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Search for "protein" in Full Text gives 623 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
- the activity of promoter and enhancer regions through cap analysis of gene expression (CAGE), TF motif instances, and expression quantitative trait loci (eQTL) to evaluate weights (evidence scores) for TF–gene isoform relationships; and iii) integration of TF-binding motifs, protein–protein
- using ST6GALNAC3-6 and also ST8SIA1/3/5. 4) Dolichol pathway: This results in the formation of the dolichol-linked 14-monosaccharide precursor oligosaccharide. This glycan is cotranslationally transferred en bloc onto Asn-X-Ser/Thr sites of the newly synthesized protein as it enters the endoplasmic
- reticulum. The enzymes involved is such synthesis include the ALG (asparagine-linked N-glycosylation) enzymes and additional proteins (part of OSTA and OSTB) involved in the transfer of the glycan to the nascent protein. 5) Complex N-glycans: This pathway includes glycogenes responsible for processing the N
Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications
Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116
- RNA–RNA kissing loop dimerization and RNA–protein binding [138]. Ly and co-workers developed Janus-wedge nucleobases that invade both dsDNA and dsRNA Watson–Crick base pairs from the minor groove side. At the time of writing, three Janus nucleobases, E, F, and I (Figure 9) have been reported for
- helix of the Antennapedia homeodomain) [167], Tat (14-amino acid peptide from HIV-1 TAT protein) [168], and transportan (chimeric 27-amino acid peptide derived from galanin and mastoparan) [169]. Corey and co-workers were the first to demonstrate that conjugation of an 11-mer PNA to penetratin peptide
Total synthesis of ent-pavettamine
Beilstein J. Org. Chem. 2021, 17, 1440–1446, doi:10.3762/bjoc.17.99
- substituted methylene linkage. Biological studies have shown that this toxin is responsible for “quick disease” (gousiekte) in ruminant animals, which causes inhibition of protein synthesis in the cardiovascular organs [13]. The unique structure coupled with the biological effects of this polyamine prompted
Double-headed nucleosides: Synthesis and applications
Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98
- neurotoxin, which is an eosinophil secretion protein and a member of the Ribonuclease A (RNase A) superfamily [36]. Double-headed nucleosides were also found to be active against orthopox viruses, vaccinia virus, and cowpox virus under in vitro conditions [11], whereas few double-headed nucleoside analogues
Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV
Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95
- degradation of antiviral RNA molecules. The present work demonstrates that VLPs (virus-like particles) allow efficient delivery of dsRNAi as antiviral therapy in shrimp. In particular, VLPs derived from a virus that infects plants, such as cowpea chlorotic mottle virus (CCMV), in which the capsid protein (CP
- of interest [12][13][14][15][16]. The antiviral response of RNAi is triggered by double-stranded RNA (dsRNA) to block the synthesis of a specific viral protein, in the case of WSSV the targets being the structural proteins VP19, VP24, VP26, and VP28, as they are involved in cell recognition, virus
- aquaculture. Materials and Methods dsRNAvp28. The VP28 dsRNA (dsRNAvp28) was generated based on the VP28 sequence of WSSV (GenBank: EU931451.1) [44]. The sequence is shown in Supporting Information File 1, Table ST1. The dsRNAvp28 was purchased from groRNA/Genolution company (South Korea). CCMV capsid protein
Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides
Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85
- modulating their protein affinity, metabolic stability, and lipophilicity. Here we described the synthesis of a series of mono-, di- and trifluorinated N-acetyl-ᴅ-glucosamine and ᴅ-galactosamine analogs. The key intermediates are the corresponding multiply fluorinated glucosazide and galactosazide
Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications
Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76
- improving metabolic stability, pairing properties (RNA affinity), protein binding and transport/cellular uptake are concerned, chemical modifications are a prerequisite for the discovery and development of oligonucleotide therapeutics [11][12][13][14][15]. Thus, the natural PS and 2'-OMe backbone
- modifications provide improved resistance to degradation by exo- and endonucleases and they both affect protein binding [16][17]. Eight of the now approved 13 oligonucleotide drugs feature the PS modification in the backbone and all four approved siRNA therapeutics: ONPATTRO® (patisiran, 2018), GIVLAARI
- nuclease-resistant probes for studying RNA–protein interactions [70]. To better elucidate the structural features of 3'-NP DNA responsible for this enhanced selective binding and stability, the Egli group determined the crystal structure of the fully modified 3'-NP DNA duplex with the sequence 5'-d
Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides
Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75
- charged peptide Tat has previously been demonstrated to be effective as an excipient species to increase the uptake through the negatively charged BBB [9][18]. Tat (sequence: H-YGRKKRRQRRR-NH2) is an arginine-rich short cell-penetrating peptide derived from the natural nuclear Tat protein of HIV-1 [19][20
- ]. The HIV-1 Tat protein itself has been shown to traverse the BBB by acting as a cell-penetrating peptide [9][20]. Other small positively charged molecules used for BBB penetration include transferrin and corresponding peptide derivatives or analogs that act as ligands for the transferrin receptor. The
- exponential enrichment (SELEX) [30]. SELEX is an iterative process that begins with a large oligonucleotide library that, through a process of negative and positive selections, ends with a few candidates that are specific for a particular protein [30][31]. Using HIV-1 as our model, we explored the use of two
DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies
Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65
