Chemical Approaches to Analyzing RNA Structure Transcriptome-Wide.
Abstract RNA molecules can fold into complex two- and three-dimensional shapes that are critical for their function. Chemical probes have long been utilized to interrogate RNA structure and are now considered invaluable resources in the goal of relating structure to function. Recently, the power of deep sequencing and careful chemical probe design have merged, permitting researchers to obtain a holistic understanding of how RNA structure can be utilized to control RNA biology transcriptome-wide. Within this review, we outline the recent advancements in chemical probe design for interrogating RNA structures inside ...
Source: Chembiochem - July 31, 2020 Category: Biochemistry Authors: England W, Garfio C, Spitale R Tags: Chembiochem Source Type: research

An Engineered Escherichia coli Strain with Synthetic Metabolism for In-cell Production of Translationally Active Methionine Derivatives.
Abstract In the last decades, it became clear that the canonical amino acid repertoire codified by the universal genetic code is not up to the needs of the emerging biotechnologies. For such reason, extensive genetic code re-engineering is essential to expand the scope of ribosomal protein translation, leading to reprogrammed microbial cells equipped with an alternative biochemical alphabet to be exploited as potentially factories for biotechnological purposes. The prerequisite for this to happen is a continuous intracellular supply of non-canonical amino acids from simple and cheap precursors via synthetic metabo...
Source: Chembiochem - July 31, 2020 Category: Biochemistry Authors: Schipp CJ, Ma Y, Al-Shameri A, D'Alessio F, Neubauer P, Contestabile R, Budisa N, di Salvo ML Tags: Chembiochem Source Type: research

Unconventional biocatalytic approaches for the synthesis of chiral sulfoxides.
Abstract Sulfoxides are a class of organic compounds that finds wide application in medicinal and organic chemistry. Several biocatalytic approaches have been developed to synthesise enantioenriched sulfoxides, mainly exploiting oxidative enzymes. Recently, the use of reductive enzymes such as Msr and Dms has emerged as new and alternative method to obtain enantiopure sulfoxides from racemic mixtures. In parallel, novel oxidative approaches, employing non-classical solvents such as ionic liquids (ILs) and deep eutectic solvents (DESs), have been developed as greener and more sustainable biocatalytic synthetic path...
Source: Chembiochem - July 31, 2020 Category: Biochemistry Authors: Anselmi S, Aggarwal N, Moody TS, Castagnolo D Tags: Chembiochem Source Type: research

Peptidyl Acyloxymethyl Ketones as Activity-Based Probes for the Main Protease of SARS-CoV-2.
Abstract The global pandemic caused by SARS-CoV-2 calls for a fast development of antiviral drugs against this particular coronavirus. Chemical tools to facilitate inhibitor discovery as well as detection of target engagement by hit or lead compounds from high throughput screens are therefore in urgent need. We here report novel, selective activity-based probes that enable detection of the SARS-CoV-2 main protease. The probes are based on acyloxymethyl ketone reactive electrophiles combined with a peptide sequence including non-natural amino acids that targets the non-primed site of the main protease substrate bin...
Source: Chembiochem - July 27, 2020 Category: Biochemistry Authors: van de Plassche MAT, Barniol-Xicota M, Verhelst S Tags: Chembiochem Source Type: research

On the Case of the Misplaced Hydrogens.
Abstract Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-...
Source: Chembiochem - July 24, 2020 Category: Biochemistry Authors: Kumar P, Agarwal PK, Cuneo MJ Tags: Chembiochem Source Type: research

Comparison of multiple factors that impact the efficiency of non-enzymatic DNA ligation: Key parameters for maximizing ligation rates and yields with carbodiimide activation.
We report a systematic study of DNA ligation using a well-defined bimolecular test system and a water-soluble carbodiimide (EDC) as a phosphate-activating agent. Our results emphasize the interplay between template-substrate complex stability and the rates of the chemical steps of ligation, with 3´ phosphate substrates providing yields near 100% after 24 hours for particularly favorable reaction conditions. Ligation rates are also shown to be sensitive to the identity of base pairs flanking a nick site, with as much as three-fold variation. Finally, the observation that DNA substrates are modified by EDC at rates tha...
Source: Chembiochem - July 23, 2020 Category: Biochemistry Authors: Obianyor C, Newnam G, Clifton B, Grover M, Hud NV Tags: Chembiochem Source Type: research

