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Chembiochem: a European Journal of Chemical Biology

Alexander Sailer, Franziska Ermer, Yvonne Kraus, Ferdinand Lutter, Carsten Donau, Maximilian Bremerich, Julia Ahlfeld, Oliver Thorn-Seshold
Druglike small molecules with photoswitchable bioactivity - photopharmaceuticals - allow biologists to perform studies with exquisitely precise and reversible, spatial and temporal control over critical biological systems inaccessible to genetic manipulation. The photoresponsive pharmacophores disclosed have been almost exclusively azobenzenes, which has limited the structural and substituent scope of photopharmacology. More detrimentally, for azobenzene reagents, it is not researchers' needs for adapted experimental tools, but rather protein binding site sterics, that typically force whether the trans (dark) or cis (lit) isomer is the more bioactive...
January 11, 2019: Chembiochem: a European Journal of Chemical Biology
Takashi Sakamoto, Rikuto Yamada
A novel label-free in situ monitoring system for hybridization chain reaction (HCR) using DNA minor-groove binding fluorophores, Hoechst 33258 (Hoe) or quinone cyanine-dithiazole (QCy-DT), has been developed. Two unmodified hairpin oligodeoxyribonucleotides having incomplete double-stranded AATT sequences enabled target-dependent formation of probe binding sites, i.e., AATT double-strand, in HCR product, and fluorescence enhancement of minor-groove binding fluorophores in situ. Using this system, target DNA can be detected by the fluorescence enhancement of Hoe and QCy-DT in a real-time in situ manner...
January 10, 2019: Chembiochem: a European Journal of Chemical Biology
C A Jabeena, Arumugam Rajavelu
The protozoan parasite Plasmodium has evolved to survive in different hosts and environments. The diverse strategies of adaptation to different niches involve differential gene expression mechanisms mediated by chromatin plasticity that are poorly characterized in Plasmodium. The parasite employs a wide variety of regulatory mechanisms to complete their life cycle and survive inside hosts. Among them, epigenetic mediated mechanisms have been implicated for controlling the chromatin organization, gene regulation, morphological differentiation, and antigenic variation...
January 10, 2019: Chembiochem: a European Journal of Chemical Biology
Hajo Kries, Aleksa Stanišić
Nonribosomal peptides are a prolific source of bioactive molecules biosynthesized on large, modular assembly-line synthetases. Synthetic biologists seek to obtain tailored peptides with tuned or novel bioactivities by engineering modules and domains of these nonribosomal peptide synthetases. The activation step catalyzed by adenylation domains primarily selects which amino acids are incorporated into nonribosomal peptides. Here, we review experimental protocols for probing the adenylation reaction that are applicable in natural product discovery and engineering...
January 10, 2019: Chembiochem: a European Journal of Chemical Biology
Marius Grote, Frank Schulz
The incorporation of new-to-nature extender units into polyketide synthesis harbours an important source for diversity yet is restricted by a limited availability of suitably activated building blocks in vivo. We here describe a straightforward workflow for the biogenic activation of commercially available new-to-nature extender units. Firstly, the substrate scope of a highly flexible malonyl co-enzyme A synthetase from Streptomyces cinnamonensis was characterized. The results were matched by in vivo experiments in which said extender units were accepted by both the polyketide synthase and the accessory enzymes of the monensin biosynthetic pathway...
January 10, 2019: Chembiochem: a European Journal of Chemical Biology
Oliver Plettenburg
Chi-Huey Wong turned 70 in August 2018: This special issue is dedicated to that event. It can be seen from the variety of topics covered that he influenced the thinking of many of his former co-workers, who then transformed and developed these thoughts into fascinating, creative and independent research areas, enriching the science of bioorganic chemistry.
January 9, 2019: Chembiochem: a European Journal of Chemical Biology
Ye Zhou, Nykola C Jones, Jannik Nedergaard Pedersen, Bianca Pérez, Søren Vrønning Hoffmann, Steen Vang Petersen, Jan Skov Pedersen, Adam Perriman, Peter Kristensen, Renjun Gao, Zheng Guo
Despite a successful application of solvent-free liquid protein (biofluids) concept to a number of commercial enzymes, the technical advantages of enzyme biofluids as hyperthermal stable biocatalysts cannot be fully utilized as up to 90-99% of native activities are lost when enzymes were made into biofluids. With a two-step strategy (site-directed mutagenesis & synthesis of variant biofluids) on Bacillus subtilis lipase A (BsLA), we elucidated a strong dependency of structure and activity on the numbers and distribution of polymer surfactant binding sites on BsLA surface...