- parallel triple-helix structure, a polypyrimidine TFO binds to dsDNA through Hoogsteen base-pairing [17], in which the cytosine bases in the TFO are protonated at the N3 atom (Figure 1B). In antisense strategies, antisense ONs (AOs) interact with RNA molecules to interfere with protein expression [18][19
Simulating the enzymes of ganglioside biosynthesis with Glycologue
Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64
- structures is evident in the knockouts of enzyme activities 8 and 9, which are unable to form terminal sialic acid or α-type structures. Knockout of ST3Gal-II (9) reduces GD1and GT1b levels in the brain by 50%, whereas brain-protein sialylation is unchanged [35]. A loss of ST3Gal-II also leads to late-onset
Designed whole-cell-catalysis-assisted synthesis of 9,11-secosterols
Beilstein J. Org. Chem. 2021, 17, 581–588, doi:10.3762/bjoc.17.52
- Pseudopterogorgia americana in 1972 (Figure 1B) [7], several others from the family have been reported [8][9][10][11][12][13][14]. The 9,11-secosterols exhibit diverse biological activities, including antihistaminic, antiproliferative, anti-inflammatory, cytotoxic and protein kinase C (PKC) inhibition activities [8
- -hydrocortisone, as a substrate [30]. For the construction of the biocatalyst, kshA5 and kshB genes from R. rhodochrous were codon-optimized for enhanced expression in E. coli and cloned into a pET21a protein expression plasmid. To obtain an active biocatalyst, the plasmid was transformed into an E. coli BL21
- (DE3) strain, and protein expression was induced by the addition of IPTG. Substrates of biocatalysis were added together with the IPTG inducer. The whole-cell biocatalysis was performed overnight at 30 °C in a rich medium with continuous shaking. Cell pellet and culture supernatant were collected the
Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement
Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40
- . We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated
- proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide
- properties. These factors may translate into an altered structure and stability of a protein containing a fluorinated fragment. What consequences fluorination would have regarding the fitness and survival of the organism relying on fluorine-containing proteins remains an open question. In this context, the
Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases
Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30
- free 4NTC by sodium periodate (Figure 2B). The specific activity (SA) of AnFaeA on 4NTC–linker–Fe (12) was determined to be 3 IU/mg of the protein (with IU corresponding to the international unit of the Fae hydrolytic activity), a value comparable to that measured on destarched wheat bran (3 IU/mg) [44
- µL of 2 M Na2CO3 after 5 min. The OD values at 530 nm were recorded on an Infinite M200 PRO (TECAN) microplate reader. One international unit (IU) of Fae specific activity (SA, expressed in µmol/min/mg or IU/mg) corresponds to the amount of released 4NTC (in µmol) per minute per milligram of protein
19F NMR as a tool in chemical biology
Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28
- fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein–protein interactions, protein–ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate
- biosynthesis and biodegradation of fluorinated organic compounds is also described. Keywords: biotransformation; chemical biology; fluorine; 19F NMR; probes; protein structure; Introduction Although fluorine is abundant in the environment, it is not a nutrient nor is it a feature of biochemistry for most
- another. With regards to probing both the structure and the interactions between biomolecules in complex settings the analytical tool 19F NMR has become invaluable. Some key highlights of how 19F NMR has been employed in this area are given in the following section. Recent advances in protein 19F
The preparation and properties of 1,1-difluorocyclopropane derivatives
Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25
Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders
Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10
- [6][7][8][9] are only few of the numerous examples for multivalent protein–protein or protein–carbohydrate interactions that underline their pivotal role in biology. Mimicking polyvalency using synthetic systems has therefore become a growing field and the high degree of functionality renders
- of multivalent interactions is the extracellular adhesion protein L-selectin. L-Selectin plays a critical role in inflammation processes by supporting the migration of leukocytes to inflammatory sites via adhesion to endothelial cells [19][20][21]. On a molecular level, a cationic binding site [22
Molecular basis for protein–protein interactions
Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1
- knowledge of protein–protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein–protein interactions and their molecular interactions is important for a number of applications, including drug
- design. Protein–protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work. Keywords: characterisation methods; heterooligomeric complex; homooligomeric complex; molecular interactions; protein–protein
- interactions; Introduction From signalling over transport to catalysis, the broad functionality of proteins is essential in the cellular machinery. To this effect, proteins can be seen as the workforce of the cell. Proteins relay some of their functionality via interactions between protein nodes called
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification
Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253
- quantification. Keywords: bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry; Introduction Protein glycosylation mainly occurs in the form of N- and O-glycosylation. N-Glycans are attached to Asn within an amino acid consensus sequence (Asn-Xxx-Ser/Thr, Xxx ≠ Pro) and O
- -glycans are attached to Ser or Thr. Glycan compositions can range from monosaccharides (e.g., Tn antigen for O-glycans [1]) to large polysaccharides (e.g., N-glycans of recombinant human erythropoietin [2]). The most common building blocks of human protein glycans are hexoses (glucose, galactose, and
