Kai Yu  Kumi Hidaka  Prof. Hiroshi Sugiyama  Prof. Masayuki Endo  Dr. Shigeyoshi Matsumura  Prof. Yoshiya Ikawa 《Chembiochem : a European journal of chemical biology》2022,23(6):e202100573

The modular architecture of naturally occurring ribozymes makes them a promising class of structural platform for the design and assembly of three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.  相似文献   

    

Kangjing Wang  Liting Zhao  Ting Li  Qian Wang  Zhongyang Ding  Dr. Weifu Dong 《Chembiochem : a European journal of chemical biology》2022,23(4):e202100497

Self-stable precipitation polymerization was used to prepare an enzyme-immobilized microsphere composite. Phosphomannose isomerase (PMI) with His-tag was successfully immobilized on Ni²⁺ charged pyridine-derived particles. The maximum amount of PMI immobilized on such particles was ∼184 mg/g. Compared with free enzyme, the activity of the immobilized enzymes was significantly improved. In addition, the immobilized enzymes showed a much better thermostability than free enzymes. At the same time, the immobilized enzymes can be reused for multiple reaction cycles. We observed that the enzyme activity did not decrease significantly after six cycles. We conclude that the pyridine-derived particles can be used to selectively immobilize His-tagged enzymes, which can couple the enzyme purification and catalysis steps and improve the efficiency of enzyme-catalyzed industrial processes.  相似文献   

    

Dr. Vipin Kumar  Prof. Dr. Eriks Rozners 《Chembiochem : a European journal of chemical biology》2022,23(3):e202100560

2,4-Difluorotoluene is a nonpolar isostere of thymidine that has been used as a powerful mechanistic probe to study the role of hydrogen bonding in nucleic acid recognition and interactions with polymerases. In the present study, we evaluated five fluorinated benzenes as nucleobase analogues in peptide nucleic acids designed for triple helical recognition of double helical RNA. We found that analogues having para and ortho fluorine substitution patterns (as in 2,4-difluorotoluene) selectively stabilized Hoogsteen triplets with U−A base pairs. The results were consistent with attractive electrostatic interactions akin to non-canonical F to H−N and C−H to N hydrogen bonding. The fluorinated nucleobases were not able to stabilize Hoogsteen-like triplets with pyrimidines in either G−C or A−U base pairs. Our results illustrate the ability of fluorine to engage in non-canonical base pairing and provide insights into triple helical recognition of RNA.  相似文献   

    

Payal Gupta  Divya Ojha  Dinesh N. Nadimetla  Dr. Sheshanath V. Bhosale  Dr. Ambadas B. Rode 《Chembiochem : a European journal of chemical biology》2022,23(12):e202200131

RNA G-quadruplex (GQs) sequences in 5′-UTRs of certain proto-oncogenes co-localize with hairpin (Hp) forming sequences resulting in intramolecular Hp-GQ conformational equilibria, which is suggested to regulate cancer development and progression. Thus, regulation of Hp-GQ equilibria with small molecules is an attractive but less explored therapeutic approach. Herein, two tetraphenylethene (TPE) derivatives, TPE−Py and TPE-MePy, were synthesized and their effect on Hp-GQ equilibrium was explored. FRET, CD and molecular docking experiments suggest that cationic TPE-MePy shifts the Hp-GQ equilibrium significantly towards the GQ conformer mainly through π-π stacking and van der Waals interactions. In the presence of TPE-MePy, the observed rate constant values for first and second folding steps were increased up to 14.6 and 2.6-fold, respectively. The FRET melting assay showed a strong stabilizing ability of TPE-MePy (ΔTm=4.36 °C). Notably, the unmethylated derivative TPE−Py did not alter the Hp-GQ equilibrium. Subsequently, luciferase assay analysis demonstrated that the TPE-MePy derivatives suppressed the translation efficiency by ∼5.7-fold by shifting the Hp-GQ equilibrium toward GQ conformers in the 5’-UTR of TRF2. Our data suggests that HpGQ equilibria could be selectively targeted with small molecules to modulate translation for therapy.  相似文献   