January 9, 2019: Chembiochem: a European Journal of Chemical Biology
Clemens Mayer
Expanding the genetic code of organisms by incorporating non-canonical amino acids (ncAAs) into target proteins through the suppression of stop codons in vivo has profoundly impacted how we perform protein modification or detect proteins and their interaction partners in their native environment. Yet, with genetic code expansion strategies maturing over the past 15 years, new applications that make use - or indeed repurpose - these techniques are beginning to emerge. This concept article highlights three of these developments: (1) the incorporation of ncAAs for the biosynthesis and selection of bioactive macrocyclic peptides with novel ring architectures, (2) synthetic biocontainment strategies based on the addiction of microorganisms to ncAAs, and (3) enzyme design strategies, in which ncAAs with unique functionalities enable the catalysis of new-to-nature reactions...
January 8, 2019: Chembiochem: a European Journal of Chemical Biology
Kabirul Islam, Shana Wagner, Megan Waldman, Simran Arora, Sinan Wang, Valerie Scott
Histone demethylases play a critical role in mammalian gene expression by removing methyl groups from lysine residues in degree- and site-specific manner. To specifically interrogate members and isoforms of this class of enzymes, we have developed demethylase variants with an expanded active site. The mutant enzymes are capable of performing lysine demethylation with wild type proficiency, but are sensitive to inhibition by cofactor-competitive molecules embellished with a complementary steric 'bump'. The selected inhibitors show more than 20-fold selectivity over the wild type demethylase, thus overcoming issues typical to pharmacological and genetic approaches...
January 7, 2019: Chembiochem: a European Journal of Chemical Biology
Nora Guidotti, Carolin C Lechner, Andreas L Bachmann, Beat Fierz
In nature, individual histones in the same nucleosome can carry identical (symmetric) or different (asymmetric) PTM patterns, increasing the combinatorial complexity. Embryonic stem cells exhibit "bivalent" nucleosomes, some of which are marked by an asymmetric arrangement of H3K36me3 (an activating PTM) and H3K27me3 (a repressive PTM). Here we describe a modular synthetic method to access such asymmetrically modified nucleosomes and show that H3K36me3 inhibits the activity of the methyltransferase PRC2 locally while still prolonging its chromatin binding time...
January 7, 2019: Chembiochem: a European Journal of Chemical Biology
Qian Liu, Dong Wang, Zhi Xu, Chunji Huang, Chun Zhang, Binfeng He, Chengde Mao, Guansong Wang, Hang Qian
Programmable DNA nanostructures are a new class of biocompatible, nontoxic nanomaterials. Nevertheless, their application in the field of biomedical research is still in its infancy, especially as drug delivery vehicles for gene therapy. In this study, a GTPase Rab26 was explored as a new potential therapeutic target using precisely tailored DNA prism for targeted lung cancer therapy. Specifically, a DNA prism platform with tunable targeting and siRNA loading capability is designed and synthesized. The DNA prisms were decorated with two functional units: a Rab26 siRNA as the drug and MUC-1 aptamers as targeting moiety for non-small cell lung cancer...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Kwan Ho Jung, Sojung Frances Kim, Yu Liu, Xin Zhang
Protein aggregation involves the assembly of partially misfolded proteins into oligomeric and higher-order structures that have been associated with several neurodegenerative diseases. However, numerous questions regarding protein aggregation remain unanswered due to the lack of available tools to visualize these species in living cells. We recently developed a fluorogenic method named Aggregation Tag (AggTag), and presented the AggTag probe P1 based on a Halo-tag ligand to report on the aggregation of a protein of interest (POI) in live cells...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Hathaichanok Seelajaroen, Marianne Haberbauer, Christine Hemmelmair, Abdalaziz Aljabour, Liviu Mihai Dumitru, Achim Walter Hassel, Niyazi Serdar Sariciftci
Microbial electrosynthesis cells containing Methylobacterium extorquens were studied for reduction of CO2 to formate via direct electron injection and redox mediator-assisted approaches with CO2 as the sole carbon source. The study revealed the formation of the biofilm on a carbon felt electrode while applying a constant potential of -0.75 V vs. Ag/AgCl under CO2-saturated condition. During the biofilm growth period, continuous H2 evolution was observed. The long-term performance for CO2 reduction of the biofilm with and without neutral red as redox mediator was studied by an applied potential of -0...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Wen-Yih Jeng, Chia-I Liu, Te-Jung Lu, Hong-Jie Lin, Nai-Chen Wang, Andrew H-J Wang