A bimane-based peptide staple for combined helical induction and fluorescent imaging.
Abstract The thiol-selective fluorescent imaging agent, dibromobimane, is repurposed to cross-link cysteine and homocysteine containing peptides, with the resulting bimane-linker acting as both a structural constraint and a fluorescent tag. Macrocyclisation was conducted on nine short peptides containing two cysteines and/or homocysteines, both on-resin and in buffered aqueous solution, to give macrocycles ranging in size from 16 ( i - i +2) to 31 ( i - i +7) atoms. The structures were defined by CD, NMR structure calculations using Xplor-NIH, NMR secondary shift and J HαNH  analyses, to ...
Source: Chembiochem - July 23, 2020 Category: Biochemistry Authors: Horsfall AJ, Dunning KR, Keeling KL, Scanlon DB, Wegener KL, Abell AD Tags: Chembiochem Source Type: research

PR10/Bet v 1-like proteins as novel contributors to plant biochemical diversity.
Abstract Pathogenesis-related (PR) proteins constitute a broad class of plant proteins with analogues found throughout nature from bacteria to higher eukaryotes. PR proteins were first noted in plants as part of the hypersensitive response but have since been assigned an array of biological roles. The PR10/Bet v 1-like proteins are a subset of PR proteins characterized by an ability to bind an wide range of lipophilic ligands, uniquely positioning them as contributors to specialized biosynthetic pathways. PR10/Bet v 1-like proteins participate in the production of plant alkaloids and phenolics including flavonoids...
Source: Chembiochem - July 23, 2020 Category: Biochemistry Authors: Morris JS, Caldo KM, Liang S, Facchini P Tags: Chembiochem Source Type: research

Synthesis of modified galacto- or fuco-clusters exploiting siderophore pathway to inhibit LecA or LecB associated virulence of Pseudomonas aeruginosa.
n F Abstract Galacto and fuco-clusters conjugated with one to three catechol or hydroxamate motifs were synthesized to target LecA and LecB lectins of Pseudomonas aeruginosa (PA) localized in the outer membrane and in the bacterium. The resulting glycocluster pseudosiderophore conjugates were evaluated as Trojan horse to cross the outer membrane of (PA) thanks to iron transport. The data suggests that glycoclusters with catechol moieties were able to hijack the iron transport while those with hydroxamates showed strong non-specific interactions. Mono- and tri-catechol galactoclusters ( G1C and G3C ) were evaluated...
Source: Chembiochem - July 23, 2020 Category: Biochemistry Authors: Madaoui M, Vidal O, Meyer A, Noël M, Lacroix JM, Vasseur JJ, Marra A, Morvan F Tags: Chembiochem Source Type: research

Photo-Biohydrogen Production by Photosensitization with Biologically Precipitated Cadmium Sulfide in Hydrogen-Forming Recombinant Escherichia coli.
In this study, we aimed to develop a new photocatalytic hydrogen production system, based on Escherichia coli whole-cell genetically engineered for the highly active hydrogen formation as a biocatalysis part. The photocatalysis part was obtained by bacterial precipitation of cadmium sulfide (CdS), which is a visible light responsive semiconductor. The recombinant E. coli cells were sequentially subjected to CdS precipitation and heterologous [FeFe]-hydrogenase synthesis, to yield a CdS@ E. coli hybrid capable of light energy conversion and hydrogen formation in a single cell. The CdS@ E. coli hybrid achieved photocatalytic...
Source: Chembiochem - July 22, 2020 Category: Biochemistry Authors: Honda Y, Shinohara Y, Watanabe M, Ishihara T, Fujii H Tags: Chembiochem Source Type: research

Triplex-Forming Peptide Nucleic Acids with Extended Backbones.
Abstract Peptide nucleic acid (PNA) forms a triple helix with double-stranded RNA (dsRNA) stabilized by a hydrogen-bonding zipper formed by PNA's backbone amides (N-H) interacting with RNA phosphate oxygens. This hydrogen-bonding pattern is enabled by the matching ~5.7 Å spacing (typical for A-form dsRNA) between PNA's backbone amides and RNA phosphate oxygens. We hypothesized that extending the PNA's backbone by one -CH2- group may bring the distance between PNA amide N-H closer to 7 Å, favourable for hydrogen-bonding to the B-form dsDNA phosphate oxygens. Extension of PNA backbone was expected to sel...
Source: Chembiochem - July 22, 2020 Category: Biochemistry Authors: Kumar V, Brodyagin N, Rozners E Tags: Chembiochem Source Type: research

