Rational design of a circularly permuted flavin-based fluorescent protein
In this study, we explored the feasibility of applying circular permutation, a valuable method for the creation of fluorescent sensors, to flavin-based fluorescent proteins. We used rational design and structural data to identify a suitable location for circular permutation in iLOV, a flavin-based reporter derived from A. thaliana. However, relocating the N- and C-termini to this position resulted in a significant reduction in fluorescence. This loss of fluorescence was reversible, however, by fusing dimerizing coiled coils at the new N- and C-termini to compensate for the increase in local chain entropy. Additionally, by ...
Source: Chembiochem - February 15, 2024 Category: Biochemistry Authors: Nolan T Anderson Jason Xie Asish N Chacko Vannie Liu Kang-Ching Fan Arnab Mukherjee Source Type: research
Identification, characterization and application of M16AT, a novel organic solvent-tolerant (R)-enantio-selective types IV amine transaminase from Mycobacterium sp. ACS1612 †
Chembiochem. 2024 Feb 13:e202300812. doi: 10.1002/cbic.202300812. Online ahead of print.ABSTRACTChiral amines widely exist in a variety of natural products and bioactive molecules. The catalytic asymmetric synthesis of chiral amines by R-selective amine transaminases (R-ATAs) has been realized. Thus, identification and characterization of novel R-ATAs will make great potential contributions to the industrial production of enantiopure chiral amines and amino acids. Here, new R-selective amine transaminases (R-ATAs) from Mycobacterium sp. ACS1612 (M16AT) using in-silico prediction combined with genome and protein database ha...
Source: Chembiochem - February 14, 2024 Category: Biochemistry Authors: Tingting Li Hai Zhu Weiwei Jia Xia Tian Ziwen Xu Jiang Zhu Wencheng Liu Yang Cao Source Type: research
Tunable electrospun scaffolds of polyacrylonitrile loaded with carbon nanotubes: from synthesis to biological applications
Chembiochem. 2024 Feb 14:e202300768. doi: 10.1002/cbic.202300768. Online ahead of print.ABSTRACTGrowing cells in a biomimetic environment is critical for tissue engineering as well for studying the cell biology underlying disease mechanisms. To this aim a range of 3D matrices have been developed, from hydrogels to decellularized matrices. They need to mimic the extracellular matrix to ensure the optimal growth and function of cells. Electrospinning has gained in popularity due to its capacity to individually tune chemistry and mechanical properties and as such influence cell attachment, differentiation or maturation. Polya...
Source: Chembiochem - February 14, 2024 Category: Biochemistry Authors: B énédicte Fromager Julien Cambedouzou Emilie Marhuenda Thomas Iskratsch Mathieu Pinault Norbert Bakalara David Cornu Source Type: research
Methylation of Phenyl Rings in Ester-Stabilized Phosphorus Ylides Vastly Enhances Their Protonophoric Activity
Chembiochem. 2024 Feb 14:e202300848. doi: 10.1002/cbic.202300848. Online ahead of print.ABSTRACTWe have recently discovered that ester-stabilized phosphorus ylides, resulting from deprotonation of a phosphonium salt such as [Ph3PCH2COOR]Br, can transfer protons across artificial and biological membranes. To create more effective cationic protonophores, we synthesized similar phosphonium salts with one ((heptyloxycarbonylmethyl)tri(p-tolyl)phosphonium bromide) or two ((butyloxycarbonylmethyl)tri(3,5-xylyl)phosphonium bromide) methyl substituents in the phenyl groups. The methylation enormously augmented both protonophoric a...
Source: Chembiochem - February 14, 2024 Category: Biochemistry Authors: Tatyana Rokitskaya Roman S Kirsanov Ljudmila S Khailova Alisa A Panteleeva Konstantin G Lyamzaev Galina A Korshunova Elena A Kotova Yuri N Antonenko Source Type: research
Biophysical and Biochemical Characterization of Structurally Diverse Small Molecules Hits for KRAS Inhibition
We describe six compounds as early hits for the development of direct inhibitors of KRAS, an important anticancer drug target. We show that these compounds bind to KRAS with affinities in the low micromolar range and exert different effects on its interactions with binding partners. Some of the compounds exhibit selective binding to the activated form of KRAS and inhibit signal transduction through both the MAPK or the phosphatidylinositide 3-kinase PI3K-protein kinase B (AKT) pathway in cells expressing mutant KRAS. Most inhibit intrinsic and/or SOS-mediated KRAS activation while others inhibit RAS-effector interaction. W...