- features, such as the linkage position and anomeric configuration, make protein glycosylation a highly complex posttranslational modification (PTM). Glycoproteomics has become important for many life science disciplines, in particular for biomedical and biopharmaceutical research [3][4][5]. Glycopeptide
Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities
Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248
- , enzyme inhibition, or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established
- ). For the biosynthesis of B. subtilis NRPs, the phosphopantetheinyl transferase Sfp is needed since it has been shown to activate the peptidyl carrier protein domains, converting it from the inactive apo-form to the active holo-form [37]. B. subtilis has four sfp-dependent SMs, of which three are
- primarily against various filamentous fungi [47][48][49][50][51]. The broad-spectrum antibiotic bacillaene, synthesised by the pksB-S gene cluster, is mainly targeting bacterial protein synthesis [52]. Still, it was also shown that it could protect cells and spores from predation [53]. We recently
Selected peptide-based fluorescent probes for biological applications
Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247
- fluorescence techniques have attracted immense interest. Synthetic peptide-based fluorescent probes are advantageous over protein-based sensors, since they are synthetically accessible, more stable, and can be easily modified in a site-specific manner for selective biological applications. Peptide receptors
- -aminobutyric acid associate with membrane-bound protein receptors and trigger changes in receptor shape and activity with subsequent signaling across the membrane. Noncovalent H-bonding and van der Waals interactions are the basis for the selective molecular recognition between a G-coupled protein receptor and
- membrane-bound receptors interact strongly with short peptidic segments of a larger protein chain, for example, recognition of the RGD sequence (arginine–glycine–aspartic acid; Arg–Gly–Asp) by integrin receptors. They use noncovalent interactions including salt bridges [5]. Vancomycin, a glycopeptide
UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation
Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240
- autofluorescence of the peptide or protein. Here, we demonstrate the use of UVRR spectroscopy with 244 nm laser excitation for the characterization of GCP as well as guanidiniocarbonyl indole (GCI), a next generation supramolecular ligand for the recognition of carboxylates. For demonstrating the feasibility of
- strengths. Various spectroscopic techniques can be employed for monitoring these changes. For example, electronic absorption or fluorescence spectroscopy can probe the spectral differences due to the complexation of the supramolecular ligand with a peptide or protein. However, electronic spectroscopies
- . In earlier studies, we have demonstrated the suitability of UVRR spectroscopy for monitoring the supramolecular binding of monovalent GCP-based ligands with peptides [12][13][14][15][16] and a trivalent GCP-based ligand with the protein leucine zipper, a protein with a single aromatic unit [17], by
Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function
Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236
- aptamer that adopts a guanine quadruplex structure was modified by four pyridine ligands [22]. The addition of Cu(II) or Ni(II) ions leads to the formation of a square-planar complex that reduces the affinity of the modified aptamer to its target protein. To the best of our knowledge, there is no
Encrypting messages with artificial bacterial receptors
Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225
- receptors is described. We show that the binding of DNA-based artificial receptors to E. coli expressing His-tagged outer membrane protein C (His-OmpC) induces a Förster resonance energy transfer (FRET) between the dyes, which results in the generation of a unique fluorescence fingerprint. Because the
- reversibly change the properties of the cell. For example, we have shown that synthetic receptors appended with a thiol or a folate group enable bacteria expressing the His-tagged outer membrane protein C (His-OmpC) to bind to gold surfaces or cancer cells, respectively [2]. We have also shown that this
- supplemented with 100 μg/mL of ampicillin at 30 °C. Then, the pre-cultured cells were diluted 1:100 in fresh LB medium supplemented with the same concentration of ampicillin, and incubated until the OD600 reached ≈0.6. In order to induce protein expression, 0.1% rhamnose and 20 μM isopropyl-β-ᴅ-1
Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response
Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223
- ]. It is a principle ubiquitously used in biology to achieve high affinity binding events with examples ranging from protein–carbohydrate interactions to host–pathogen interactions or cell surface adhesion [12][13][14]. The high affinity originates from the simultaneous interactions of multiple sites in
Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides
Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221
- noncovalent synthesis [41][42] in a cellular environment. Results and Discussion Molecular design We designed the branched peptides including the DEXXXLLI sequences [43] for this study. The DEXXXLLI (X is any amino acid) sequences are sorting signals of adaptor protein (AP) complexes, which play a critical
- concentrations, exhibit the same morphological appearances, agreeing with the statement that the nanofibers likely are made of Nap-ffky. Cytotoxicity, cell lysates, and protein delivery We investigated the cell compatibility of 1 and 2 by incubation with two kinds of mammalian cells, HeLa and Saos-2 cells, using
- nanofibers in the HeLa cells. Then, we used confocal laser scanning microscopy (CLSM) to examine whether these compounds deliver RPE into HeLa cells. After mixing R-phycoerythrin (RPE) [49], a red fluorescent protein, with 1 or 2 at different concentrations, we incubated the mixtures with HeLa cells for 2 h
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