Understanding the glycopeptide antibiotic crosslinking cascade - in vitro approaches revealing the details of a complex biosynthesis pathway.
Abstract The glycopeptide antibiotics (GPAs) are a fascinating example of complex natural product biosynthesis, with the non-ribosomal synthesis of the peptide core coupled to a cytochrome P450-mediated cyclisation cascade that crosslinks aromatic side chains within this peptide. Given the challenges associated with the synthesis of GPAs stems from their highly crosslinked structure, there is great interest in understanding how biosynthesis accomplishes this challenging set of transformations. In this regard, the use of in vitro experiments has delivered important insights into this process, including the identifi...
Source: Chembiochem - July 21, 2020 Category: Biochemistry Authors: Zhao Y, Ho YTC, Tailhades J, Cryle MJ Tags: Chembiochem Source Type: research

Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue.
Abstract Kasumigamide is an antialgal hybrid peptide-polyketide isolated from the freshwater cyanobacterium  Microcystis aeruginosa (NIES-87).    The biosynthetic gene cluster was identified from not only the cyanobacterium but also  Candidatus  "Entotheonella", associated with the Japanese marine sponge Discodermia calyx .    Therefore, kasumigamide is considered to play a key role in microbial ecology, regardless of the terrestrial and marine habitats.   We now report the synthetic studies on this intriguing natural product, leading to the structural revisio...
Source: Chembiochem - July 21, 2020 Category: Biochemistry Authors: Kuranaga T, Matsuda K, Takaoka M, Tachikawa C, Sano A, Itoh K, Enomoto A, Fujita K, Abe I, Wakimoto T Tags: Chembiochem Source Type: research

Distinct mechanisms for processing autophagy protein LC3-PE by RavZ and ATG4B.
Abstract Autophagy is a conserved catabolic process involved in the elimination of proteins, organelles and pathogens. Lipidated LC3 proteins that are conjugated to phosphatidylethanolamine (PE) play a key role in autophagosome biogenesis. Endogenous ATG4-mediated deconjugation of LC3-PE is required for LC3 recycling. However, the Legionella effector RavZ irreversibly deconjugates LC3-PE to inhibit autophagy. It is not clear how ATG4 and RavZ process LC3-PE with distinct modes. Herein, a series of semi-synthetic LC3-PE proteins containing C-terminal mutations or insertions were used to investigate the relationship...
Source: Chembiochem - July 20, 2020 Category: Biochemistry Authors: Yang A, Pantoom S, Wu Y Tags: Chembiochem Source Type: research

Lanthanide Tagging of Oligonucleotides to Nucleobase for Paramagnetic NMR.
inger C Abstract Although lanthanide tags, which have large anisotropic magnetic susceptibilities, have already been introduced to enrich the NMR parameters by long ranging pseudoconact shifts (PCSs) and residual dipolar couplings (RDCs) of proteins, their application to nucleotides has so far been limited to one previous report, due to the high affinities of lanthanides to the phosphodiester backbone of nucleotides and difficult organic synthesis. Here we report successful attachment of a lanthanide tag to a chemically synthesized oligonucleotide via a disulfide bond. NMR experiments reveal PCSs up to 1 ppm and H...
Source: Chembiochem - July 20, 2020 Category: Biochemistry Authors: Täubert S, Zhang YH, Maestre-Martinez M, Siepel F, Wöltjen E, Leonov A, Griesinger C Tags: Chembiochem Source Type: research

Methyltransferase contingencies in the pathway of everninomicin D antibiotics and analogs.
Abstract Everninomicins are orthoester oligosaccharide antibiotics with potent activity against multidrug-resistant (MDR) bacterial pathogens. Everninomicins act via disruption of ribosomal assembly in a distinct region in comparison to clinically prescribed drugs. We employed microporous intergeneric conjugation with Escherichia coli to manipulate Micromonospora for targeted gene-replacement studies of multiple putative methyltransferases across the octasaccharide scaffold of everninomicin effecting the A1 , C, F, and H-rings. Analyses of gene-replacement and genetic complementation mutants established the mutabi...
Source: Chembiochem - July 19, 2020 Category: Biochemistry Authors: Limbrick EM, Ynigez-Gutierrez AE, Dulin CC, Derewacz DK, Spraggins JM, McCulloch KM, Iverson TM, Bachmann BO Tags: Chembiochem Source Type: research

Tryptophan Synthase: Biocatalyst Extraordinaire.
Abstract Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond forming reaction between indole and serine (Ser) to make l -tryptophan (Trp); native TrpS complexes possess fairly broad specificity for indole analogs, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteri...
Source: Chembiochem - July 16, 2020 Category: Biochemistry Authors: Watkins-Dulaney EJ, Straathof S, Arnold FH Tags: Chembiochem Source Type: research

