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Search for "proteins" in Full Text gives 471 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria
Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75
- contaminants but are either undissociated higher oligomer states or are oligomers whose formation is induced by SDS treatment, which has been observed for other proteins [29][30]. To characterize these oligomer states of native protein, analytical size exclusion chromatography data were collected (Figure 2B
- nm/A280 nm ratio for each homolog was greater than 1.0, consistent with high occupancy of heme incorporation in the proteins. Iron analyses of each of the homologs were consistent with this conclusion; the heme iron concentrations per protein were consistent with stoichiometric or nearly
- structure of oligomeric proteins [31]. The highest ranked model is shown in Figure 5. AlphaFold predicted a canonical α/β fold with high confidence, between residues Arg16 and Gly146 (Figure 5A). Structural clustering using Foldseek Cluster identified substantial similarities to other PAS domain proteins
Methodology for awakening the potential secondary metabolic capacity in actinomycetes
Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69
- chaxalactins A–C (16–18), and polycyclic polyether natural products designated terrosamycins A and B (19, 20), respectively [55][56]. Thus, the OSMAC strategy has been successfully applied over the last 10 years to generate new secondary metabolites from a single microbial strain. Sensor proteins for medium
- structure. Saito et al. are now interested in determining how and why these HSMs are produced. First, when actinomycetes sense heat stress, repression mediated by heat shock sensor proteins such as HrcA, HspR, and RheA is released. The expression of various genes, such as those encoding heat shock proteins
- is regulated by such heat shock sensors. Although long-term high-temperature culture experiments are employed in this study, reactive oxygen species (ROS) may exert a stronger effect than high temperature. In actinomycetes, several sensor proteins for ROS have been reported (e.g., SoxR and OxyR
Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins
Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68
- , and UGTs are the key players in crocin biosynthesis. Empowered by the genomic, transcriptomic, and metabolomic analysis and biochemical characterization, many such enzymes have been identified. Some proteins, exemplified by GjCCD4a and GjUGT94E13, exhibit broad substrate promiscuity and high catalytic
Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis
Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67
- : the acyl transferases (AT) for loading of the starter or extender units, the acyl carrier proteins (ACP) for anchoring the growing polyketide chain, and the ketosynthases (KS) for merging of the next extender unit with the existing chain by a decarboxylative Claisen condensation [2][4]. Today a high
- is still important. Previous approaches to determine KS domain specificities have involved mass spectrometry (MS)-based methods [22][23], MS analysis of trypsin-digested proteins [24], and radiochemical assays [25]. Here, we report on a new method using 13C-labelled substrate surrogates in
Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization
Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66
- peptides and even small proteins. In the chemoenzymatic synthesis of macrocyclic peptides, SPPS strategies provide highly efficient routes to access linear precursors, accelerating the development of enzymatic macrocyclization. The tyrocidines Tyrocidine A (1), a cyclic decapeptide isolated from Bacillus
- domains along with their associated peptidyl carrier proteins (PCPs): daptomycin and A54145 PCP-TE [55]. A series of thiophenol-activated precursors were tolerated by these enzymes to produce daptomycin derivatives, A54145 as well as hybrid molecules of the two compounds, which pushed forward the better
- exhibit a potent ability to induce tubulin depolymerization [77], originally isolated from the cyanobacteria Nostoc sp. ATCC 53789 [78]. Notably, the cryptophycins cannot serve as substrates for P-glycoprotein and multiple drug resistance-associated proteins, making them attractive as chemotherapeutic
Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari
Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65
- TCs, AsPS and AsCPS, in the fungus Arthrinium sacchari. AsPS consists of catalytically active α and inactive β domains, whereas AsCPS contains βγ domains and a truncated α domain. Heterologous expression in Aspergillus oryzae and biochemical characterization of recombinant proteins demonstrated that
- determined to be (−)-sandaracopimaradiene (Figure 3B). We then turned our attention to the individual function of these enzymes. With this aim, AsPS and AsCPS were expressed in Escherichia coli as N-terminal hexa-histidine-tagged proteins and purified by Ni-affinity chromatography (see Supporting Information
- File 1, Figure S3). The purified proteins were incubated in the presence of GGPP and Mg2+. GC–MS analysis of the hexane extract revealed the enzyme-dependent formation of compound 1 (Figure 4A and Figure S2 in Supporting Information File 1). The formation of 1 was not observed when either AsPS or AsCPS
Recent developments in the engineered biosynthesis of fungal meroterpenoids
Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50
- chair–chair stereocontrol, the structure basis of InsA7 should be unique. A structural comparison of InsB2 and InsA7 will help to clarify the differences in their structural bases. Recent advances in artifical intelligence (AI) have even made the structural modeling of membrane-bound proteins possible
Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study
Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49
- of molecules based on nanoscience can lead to a better understanding of the behavior of target biomaterials and improve the sensitivity of specific dynamical systems, such as biosensors. In this study, we investigate the behavior of proteins immobilized with linker molecules on graphene substrates
- . It is known that graphene may not easily adsorb proteins [1]. On the other hand, proteins can be immobilized on graphene by using appropriate linker molecules, such as 1-pyrenebutanoic acid succinimidyl ester (PASE). Actually, pyrene and its derivatives have been demonstrated to form stable bindings
- can be expected for proteins immobilized on graphene. As a result, we propose a strategy for improving the accuracy of the sensing process in elastic wave measurement sensors through antigen/antibody reactions. Results and Discussion PASE and PASE-derivatives on graphene Among pyrene derivatives, PASE
Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors
Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46
- with emphasis on the structural diversity of small-molecule ligands. In this context, acyl-acyl carrier protein (acyl-ACP) thioesterase inhibitors have shown a remarkable variability. Fatty acid thioesterase (FAT) enzymes represent a family of proteins exclusively found in higher plants. They mediate
Switchable molecular tweezers: design and applications
Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45
Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells
Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39
- biosynthesis by using small molecules can help to elucidate their natural functions and their potential as therapeutic targets. NRPs are synthesized by large, versatile, and multifunctional proteins called nonribosomal peptide synthetases (NRPSs), which are composed of multiple modules and subdivided domains
- differences in the composition of cell membranes and presence of efflux pumps [9]. Specific protein labeling using a chemical probe can help to identify, characterize, and visualize target proteins [10][11]. The first chemical probe used for A-domains in NRPSs was reported by Marahiel et al. [8]. They
- derivatives can penetrate cells and interact with A-domains in live bacterial cells, resulting in the competitive inhibition of the labeling by ʟ-Phe-AMS-BPyne. The substituent group (R; gray) of ʟ-Phe-AMS derivatives could facilitate their cell penetration. After UV irradiation (365 nm), the labeled proteins
Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles
Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36
- reduction in the concentration of these cytokines, as well as, increased intestinal permeability and improved expression of tight junction proteins that control the polarity of cells when using DIM in Caco-2 human cells [3]. BIMs have also been linked with the therapy of various cancers with one of their
- ]. DIM has also been found to initiate the expression of tumor suppressing proteins (ATM, p21, p27kip), which control cell growth and protect cells against ionizing radiation, which can cause DNA mutations, decreasing the overall risk of breast cancer [1][5][6]. The cytotoxicity of DIM and BIMs in
- antiviral properties. BIMs function as selective antibacterial agents against several virulent Escherichia coli (E. coli) strains, which can cause many gut and urinary tract infections. They act by damaging DNA molecules and inhibiting their replication in bacteria, while also targeting the proteins that
Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin
Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31
- biology, and biomedicine. These carbohydrate-binding proteins boast a range of functions, acting as recognition modules in cell–molecule and cell–cell interactions, thereby playing vital roles in immune defense, regulation of growth, and apoptosis [1]. In plants, they serve as essential components in
- hexa-His tag, cleavable by TEV (Tobacco etch virus) protease. Despite the presence of the DsbC signal peptide, we did not observe periplasmic localization, and all proteins were instead purified from the cytoplasm. Ni-NTA affinity chromatography followed by TEV protease cleavage of the fusion construct
- , Merck, #56749) to remove all contaminants and unbound proteins. CMA1 was eluted by a 20 mL linear gradient from 50 mM to 500 mM imidazole in buffer A. The fractions were analyzed by SDS-PAGE with 15% gel and those containing CMA1 were collected and deprived of imidazole by buffer exchange in buffer A
Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway
Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1
- biosynthesis by heterologous expression of the cma cluster and in vitro enzyme assays using recombinant Cma proteins. The ATP-dependent diazotase CmaA6 catalyzed the diazotization of both 3-aminocoumaric acid and 3-aminoavenalumic acid using nitrous acid in vitro. In addition, the high efficiency of the CmaA6
- on an ava cluster-related BGC in Kutzneria albida JCM 3240. We showed that this BGC is involved in p-coumaric acid biosynthesis by heterologous expression in Streptomyces albus J1074 and several in vitro biochemical experiments using recombinant proteins. CmaA6 was shown to catalyze the diazotization
- confirmed that the cma cluster is responsible for p-coumaric acid (5) biosynthesis, in which the number of condensations of the malonyl units was one time less than that in the biosynthesis of avenalumic acid. In vitro analysis of recombinant Cma proteins To further understand the biosynthetic machinery
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144
- proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is