    

Donghong Liu  Xiao Shu  Siying Xiang  Tengwei Li  Chenyang Huang  Mohan Cheng  Dr. Jie Cao  Prof. Dr. Yuejin Hua  Prof. Dr. Jianzhao Liu 《Chembiochem : a European journal of chemical biology》2022,23(13):e202200143

DNA tagging with base analogues has found numerous applications. To precisely record the DNA labelling information, it would be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases following a mild, efficient and bioorthogonal chemical treatment. Here we reported such a DNA tag, N⁴-allyldeoxycytidine (a⁴dC), for labeling and identifying DNA by in vitro assays. The iodination of a⁴dC led to fast and complete formation of 3 , N⁴-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a⁴dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic marker N⁴-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a⁴dC. Our study sheds light on the design of next generation DNA tags with chemical sequencing power.  相似文献   

    

Romina Fernández Varela  Dr. Ana Laura Valino  Dr. Eman Abdelraheem  Dr. Rosario Médici  Dr. Melisa Sayé  Dr. Claudio A. Pereira  Dr. Peter-Leon Hagedoorn  Prof. Ulf Hanefeld  Prof. Adolfo Iribarren  Prof. Elizabeth Lewkowicz 《Chembiochem : a European journal of chemical biology》2022,23(13):e202200147

In nature 2-deoxy-D-ribose-5-phosphate aldolase (DERA) catalyses the reversible formation of 2-deoxyribose 5-phosphate from D-glyceraldehyde 3-phosphate and acetaldehyde. In addition, this enzyme can use acetaldehyde as the sole substrate, resulting in a tandem aldol reaction, yielding 2,4,6-trideoxy-D-erythro-hexapyranose, which spontaneously cyclizes. This reaction is very useful for the synthesis of the side chain of statin-type drugs used to decrease cholesterol levels in blood. One of the main challenges in the use of DERA in industrial processes, where high substrate loads are needed to achieve the desired productivity, is its inactivation by high acetaldehyde concentration. In this work, the utility of different variants of Pectobacterium atrosepticum DERA (PaDERA) as whole cell biocatalysts to synthesize 2-deoxyribose 5-phosphate and 2,4,6-trideoxy-D-erythro-hexapyranose was analysed. Under optimized conditions, E. coli BL21 (PaDERA C-His AA C49M) whole cells yields 99 % of both products. Furthermore, this enzyme is able to tolerate 500 mM acetaldehyde in a whole-cell experiment which makes it suitable for industrial applications.  相似文献   

    

Claudius Lenz  Sebastian Dörner  Felix Trottmann  Prof. Dr. Christian Hertweck  Alexander Sherwood  Prof. Dr. Dirk Hoffmeister 《Chembiochem : a European journal of chemical biology》2022,23(13):e202200183

Psilocybin ( 1 ) is the major alkaloid found in psychedelic mushrooms and acts as a prodrug to psilocin ( 2 , 4-hydroxy-N,N-dimethyltryptamine), a potent psychedelic that exerts remarkable alteration of human consciousness. In contrast, the positional isomer bufotenin ( 7 , 5-hydroxy-N,N-dimethyltryptamine) differs significantly in its reported pharmacology. A series of experiments was designed to explore chemical differences between 2 and 7 and specifically to test the hypothesis that the C-4 hydroxy group of 2 significantly influences the observed physical and chemical properties through pseudo-ring formation via an intramolecular hydrogen bond (IMHB). NMR spectroscopy, accompanied by quantum chemical calculations, was employed to compare hydrogen bond behavior in 4- and 5-hydroxylated tryptamines. The results provide evidence for a pseudo-ring in 2 and that sidechain/hydroxyl interactions in 4-hydroxytryptamines influence their oxidation kinetics. We conclude that the propensity to form IMHBs leads to a higher number of uncharged species that easily cross the blood-brain barrier, compared to 7 and other 5-hydroxytryptamines, which cannot form IMHBs. Our work helps understand a fundamental aspect of the pharmacology of 2 and should support efforts to introduce it (via the prodrug 1 ) as an urgently needed therapeutic against major depressive disorder.  相似文献   