HaloTag-targeted Sirtuin rearranging ligand (SirReal) for the development of proteolysis targeting chimeras (PROTACs) against the lysine deacetylase Sirtuin 2 (Sirt2).
te;di J, Jung M Abstract We have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis targeting chimera (PROTAC), enabled small molecule-induced degradation of Sirt2. Here, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 deg...
Source: Chembiochem - July 16, 2020 Category: Biochemistry Authors: Schiedel M, Lehotzky A, Szunyogh S, Oláh J, Hammelmann S, Wössner N, Robaa D, Einsle O, Sippl W, Ovádi J, Jung M Tags: Chembiochem Source Type: research

Effect of metal shielding on the enzymatic construction of artificial base pairs.
stein M Abstract Formation of metal base pairs is a versatile method for the introduction of metal cations into nucleic acids that has been applied in numerous applications including the construction of metal nanowires, development of energy, charge transfer devices and expansion of the genetic alphabet. As an alternative, enzymatic construction of metal base pairs represents an alluring strategy that grants access to longer sequences and offers the possibility of using such unnatural base pairs (UBPs) in SELEX experiments for the identification of functional nucleic acids. This method remains rather underexplored...
Source: Chembiochem - July 16, 2020 Category: Biochemistry Authors: Flamme M, Levi-Acobas F, Hensel S, Naskar S, Röthlisberger P, Sarac I, Gasser G, Müller J, Hollenstein M Tags: Chembiochem Source Type: research

Bioimaging and Biodistribution of the Metal Ion Controlled Self-Assembly of PYY3-36 Studied by SPECT/CT.
ml;feli UO, Jensen KJ Abstract Controlled self-assembly of peptide- and protein-based pharmaceuticals is of central importance for their mode of action and tuning of their properties. Peptide YY 3-36 (PYY 3-36 ) is a 36 amino acid peptide hormone that reduces food intake when peripherally administered. Herein, we describe the synthesis of a PYY 3-36 analogue functionalized with a metal ion binding 2,2'-bipyridine ligand which enables self-assembly through metal complexation. Upon addition of Cu(II), the bipyridine-modified PYY 3-36 peptide binds stoichiometric quantities of metal ions in solution and contributes t...
Source: Chembiochem - July 15, 2020 Category: Biochemistry Authors: Kalomoiri P, Rodríguez-Rodríguez C, Sørensen KK, Bergamo M, Saatchi K, Häfeli UO, Jensen KJ Tags: Chembiochem Source Type: research

Self-Emergent Protocells Generated in an Aqueous Solution with Binary Macromolecules through Liquid-Liquid Phase Separation.
We report that in the presence of phospholipids, cell-sized liposomes are spontaneously formed in an aqueous solution, which exhibit the properties of LLPS, by using the macromolecules polyethylene glycol (PEG) and dextran. In this system, LLPS is generated through the depletion effect of macromolecules. The results showed that cell-like micro-droplets entrapping DNA wrapped by a phospholipid layer emerge in a self-organized manner. PMID: 32667694 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - July 15, 2020 Category: Biochemistry Authors: Sakuta H, Fujita F, Hamada T, Hayashi M, Takiguchi K, Tsumoto K, Yoshikawa K Tags: Chembiochem Source Type: research

Multiparameter kinetic analysis for covalent fragment optimization using quantitative irreversible tethering (qIT).
We describe a new technique in covalent probe discovery that enables data driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing methods for covalent fragment hit identification by facilitating rapid multiparameter kinetic analysis of covalent structure-activity relationships through simultaneous determination of Ki, kinact and intrinsic reactivity. We apply this approach to develop novel probes against electrophile sensitive kinases and showcase how multiparameter kinetic analysis enabled a successful fragment merging strategy. PMID: 32659037 [PubMed - as supplied ...
Source: Chembiochem - July 13, 2020 Category: Biochemistry Authors: Craven GB, Affron DP, Kösel T, Wong TLM, Jukes ZH, Liu CT, Morgan RML, Armstrong A, Mann DJ Tags: Chembiochem Source Type: research

Towards Zwitterionic Oligonucleotides with Improved Properties: the NAA/LNA-Gapmer Approach.
Abstract Oligonucleotides (ON) are promising therapeutic candidates, for instance by blocking endogenous mRNA (antisense mechanism). However, ON usually require structural modifications of the native nucleic acid backbone to ensure satisfying pharmacokinetic properties. One such strategy to design novel antisense oligonucleotides is the replacement of native phosphate diester units by positively charged artificial linkages, thus leading to (partially) zwitterionic backbone structures. Herein, we report a gapmer architecture comprised of one zwitterionic central segment ('gap') containing nucleosyl amino acid (NAA)...
Source: Chembiochem - July 13, 2020 Category: Biochemistry Authors: Wojtyniak M, Schmidtgall B, Kirsch P, Ducho C Tags: Chembiochem Source Type: research

