enzyme is capable of stabilizing both anionic and neutral flavin semiquinone species. The presence of a radical scavenger decreases the activity in a concentration-dependent manner...
May 18, 2018: Chembiochem: a European Journal of Chemical Biology
Aranzazu Del Campo, Roshna V Nair, Aleeza Farrukh
The integrin α5β1 is overexpressed in colon, breast, ovarian, lung and brain tumors and has been identified as key component in mechanosensing. In order to study how dynamic changes of α5β1 engagement affect cellular behaviour, photoactivatable derivatives of α5β1 specific ligands are presented in this article. A photoremovable protecting group (PRPG) was introduced into the ligand structure at a relevant position for integrin recognition. The presence of the chromophore temporally inhibited ligand bioactivity...
May 18, 2018: Chembiochem: a European Journal of Chemical Biology
Khashti Ballabh Joshi, Ramesh Singh, Narendra Kumar Mishra, Vikas Kumar, Vandana Vinayak
We report the design and synthesis of biocompatible small peptide based molecule for the controlled and targeted delivery of the encapsulated bioactive metal ions via transforming their internal nanostructures. Tyrosine based short peptide amphiphile (sPA) was synthesized which self-assembled into β-sheet like secondary structures. The self assembly of the designed sPA was modulated by using different bioactive transition metal ions which is confirmed by spectroscopic and microscopic techniques. These bioactive metal ions conjugated sPA hybrid structures are further used to develop antibacterial materials...
May 17, 2018: Chembiochem: a European Journal of Chemical Biology
Koh K Takita, Kazunori K Fujii, Tetsuya Kadonosono, Ryo Masuda, Takaki Koide
We report here a novel class of collagen-binding peptides, cyclic collagen-mimetic peptides (cCMPs), which efficiently hybridize with triple helix-forming portions of collagen. cCMPs are composed of two parallel collagen-like (Xaa-Yaa-Gly)n strands with both termini tethered by covalent linkages. Enzyme-linked immunosorbent assay and western blotting analysis showed that cCMPs exhibit more potent affinity toward collagen than reported collagen-binding peptides and specifically detect different collagen polypeptides in a mixture of proteins...
May 14, 2018: Chembiochem: a European Journal of Chemical Biology
Pallavi Gosavi, Megha Jayachandran, Joel Rempillo, Oleksii Zozulia, Olga Makhlyents, Ivan Korendovych
A computationally designed allosterically regulated catalyst (CaM M144H) produced by substituting a single residue in calmodulin, a non-enzymatic protein, is capable of efficient and site selective post-translational acylation of lysines in peptides with highly diverse sequences. Calmodulin binding partners are involved in regulating a large number of cellular processes, this new chemical biology tool will help identify them and provide structural insight into their interactions with calmodulin.
May 13, 2018: Chembiochem: a European Journal of Chemical Biology
David H Sherman, Ashootosh Tripathi, Sung Ryeol Park, Andrew Sikkema, Hyo Je Cho, Jianfeng Wu, Brian Lee, Chuanwu Xi, Janet L Smith
Cahuitamycins are biofilm inhibitors biosynthesized by a convergent NRPS pathway. Previous genetic analysis indicated that a discrete enzyme, CahJ, serves as a gatekeeper for cahuitamycin structural diversification. Herein, the CahJ protein was probed structurally, functionally and through mutasynthesis. This analysis enabled production of a new cahuitamycin congener through targeted precursor incorporation.
May 9, 2018: Chembiochem: a European Journal of Chemical Biology
Dennis Gillingham, Basilius Sauter
Drugs that covalently modify DNA are components of most chemotherapy regimens, often serving as first-line treatments. Classically the chemical reactivity of DNA alkylators has been determined in vitro with short oligonucleotides. Here we use next generation RNA sequencing to report on the chemoselectivity of alkylating agents. We develop the method with the well-known clinically used DNA modifiying drugs streptozotocin and temozolomide, and then apply the technique to profile RNA modification with uncharacterized alkylation reactions such as with powerful electrophiles like trimethylsilyldiazomethane...