Endoglucanase CtCel9Q is one of the enzyme components of the cellulosome, which is an active cellulase system in the thermophile Clostridium thermocellum. The precursor form of CtCel9Q comprises a signal peptide, a glycoside hydrolase family 9 (GH9) catalytic domain, a type 3c carbohydrate binding module (CBM), and a type I dockerin domain. Here, we report the crystal structures of the C-terminally truncated CtCel9Q (CtCel9QΔc) complexed with Tris, Tris + cellobiose, cellobiose + cellotriose, cellotriose, and cellotetraose at resolutions of 1...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Bao-Qing Zhao, Wen-Long Ding, Zi-Zhu Tan, Qi-Ying Tang, Kai-Hong Zhao
While phycobiliproteins are organized as the phycobilisomes, they can harvest orange, red and/or far-red lights for photosynthesis in cyanobacteria and red algae, phycobiliproteins in the phycobilisome cores such as allophycocyanins absorb far-red light for funneling the energy to the reaction centers. The allophycocyanin subunits have been engineered as far-red fluorescent proteins such as BDFP1.6. However, most current fluorescent probes have small Stokes shifts, which limits their applications in multicolor bioimaging...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Verrill M Norwood Iv, Robert William Huigens Iii
Indole-containing compounds demonstrate an array of biological activities relevant to numerous human diseases. The biological activities of diverse indole-based agents are driven by molecular interactions between indole agent and critical therapeutic target. The chemical inventory of medicinally useful or promising indole compounds spans the entire structural spectrum, from simple synthetic indoles to highly complex indole alkaloids. In an analogous fashion, the chemistry behind the indole heterocycle is unique and provides rich opportunities for extensive synthetic chemistry enabling the construction and development of novel indole compounds to explore chemical space...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
Nishant Pappireddi, Lance Martin, Martin Wühr
Over the last few decades, mass spectrometry-based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which in a single experiment enable the global quantification of proteins across multiple samples. In this review, we refer to these methods as multiplexed proteomics. We discuss the principles, advantages, and drawbacks of various multiplexed proteomics techniques, and compare them to alternative approaches...
January 4, 2019: Chembiochem: a European Journal of Chemical Biology
H Ulrich Göringer, W-Matthias Leeder, Fabian Giehler, Juliane Joswig
Humans have evolved a natural immunity against Trypanosoma brucei infections, which is executed by two serum (lipo)protein complexes known as trypanolytic factors (TLF). Active TLF-ingredient is the primate-specific apolipoprotein L1 (ApoL1). The protein has a pore-forming activity that kills parasites by lysosomal and mitochondrial membrane fenestration. Of the many trypanosome subspecies only two are able to counteract the activity of ApoL1, which illustrates its evolutionary optimized design and trypanocidal potency...
January 3, 2019: Chembiochem: a European Journal of Chemical Biology
Alison Narayan, April L Lukowski
Natural product biosynthetic pathways are composed of enzymes that use powerful chemistry to assemble complex molecules. Small molecule neurotoxins are examples of natural products with intricate scaffolds which often have high affinities for their biological targets. The focus of this review is small molecule neurotoxins targeting voltage-gated sodium channels (VGSCs) and the state of knowledge on their associated biosynthetic pathways. There are three small molecule neurotoxin receptor sites on VGSCs associated with three different classes of molecules: guanidinium toxins, alkaloid toxins, and ladder polyethers...
January 3, 2019: Chembiochem: a European Journal of Chemical Biology
David O'Hagan, Davide Bello, Maria Grazia Rubanu, Nouchali Bandaranayaka, Jan P Götze, Michael Bühl
In this study we probe inhibition of pig heart citrate synthase (E. C. by synthesis of seven analogues designed to mimic either the proposed enolate intermediate in this enzyme reaction or develop from historical inhibitors. The most potent inhibitor was fluorovinyl thioether 9 (Ki = 4.3 μM), where a fluorine replaces the oxygen atom of the enolate. A comparison of the potency of 9 versus its non-fluorinated vinyl thioether analogue 10 (Ki = 68.3 μM), revealed a clear 'fluorine effect' favouring 9 by an order of magnitude...
January 3, 2019: Chembiochem: a European Journal of Chemical Biology
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