    

Philipp Wolf  Alexander Mohr  Georgina Gavins  Victoria Behr  Karin Mörl  Prof. Oliver Seitz  Prof. Annette G. Beck-Sickinger 《Chembiochem : a European journal of chemical biology》2022,23(6):e202100340

Fine-tuning of G protein-coupled receptor (GPCR) signaling is important to maintain cellular homeostasis. Recent studies demonstrated that lateral GPCR interactions in the cell membrane can impact signaling profiles. Here, we report on a one-step labeling method of multiple membrane-embedded GPCRs. Based on short peptide tags, complementary probes transfer the cargo (e. g. a fluorescent dye) by an acyl transfer reaction with high spatial and temporal resolution within 5 min. We applied this approach to four receptors of the cardiovascular system: the endothelin receptor A and B (ET_AR and ET_BR), angiotensin II receptor type 1, and apelin. Wild type-like G protein activation after N-terminal modification was demonstrated for all receptor species. Using FRET-competent dyes, a constitutive proximity between hetero-receptors was limited to ET_AR/ET_BR. Further, we demonstrate, that ET_AR expression regulates the signaling of co-expressed ET_BR. Our orthogonal peptide-templated labeling of different GPCRs provides novel insight into the regulation of GPCR signaling.  相似文献   

    

Hiroshi Takagi  Kohei Kozuka  Kenta Mimura  Prof. Dr. Shogo Nakano  Prof. Dr. Sohei Ito 《Chembiochem : a European journal of chemical biology》2022,23(8):e202100447

Glutamate decarboxylase (GAD) catalyses the decarboxylation of L-glutamate to gamma-aminobutyric acid (GABA). Improvement of the enzymatic properties of GAD is important for the low-cost synthesis of GABA. In this study, utilizing sequences of enzymes homologous with GAD from lactic acid bacteria, highly mutated GADs were designed using sequence-based protein design methods. Two mutated GADs, FcGAD and AncGAD, generated by full-consensus design and ancestral sequence reconstruction, had more desirable properties than native GADs. With respect to thermal stability, the half-life of the designed GADs was about 10 °C higher than that of native GAD. The productivity of FcGAD was considerably higher than those of known GADs; more than 250 mg/L of purified enzyme could be produced in the E. coli expression system. In a production test using 26.4 g of l -glutamate and 3.0 g of resting cells, 17.2 g of GABA could be prepared within one hour, without purification, in a one-pot synthesis.  相似文献   

    

Zi-Xuan Hu  Cheng Cheng  Yu-Qian Li  Xiao-Han Qi  Dr. Ting Wang  Prof. Dr. Li Liu  Prof. Dr. Josef Voglmeir 《Chembiochem : a European journal of chemical biology》2022,23(13):e202200074

Aldolases are enzymes that reversibly catalyze the cleavage of carbon-carbon bonds. Here we describe a recombinant sialic acid aldolase originating from the freshwater snail Biomphalaria glabrata (sNPL), and compare its substrate spectrum with a sialic acid aldolase originating from chicken (chNPL). In contrast to vertebrate animals which can synthesize, degrade, and incorporate sialic acids on glycoconjugate ubiquitously, snails (as all mollusks) cannot synthesize sialic acids endogenously, and therefore the biological function and substrate scope of sNPL ought to differ significantly from vertebrate sialic aldolases such as chNPL. sNPL was active towards a series of sialic acid derivatives but was in contrast to chNPL unable to catalyze the cleavage of N-acetylneuraminic acid into N-acetylmannosamine and pyruvate. Interestingly, chNPL and sNPL showed contrasting C4(R)/(S) diastereoselectivity towards the substrates d -mannose and d -galactose in the presence of pyruvate. In addition, sNPL was able to synthesize a series of 4-hydroxy-2-oxoates using the corresponding aliphatic aldehyde substrates in the presence of pyruvate, which could be not achieved by chNPL.  相似文献