May 6, 2018: Chembiochem: a European Journal of Chemical Biology
Yashoda Krishna Sunkari, Kiran Kumar Pulukuri, Pancham Singh Kandiyal, Jayanti Vaishnav, Ravi Sankar Ampapathi, Tushar Kanti Chakraborty
Sugar amino acid (SAA) based foldamers with well-defined secondary structures were appended with GalNAc sugars to access sequence-defined, multidentate glycoconjugates with full control over number, spacing and position. Conformational analysis of these glycopeptides by extensive NMR studies revealed that the appended GalNAc units had profound influence on the native conformational behaviour of the SAA foldamers. While the "2,5-cis" glycoconjugate showed helical structure in water comprising of two consecutive 16-member hydrogen bondings, its "2,5-trans" congener displayed an unprecedented 16/10-mixed turn structure, not seen before in any glycopeptide foldamer...
May 4, 2018: Chembiochem: a European Journal of Chemical Biology
Zhihong Guo, Mingming Qin, Haigang Song, Xin Dai, Chi-Kong Chan, Wan Chan
MenD, or (1R, 2S, 5S, 6S)-2-succinyl -5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, uses a thiamine diphosphate (ThDP)-dependent tetrahedral Breslow intermediate rather than the canonical enamine for catalysis in vitamin K biosynthesis. By real-time monitoring of the cofactor chemical state with circular dichroism spectroscopy, we found that a new post-decarboxylation intermediate is formed from a multiple-step process rate-limited by binding of the α-ketoglutarate substrate before quickly relaxing to the characterized tetrahedral Breslow intermediate...
May 3, 2018: Chembiochem: a European Journal of Chemical Biology
Tian Xie, Zhongchuan Liu, Ganggang Wang
In laccase, type-1 copper (Cu1) was connected to the trinuclear copper center (TNC) by the conserved Cys-His bridge. An allosteric coupling between the two redox sites has been reported; however, the molecular mechanism underlining the allosteric coupling is unknown. In this study, ligands of the two type 3 copper sites, including His491 and His493, in CotA were mutated to Cys or Ala. The crystal structures revealed that mutation at His491 and His493 caused rearrangement of the hydrogen bond network and geometric distortion of the TNC, which severely impaired the activities of mutants H493A, H493C and H491C...
May 3, 2018: Chembiochem: a European Journal of Chemical Biology
Florian Witzgall, Tobias Depke, Michael Hoffmann, Martin Empting, Mark Brönstrup, Rolf Müller, Wulf Blankenfeldt
Pseudomonas aeruginosa is a bacterial pathogen that causes life-threatening infections in immunocompromised patients. It produces a large armory of saturated and mono-unsaturated 2-alkyl-4(1H)-quinolones (AQs) or AQ N-oxides (AQNOs) that serve as signaling molecules to control the production of virulence factors, are involved in membrane vesicle formation and iron chelation and also have e.g. antibiotic properties. It has been shown that the FabH-like heterodimeric enzyme PqsBC catalyzes the last step in the biosynthesis of the most abundant AQ congener 2-heptyl-4(1H)-quinolone (HHQ) by condensing octanoyl-coenzyme A (CoA) with 2-aminobenzoylacetate (2-ABA), but the basis for the large number of other AQs/AQNOs produced by P...
May 3, 2018: Chembiochem: a European Journal of Chemical Biology
Andreas Sebastian Klein, Hannah Ursula Clara Brass, David Klebl, Thomnas Classen, Anita Loeschcke, Thomas Drepper, Sonja Sievers, Karl-Erich Jaeger, Joerg Pietruszka
Prodiginines are a group of naturally occurring pyrrole alkaloids produced by various microorganisms, which are known for their broad biological activities. The production of nature inspired cyclic prodignines was enabled by combining organic syntheses with a mutasynthesis approach using the GRAS (generally recognized as safe) certified host strain Pseudomonas putida. The newly prepared prodiginines exerted an antimicrobial effect against relevant alternative biotechnological microbial hosts while P. putida exhibited remarkable tolerance against all tested prodiginines, corroborating the bacterium's exceptional suitability as a mutasynthesis host for the production of these cytotoxic secondary metabolites...