Source: Chembiochem - February 13, 2024 Category: Biochemistry Authors: Cynthia Pagba Amit K Gupta Kasuni Dilsha Parisa Sadrpour Jacob Jakubec Priyanka Prakash Dharini van der Hoeven Kwang-Jin Cho Scott Gilbertson Alemayehu A Gorfe Source Type: research
Aldehyde Reductase Activity of Carboxylic Acid Reductases
Chembiochem. 2024 Feb 13:e202400121. doi: 10.1002/cbic.202400121. Online ahead of print.ABSTRACTCarboxylic acid reductase enzymes (CARs) are well known for the reduction of a wide range of carboxylic acids to the respective aldehydes. One of the essential CAR domains - the reductase domain (R-domain) - was recently shown to catalyze the standalone reduction of carbonyls, including aldehydes, which are typically considered to be the final product of carboxylic acid reduction by CAR. We discovered that the respective full-length CARs were equally able to reduce aldehydes. Herein we aimed to shed light on the impact of this a...
Source: Chembiochem - February 13, 2024 Category: Biochemistry Authors: Margit Winkler Hannah Breuer Lukas Schober Source Type: research
Human 2 ´-Deoxynucleoside 5´-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80
Chembiochem. 2024 Feb 13:e202400047. doi: 10.1002/cbic.202400047. Online ahead of print.ABSTRACTThe human enzyme 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (HsDNPH1) catalyses the hydrolysis of 5-hydroxymethyl-2'-deoxyuridine 5'-phosphate to generate 5-hydroxymethyluracil and 2-deoxyribose-5-phosphate via a covalent 5-phospho-2-deoxyribosylated enzyme intermediate. HsDNPH1 is a promising target for inhibitor development towards anticancer drugs. Here, site-directed mutagenesis of conserved active-site residues, followed by HPLC analysis of the reaction and steady-state kinetics are employed to reveal the importance of e...
Source: Chembiochem - February 13, 2024 Category: Biochemistry Authors: Anna E Carberry Suneeta Devi David J Harrison Rafael G da Silva Source Type: research
Organocatalytic Synthesis and DNA Interactive Studies of New 1,2,3-Triazolyl-thiazolidines Hybrids
Chembiochem. 2024 Feb 9:e202300844. doi: 10.1002/cbic.202300844. Online ahead of print.ABSTRACTAn organocatalytic [3 + 2] cycloaddition reaction between thiazolidine-containing β-ketoester 1 and aryl azides 2 was employed to synthesize new 1,2,3-triazolyl-thiazolidine hybrids 3. In this metal-free approach, twelve compounds were isolated in yields ranging from 23% to 96% by using diethylamine (10 mol%) and DMSO at 75 °C for 24 hours. DNA-binding assays were conducted through absorption, emission spectroscopy and viscosimetry analysis, to evaluate the interaction capacity of the studied derivatives with nucleic acids. All...
Source: Chembiochem - February 10, 2024 Category: Biochemistry Authors: Allya Larroza Liane K Soares Roberto B Moraes Mariana F Bach Caroline G Jacoby Bernardo A Iglesias Paulo Henrique Schneider Diego Alves Source Type: research
Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.PMID:38334959 | DOI:10.1002/cbic.202400043 (Source: Chembiochem)
Source: Chembiochem - February 9, 2024 Category: Biochemistry Authors: Michela Vargiu Yanli Xu Oscar Kuipers Gerard Roelfes Source Type: research
The Biological Activities of Polyether Ionophore Antibiotic Routiennocin is Independent of Absolute Stereochemistry
Chembiochem. 2024 Feb 8:e202400013. doi: 10.1002/cbic.202400013. Online ahead of print.ABSTRACTCarboxylic polyether ionophores (CPIs) are among the most prevalent agricultural antibiotics (notably in the US) and these compounds have been in use for decades. The potential to reposition CPIs beyond veterinary use, e.g. through chemical modifications to enhance their selectivity window, is an exciting challenge and opportunity, considering their general resilience towards resistance development. Given the very large societal impact of these somewhat controversial compounds, it is surprising that many aspects of their mechanis...