- ) with three different proteins (basic fibroblast growth factor, acidic fibroblast growth factor, and cathepsin K). The main focus of our study was to evaluate whether the US approach is able to reproduce experimentally obtained structures, and how useful it can be for getting a deeper understanding of
- be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse
N-Boc-α-diazo glutarimide as efficient reagent for assembling N-heterocycle-glutarimide diads via Rh(II)-catalyzed N–H insertion reaction
Beilstein J. Org. Chem. 2023, 19, 1841–1848, doi:10.3762/bjoc.19.136
- ubiquitin-proteasome degradation system, it has been achieved to approach previously considered undruggable targets and conceive remedies for drug-resistant targets [4]. The given TPD's benefit over traditional inhibition; numerous proteins have been set for proteasomal degradation by transmuting accessible
- small molecule inhibitors into PROTACs. The RAS proteins, once seen as drug-resistant, became susceptible and a series of covalent inhibitors [5][6][7] were synthesized to bind to KRASG12C. The application of the PROTAC principle has demonstrated the feasibility of endogenous degradation of KRAS [8][9
GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data
Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134
- impact for the society in regard to the United Nations sustainable development goal [1]. The major roadblock to carbohydrate sequencing is intrinsically due to their unique molecular properties, among biopolymers. In contrast with proteins and DNA, which are linear polymers made of a limited number of
Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect
Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117
- potent compound 7 was found to significantly inhibit the production of IL-1β and IL-6 proteins, as revealed by the analysis of culture supernatants. Keywords: anti-inflammatory; Breynia disticha; RAW 264.7 cells; sesquiterpenoids; sulfur-containing compounds; Introduction Breynia disticha J.R.Forst
Radical chemistry in polymer science: an overview and recent advances
Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116
- consists of a bundle of disc-tipped acellular thread called byssus, which connect the mussel to the surfaces of substrates [10]. A family of proteins called mussel foot proteins (mfp’s) distribute throughout the whole length of byssus while there is an extremely high concentration of mfp’s at the plaque
- amino acid sequence of mfp-1, mfp-3, and mfp-5 (Y: DOPA, K: lysine). B) Scheme showing examples of the adhesive and cohesive properties of catechol-containing proteins. R represents the remainder of the mfp’s. Scheme 3 redrawn from [10]. Activation–deactivation equilibrium in nitroxide-mediated
Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration
Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115
- cellular processes, (e.g., signaling transduction, proteins trafficking, etc.) [19]. However, many discrepancies could be found in the literature regarding the existence of lipid rafts in synthetic membranes, especially CHOL–lipid binary mixtures. Studies of DPPC:CHOL bilayers have elucidated the formation
Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials
Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108
- complicated by both berberine and chelerythrine having multiple pathways associated with their antimicrobial activity [11][12][13][14][15][16][17][18][24]. In an effort to better understand the differences seen with our variants, we chose to focus on their effects on leakage of intercellular proteins, as
Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs
Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104
- cloned individually, heterologously expressed as N-terminally His-tagged proteins in Escherichia coli and purified (Supporting Information File 1, Figure S1). Also full length 2MIBS from S. coelicolor was obtained in the same way. The relative production of 1 from 2-Me-GPP was tested in triplicate
Functional characterisation of twelve terpene synthases from actinobacteria
Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100
- ). The genes coding for all fifteen enzymes were amplified by PCR from genomic DNA, cloned and expressed in Escherichia coli. The purified recombinant proteins (Figure S1, Supporting Information File 1) were used in test incubations with geranyl pyrophosphate (GPP), farnesyl pyrophosphate (FPP
Synthesis of ether lipids: natural compounds and analogues
Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96
- ) that exhibit promising anticancer properties renew the interest in this class of compounds. Indeed, ether lipid represent a new and promising class of compounds featuring the capacity to modulate selectively the activity of some membrane proteins or, for other compounds, feature antiproliferative
- with biomembranes via supramolecular interactions with the lipids and proteins that are embedded in these membranes. We can hypothesis that their mechanism of action occurs via a direct interaction with membrane proteins or by a modification of the biophysical properties of the membranes. It must be
- noted that the design of new bioactive ELs is an alternative to others strategies (e.g., small molecules, antibodies) to modulate membrane proteins functions. Recent results from our group [41][42] and others renew the interest to develop new ether lipids with promising perspectives to address the
Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1
Beilstein J. Org. Chem. 2023, 19, 909–917, doi:10.3762/bjoc.19.69
- photosynthesis, respiration or nitrogen fixation, in which iron-containing proteins are engaged in electron transfer reactions. In fact, the transition metal is perfectly suited for shifting electrons due to its ability to easily interconvert between a reduced ferrous (Fe2+) and an oxidized ferric state (Fe3
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