May 2, 2018: Chembiochem: a European Journal of Chemical Biology
Wuyu Mao, Yaqun Wang, Xiana Qian, Lingying Xia, Hexin Xie
Metallo-ß-lactamase has been one of the major clinical threats because this ß-lactam-hydrolyzing enzyme confers significant resistance to most ß-lactam antibiotics, including carbapenems, among bacterial pathogens. Reported herein is a novel fluorogenic sensor for the specific detection of metallo-ß-lactamase activities. This carbapenem-based reagent exhibits excellent selectivity to metallo-ß-lactamase over other serine-ß-lactamases, including serine-carbapenemases. The usefulness of this probe was further demonstrated in the rapid identification of metallo-ß-lactamase-expressing pathogenic bacteria...
May 2, 2018: Chembiochem: a European Journal of Chemical Biology
Kosei Kudo, Chengwei Liu, Tomoyuki Matsumoto, Atsushi Minami, Taro Ozaki, Hiroaki Toshima, Katsuya Gomi, Hideaki Oikawa
Indole sesquiterpene sespendole, isolated from filamentous fungus Pseudobotrytis terrestris FKA-25, is a specific inhibitor of lipid droplet synthesis in mouse macrophages. The biosynthetic pathway that involves genes encoding six enzymes (spdEMBQHJ) was elucidated through heterologous expression of spd genes in Aspergillus oryzae, biotransformation experiments, and in vitro enzymatic reactions with a recombinant protein, thereby revealing the mechanism underlying the characteristic modification on the indole ring, catalyzed by a set of prenyltransferase (SpdE)/cytochrome P450 (SpdJ) enzymes...
May 2, 2018: Chembiochem: a European Journal of Chemical Biology
Ilaria Bargigia, Elena Zucchetti, Ajay Ram Srimath Kandada, Miguel Moreira, Caterina Bossio, Walter Wong, Paulo Miranda, Paolo Decuzzi, Cesare Soci, Cosimo D'Andrea, Guglielmo Lanzani
In this work the photo-physics of poly(3-hexyltiophene) nanoparticles (NPs) is investigated in the context of their biological applications. The NPs made as colloidal suspensions in aqueous buffers present a distinct absorption band in the low energy region. Based on systematic analysis of absorption and transient absorption spectra taken under different pH conditions, this band is associated to charge transfer states generated by the polarization of loosely bound polymer chains and originated from complexes formed with electron withdrawing species...
May 1, 2018: Chembiochem: a European Journal of Chemical Biology
Yunus Ensari, Gaurao V Dhoke, Mehdi D Davari, Anna Joelle Ruff, Ulrich Schwaneberg
Positions identified in directed evolution campaigns or by (semi-) rational design can be recombined iteratively or simultaneously. Iterative recombination (CAST method) yielded many success stories and is beneficially used if screening capabilities are limited (four iterative SSMs generated 20x4= 80 different enzyme variants). Simultaneous site saturation mutagenesis offers a significantly higher diversity (204=160000 variants) and enables to find higher improvements especially if the selected positions are in close proximity to each other (cooperative effects)...
April 30, 2018: Chembiochem: a European Journal of Chemical Biology
Wes Brown, Jihe Liu, Michael Tsang, Alexander Deiters
Cell lineage tracing is used to study embryo development, stem cell differentiation, and to document tumor cell heterogeneity. Cre recombinase-mediated cell labelling is the preferred approach; however, its utility is restricted by when and where DNA recombination takes place. We generated a photoactivatable Cre recombinase by replacing a critical residue in its active site with a photocaged lysine derivative through genetic code expansion in zebrafish embryos. This allows for high spatiotemporal control of DNA recombination using 405 nm light...
April 27, 2018: Chembiochem: a European Journal of Chemical Biology
Bassam Alkotaini, Samantha L Tinucci, Stuart J Robertson, Kamrul Hasan, Shelley D Minteer, Matteo Grattieri
A microbial fuel cell (MFC) based on a new wild-type strain of Salinivibrio sp. allowed the self-sustained treatment of hypersaline solutions (100 g L-1 , 1.71 m NaCl), reaching a removal of (87±11) % of the initial chemical oxygen demand after five days of operation, being the highest value achieved for hypersaline MFC. The degradation process and the evolution of the open circuit potential of the MFCs were correlated, opening the possibility for online monitoring of the treatment. The use of alginate capsules to trap bacterial cells, increasing cell density and stability, resulted in an eightfold higher power output, together with a more stable system, allowing operation up to five months with no maintenance required...
April 27, 2018: Chembiochem: a European Journal of Chemical Biology
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