Quantitative elemental analysis of a single cell using inductively coupled plasma-mass spectrometry in fast time-resolved analysis mode.
Abstract The elemental composition of a single cell such as yeast, green alga, and red blood cells (RBC) was precisely determined using inductively coupled plasma-mass spectrometry (ICP-MS) operating in fast time-resolved analysis (TRA) mode. The technique is known as single cell ICP-MS (SC-ICP-MS). Phosphorus (P), sulfur (S), magnesium (Mg), zinc (Zn), and iron (Fe) were detected in the three types of cell. The elemental composition of yeast and green alga obtained by SC-ICP-MS was consistent with results obtained by conventional ICP-MS measurements following acid digestion of the cells. Slight differences were f...
Source: Chembiochem - July 13, 2020 Category: Biochemistry Authors: Tanaka YK, Iida R, Takada S, Kubota T, Yamanaka M, Sugiyama N, Abdelnour Y, Ogra Y Tags: Chembiochem Source Type: research

Production of Propene from n-Butanol: A Three-Step Cascade Utilizing the Cytochrome P450 Fatty Acid Decarboxylase OleTJE.
Abstract Propene is one of the most important starting materials in the chemical industry. Herein, we report an enzymatic cascade reaction for the biocatalytic production of propene starting from n-butanol, thus offering a biobased production from glucose. In order to create an efficient system, we faced the issue of an optimal cofactor supply for the fatty acid decarboxylase OleTJE, which is said to be driven by either NAD(P)H or H2O2. In the first system, we used an alcohol and aldehyde dehydrogenase coupled to OleTJE via the electron transfer complex putidaredoxin reductase/putidaredoxin, allowing regeneration ...
Source: Chembiochem - July 12, 2020 Category: Biochemistry Authors: Bauer D, Zachos I, Sieber V Tags: Chembiochem Source Type: research

Cyclotide structures revealed by NMR, with a little help from X-ray crystallography.
This article highlights the predominant role that NMR has had in determining the structures of cyclotides, a fascinating class of macrocyclic peptides found in plants. Cyclotides contain a cystine knot, a compact structural motif that is constrained by three disulfide bonds and able to resist chemical and biological degradation. Their resistance to proteolytic degradation has made cyclotides appealing as drug leads. Here we examine the developments that led to the identification and conclusive determination of the disulfide connectivity of cyclotides and describe in detail the structural features of exemplar cyclotides. We...
Source: Chembiochem - July 12, 2020 Category: Biochemistry Authors: Handley TNG, Harvey PJ, Wang CK, Lawrence N, Craik D Tags: Chembiochem Source Type: research

Macrocyclization of a ligand targeting a toxic RNA dramatically improves potency.
Abstract RNA molecules both contribute to and are causative of many human diseases. One method to perturb RNA function is to target its structure with small molecules. However, discovering bioactive ligands for RNA targets is challenging. Here, we show that the bioactivity of a linear dimeric ligand that inactivates the RNA trinucleotide repeat expansion that causes myotonic dystrophy type 1 [DM1; r(CUG)exp] can be improved by macrocyclization. Indeed, the macrocyclic compound is 10-fold more potent than the linear compound for improving DM1-associated defects in cells, including in patient-derived myotubes (muscl...
Source: Chembiochem - July 10, 2020 Category: Biochemistry Authors: Benhamou R, Vezina-Dawod S, Choudhary S, Wang KW, Meyer SM, Yildirim I, Disney M Tags: Chembiochem Source Type: research

Predicting the substrate scope of the flavin-dependent halogenase BrvH.
Abstract The recently described flavin-dependent halogenase BrvH is able to catalyze both bromination and chlorination of indole, but shows significantly higher bromination activity. BrvH was annotated as a tryptophan halogenase, but does not accept tryptophan as a substrate. Its native substrate remains unknown. A predictive model with the data available for BrvH was analysed. A training set of compounds tested in vitro was docked into the active site of a complete protein model based on the X-ray structure of BrvH. The atoms not resolved experimentally have been modelled using molecular mechanics force fields to...
Source: Chembiochem - July 9, 2020 Category: Biochemistry Authors: Neubauer PR, Pienkny S, Wessjohann LA, Brandt W, Sewald N Tags: Chembiochem Source Type: research

Cancer Cell Metabolites: Updates on Current Tracing Methods.
Abstract Cancer is the second leading cause of death and, 1 in 6 deaths globally is due to cancer. Cancer metabolism is a complex and one of the most actively researched area in cancer biology. Metabolic reprogramming in cancer cells entails activities which involves several enzymes and metabolites to convert nutrient into building blocks that alter energy metabolism to fuel rapid cell division. Metabolic dependencies in cancer generate signature metabolites that have key regulatory roles in tumorigenesis. In this minireview, we highlight recent advances of the popular methods ingrained in biochemistry research su...
Source: Chembiochem - July 8, 2020 Category: Biochemistry Authors: Maniam S, Maniam S Tags: Chembiochem Source Type: research