Source: Chembiochem - February 8, 2024 Category: Biochemistry Authors: S øren Møller Michelle Rasmussen Jun Li Esben Svenningsen Gustav W ørmer Thomas T ørring Thomas Bj ørnskov Poulsen Source Type: research
Systematic Analysis of the MIO-forming Residues of Aromatic Ammonia Lyases
Chembiochem. 2024 Feb 7:e202400016. doi: 10.1002/cbic.202400016. Online ahead of print.ABSTRACTAromatic ammonia lyases (AALs) and tyrosine/phenylalanine ammonia mutases (TAM/PAM) are 3,5-dihydro-5-methylidene-4H-imidazol-4-one- (MIO) dependent enzymes. Usually, the MIO moiety is autocatalytically formed from the tripeptide Ala-Ser-Gly (ASG) and acts as an electrophile during the enzymatic reaction. However, the MIO-forming residues (ASG) have some diversity in this enzyme class. In this work, a systematic investigation on the variety of MIO-forming residues was carried out using in-depth sequence analyses. Several protein ...
Source: Chembiochem - February 7, 2024 Category: Biochemistry Authors: Yannik Brack Chenghai Sun Dong Yi Uwe Bornscheuer Source Type: research
Endogenous Production and Vibrational Analysis of Heavy-Isotope-Labeled Peptides from Cyanobacteria
In this study, a cyanobacterium was cultured in 15N/13C-enriched media to endogenously produce labeled, bioactive oligopeptides. The extent of heavy isotope incorporation in these peptides was determined with LC-MS, while the overall extent of heavy isotope incorporation in whole cells was studied with nanoSIMS and AFM-IR. Up to 98% heavy isotope incorporation was observed in labeled cells. Three of the most abundant peptides, microcystin-LR (MCLR), cyanopeptolin-A (CYPA), and aerucyclamide-A (ACAA), were isolated and further studied with Raman and FTIR spectroscopies and DFT calculations. This revealed several IR and Rama...
Source: Chembiochem - February 4, 2024 Category: Biochemistry Authors: John G Ricca Xavier Mayali Jing Qu Peter K Weber Gerald Poirier Craig P Dufresne J William Louda Andrew C Terentis Source Type: research
Fus-SMO: Kinetics, Biochemical Characterisation and In Silico Modelling of a Chimeric Styrene Monooxygenase Demonstrating Quantitative Coupling Efficiency
Chembiochem. 2024 Feb 2:e202300833. doi: 10.1002/cbic.202300833. Online ahead of print.ABSTRACTThe styrene monooxygenase, a two-component enzymatic system for styrene epoxidation, was characterised through the study of Fus-SMO-a chimera resulting from the fusion of StyA and StyB using a flexible linker. Notably, it remains debated whether the transfer of FADH2 from StyB to StyA occurs through diffusion, channeling, or a combination of both. Fus-SMO was identified as a trimer with one bound FAD molecule. In silico modelling revealed a well-distanced arrangement (45-50 Å) facilitated by the flexible linker's loopy structure...
Source: Chembiochem - February 2, 2024 Category: Biochemistry Authors: Tanja Knaus Peter Macheroux Francesco Mutti Source Type: research
Effect of DNA Origami Nanostructures on Bacterial Growth
Chembiochem. 2024 Feb 1:e202400091. doi: 10.1002/cbic.202400091. Online ahead of print.ABSTRACTDNA origami nanostructures are a powerful tool in biomedicine and can be used to combat drug-resistant bacterial infections. However, the effect of unmodified DNA origami nanostructures on bacteria is yet to be elucidated. With the aim to obtain a better understanding of this phenomenon, the effect of three DNA origami shapes, i.e., DNA origami triangles, six-helix bundles (6HBs), and 24-helix bundles (24HBs), on the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis is investigated. These results reveal...
Source: Chembiochem - February 1, 2024 Category: Biochemistry Authors: Jaime Andres Garcia-Diosa Guido Grundmeier Adrian Keller Source Type: research
Aminic Organoselenium Compounds as Glutathione Peroxidase Mimics and Inhibitors of Ferroptosis
This study revealed that the methoxy-substituted organoselenium compounds showed significant effect on the GPx-like activity. The catalytic parameters for the most efficient catalysts were also determined. The anti-ferroptotic activity for all GPx-mimics evaluated in a 4-OH-tamoxifen (TAM) inducible GPx4 knockout cell line using liproxstatin as standard.PMID:38293899 | DOI:10.1002/cbic.202400074 (Source: Chembiochem)
Source: Chembiochem - January 31, 2024 Category: Biochemistry Authors: Babli Chhillar Rajni Kadian Manish Kumar Manisha Yadav Nikhil Sodhi Thamara Nishida Xavier da Silva Jose Pedro Friedmann Angeli Vijay P Singh Source Type: research