Catalytic promiscuity of cGAS: A facile enzymatic synthesis of 2'-3' linked cyclic dinucleotides.
z S Abstract Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that catalyzes the synthesis of cyclic GMP-AMP dinucleotide 2'3'-cGAMP. 2'3'-cGAMP functions as inducer for the production of type I interferons. Derivatives of this important second messenger are highly valuable for pharmaceutical applications. However, the production of these analogs requires complex, multistep synthesis. Herein, human cGAS is shown to react with a series of non-natural nucleotides, thus leading to novel cyclic dinucleotides. Most substrate derivatives were accepted with modifications at the nucleobase, ribose, as well as the ...
Source: Chembiochem - July 7, 2020 Category: Biochemistry Authors: Rosenthal K, Becker M, Rolf J, Siedentop R, Hillen M, Nett M, Lütz S Tags: Chembiochem Source Type: research

Perfluorocarbons in Chemical Biology.
Abstract Perfluorocarbons, saturated carbon chains where all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass-spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to under...
Source: Chembiochem - July 6, 2020 Category: Biochemistry Authors: Miller MA, Sletten E Tags: Chembiochem Source Type: research

The Ubiquitin Enigma: Progress in the Detection and Chemical Synthesis of Branched Ubiquitin Chains.
Abstract Ubiquitin chains with distinct topologies play essential roles in eukaryotic cells. Recently, it was discovered that multiple ubiquitin units can be ligated to more than one lysine residue in the same ubiquitin to form diverse branched ubiquitin chains. Although there is increasing evidence implicating these branched chains in a plethora of biological functions, few mechanistic details have been elucidated. This concept article introduces the function, detection and chemical synthesis of branched ubiquitin chains; and offers some future perspective for this exciting new field. PMID: 32621561 [PubMed ...
Source: Chembiochem - July 4, 2020 Category: Biochemistry Authors: Li Y, Hua X, Chu G Tags: Chembiochem Source Type: research

Morphological profiling enables the identification of common mode of action for small molecules with different targets.
Abstract Unbiased morphological profiling of bioactivity, e. g. in the cell painting assay (CPA), enables identification of small-molecule mode of action based on similarity to bioactivity of reference compounds and irrespective of biological target and chemical similarity. This is particularly important for small molecules with non-protein targets as those are rather difficult to identify with widely employed target identification methods. We employed morphological profiling using the CPA to identify compounds that are biosimilar to the iron chelator deferoxamine. Structurally different compounds with different a...
Source: Chembiochem - July 3, 2020 Category: Biochemistry Authors: Schneidewind T, Brause A, Pahl A, Burhop A, Mejuch T, Sievers S, Waldmann H, Ziegler S Tags: Chembiochem Source Type: research

Reexamination of the Ergothioneine Biosynthetic Methyltransferase EgtD from Mycobacterium tuberculosis as a Protein Kinase Substrate.
In this report, we show that, under in vitro conditions, EgtD is not a substrate of protein kinase PknD. PMID: 32614492 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - July 2, 2020 Category: Biochemistry Authors: Maurer A, Seebeck FP Tags: Chembiochem Source Type: research

The molecular basis for purine binding selectivity in the bacterial ATP synthase ε subunit.
In this study, the purine triphosphate selectivity is rationalized via results from MD simulations and free energy calculations for the R103A/R115A mutant of the ε subunit from Bacillus PS3, which binds ATP stronger than the wild-type (WT) protein. Our results are in good agreement with experimental data, and the elucidated molecular basis for selectivity could help to guide the design of novel GTP sensors. PMID: 32608105 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - June 30, 2020 Category: Biochemistry Authors: Krah A, Huber RG, McMillan DGG, Bond PJ Tags: Chembiochem Source Type: research

Genetic code expansion strategies for vaccine development.
Abstract By providing long-term protection against infectious diseases vaccinations have significantly reduced death and morbidity world-wide. In the 21 st century, (bio)technological advances have paved the way for developing prophylactic vaccines that are safer and more effective as well as enabled the use of vaccines as therapeutics to treat human diseases. Here, we provide a focused review on the utility of genetic code expansion as an emerging tool for the development of vaccines. Specifically, we discuss how the incorporation of immunogenic non-canonical amino acids can aid in eliciting immune responses agai...
Source: Chembiochem - June 30, 2020 Category: Biochemistry Authors: Fok JA, Mayer C Tags: Chembiochem Source Type: research

Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.
Abstract Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein engineering strategy for tailoring functional diversity. However, domain-swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member, hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, demonstrating a strategy for fold co...
Source: Chembiochem - June 30, 2020 Category: Biochemistry Authors: Geiger JH, Ghanbarpour A, Santos EM, Pinger CH, Assar Z, Nasr SH, Vasileiou C, Spence D, Borhan BH Tags: Chembiochem Source Type: research

Environmental performance of Pseudomonas putida with a uracylated genome.
ía E Abstract A variant of the soil bacterium Pseudomonas putida with a genome containing a ∼ 20% replacement of the whole of thymine (T) by uracil (U) was made by deleting genes ung (uracil DNA glycosylase) and dut ( deoxyuridine 5'-triphosphate nucleotide hydrolase) . Proteomic comparisons revealed of 281 up-regulated and 96 down-regulated proteins in the ∆ ung ∆ dut cells as compared to the wild-type, many of them involved in nucleotide metabolism. Unexpectedly, genome uracylation did not change much the gross environmental endurance profile of P. putida , increased spontaneous mutagenesis by onl...
Source: Chembiochem - June 29, 2020 Category: Biochemistry Authors: Algar E, Al-Ramahi Y, de Lorenzo V, Martínez-García E Tags: Chembiochem Source Type: research

Structure-based design of fluorogenic substrates selective for human proteasome subunits.
Abstract Proteasomes are established therapeutic targets for hematological cancers and promising targets for autoimmune diseases. In the past we designed and synthesized mechanism-based proteasome inhibitors selective for individual catalytic activities of human constitutive proteasomes and immunoproteasomes: β1c, β1i, β2c, β2i, β5c and β5i. We show here that by taking the oligopeptide recognition element and substituting the electrophile for a fluorogenic leaving group fluorogenic substrates are obtained that report on the proteasome catalytic activity also targeted by the parent inh...
Source: Chembiochem - June 29, 2020 Category: Biochemistry Authors: Maurits E, Degeling CG, Kisselev AF, Florea B, Overkleeft HS Tags: Chembiochem Source Type: research

Inducible genetic code expansion in eukaryotes.
Abstract Genetic code expansion (GCE) is a versatile tool to site-specifically incorporate a noncanonical amino acid (ncAA) into a protein to e.g. perform fluorescent labeling inside living cells. To this end, an orthogonal aminoacyl-tRNA-synthetase/tRNA (RS/tRNA) pair is used to insert the ncAA in response to an amber stop codon in the protein of interest.  One of the drawbacks of this system is that in order to achieve maximum efficiencies high levels of the orthogonal tRNA are required which could interfere with host cell functionality. To minimize adverse effects on the host, we developed an inducible GCE...
Source: Chembiochem - June 29, 2020 Category: Biochemistry Authors: Koehler C, Estrada Girona G, Reinkemeier CD, Lemke EA Tags: Chembiochem Source Type: research

Trimethylation of the R5 silica-precipitating peptide increases silica particle size by redirecting orthosilicate binding.
Abstract The unmodified R5 peptide from silaffin in the diatom Cylindrotheca fusiformis rapidly precipitates silica particles from neutral aqueous solutions of orthosilicic acid. A range of post-translational modifications found in R5 contribute toward tailoring silica morphologies in a species-specific manner. We investigated the specific effect of R5 lysine side-chain trimethylation, which adds permanent positive charges, on silica particle formation. Our studies revealed that a doubly trimethylated R5K3,4me3 peptide has reduced maximum activity yet, surprisingly, generates larger silica particles. Molecular dyn...
Source: Chembiochem - June 28, 2020 Category: Biochemistry Authors: Buckle EL, Sampath J, Michael N, Whedon SD, Leonen CJA, Pfaendtner J, Drobny GP, Chatterjee C Tags: Chembiochem Source Type: research

Complete Photochemical Regulation of 8-17 DNAzyme Activity using Reversible DNA Photo-cross-linking.
Abstract The regulation of DNAzyme activity is an important problem for its in vivo applications. We achieved photochemical regulation of DNAzyme activity using reversible DNA photo-cross-linking of 3-cyanovinylcarbazole ( CNV K). The ODN containing CNV K photo-cross-linked to pyrimidine base in complementary strand with a few seconds of photoirradiation and its photoadduct was photo-split by photoirradiation with another wavelength. The activity of photo-cross-linked DNAzyme having CNV K was completely inhibited (OFF state). In contrast, after 312 nm irradiation, the DNAzyme activity was recovered upon addition o...
Source: Chembiochem - June 28, 2020 Category: Biochemistry Authors: Watanabe Y, Fujimoto K Tags: Chembiochem Source Type: research

Efficient Chemoenzymatic Synthesis of N-Glycans with a  β1,4-Galactosylated Bisecting-GlcNAc Motif.
Efficient Chemoenzymatic Synthesis of N-Glycans with a β1,4-Galactosylated Bisecting-GlcNAc Motif. Chembiochem. 2020 Jun 28;: Authors: Weiss M, Ott D, Karagiannis T, Weishaupt M, Niemietz M, Eller S, Lott M, Martínez-Orts M, Canales A, Razi N, Paulson J, Unverzagt C Abstract In human serum immunoglobulin G (IgG) a rare modification of biantennary complex N-glycans leads to a  b 1,4-galactosylated bisecting-GlcNAc branch. We found that the bisecting-GlcNAc on a biantennary core-fucosylated N-glycan was enzymatically galactosylated under stringent reaction conditions. Further optim...
Source: Chembiochem - June 28, 2020 Category: Biochemistry Authors: Weiss M, Ott D, Karagiannis T, Weishaupt M, Niemietz M, Eller S, Lott M, Martínez-Orts M, Canales A, Razi N, Paulson J, Unverzagt C Tags: Chembiochem Source Type: research

First Workshop on Metals in Medicine (2019): Translational Research in Medicinal Bioinorganic Chemistry.
Abstract On the 14-15th November 2019, the first workshop on Metals in Medicine took place in Paris at Chimie ParisTech, PSL University. Organised with the aim of having invited speakers share their experience in bringing metal-based drugs to (pre-)clinical trials, this event gathered 135 attendees from six continents to Paris. A special collection on this event has now been published in ChemBioChem, combining more than 20 articles on different topics related to metals in medicine. PMID: 32588495 [PubMed - as supplied by publisher] (Source: Chembiochem)
Source: Chembiochem - June 26, 2020 Category: Biochemistry Authors: Notaro A, Gasser G Tags: Chembiochem Source Type: research

Deacylation of calcium-dependent antibiotics from Streptomyces violaceoruber in co-culture with Streptomyces sp. MG7-G1.
Abstract When Streptomyces violaceoruber grows together with Streptomyces sp. MG7-G1, it reacts with strongly induced droplet production on its aerial mycelium. Initially the metabolite profile of droplets from S. violaceoruber in co-culture with Streptomyces sp. MG7-G1 was compared to samples from S. violaceoruber in single-culture using high-performance liquid chromatography-mass spectrometry (HPLC-MS). Then, also the exudate from agar plates of co-cultures and single cultures (after freezing and thawing) was analysed. Several compounds were only observed when S. violaceoruber was grown in co-culture. Based on t...
Source: Chembiochem - June 25, 2020 Category: Biochemistry Authors: Schindl K, Sharma D, Spiteller DS Tags: Chembiochem Source Type: research

A hydroxyquinoline-based unnatural amino acid for the design of novel artificial metalloenzymes.
fes G Abstract Here we examine the potential of the non-canonical amino acid (8-hydroxyquinolin-3-yl)alanine (HQAla) for the design of artificial metalloenzymes. HQAla, a versatile chelator of late transition metals, was introduced into the Lactococcal multidrug resistance regulator (LmrR) via stop codon suppression methodology. LmrR_HQAla was shown to efficiently complex with three different metal ions, Cu II- , Zn II and Rh III to form unique artificial metalloenzymes. The catalytic potential of the Cu II bound LmrR_HQAla enzyme was shown through its ability to catalyze asymmetric Friedel-Craft alkylation and wa...
Source: Chembiochem - June 25, 2020 Category: Biochemistry Authors: Drienovská I, Scheele RA, de Souza CG, Roelfes G Tags: Chembiochem Source Type: research

Cationic Ru(II) cyclopentadienyl complexes with antifungal activity against several  Candida species.
Cationic Ru(II) cyclopentadienyl complexes with antifungal activity against several Candida species. Chembiochem. 2020 Jun 23;: Authors: Golbaghi G, Groleau MC, López de Los Santos Y, Doucet N, Déziel E, Castonguay A Abstract Fungal infections, including those caused by antifungal-resistant  Candida , are a very challenging health problem worldwide. Whereas different ruthenium complexes were previously studied for their anti- Candida  potential, Ru-cyclopentadienyl complexes were overlooked. Here, we report an antifungal activity assessment of three Ru-cyclo...
Source: Chembiochem - June 23, 2020 Category: Biochemistry Authors: Golbaghi G, Groleau MC, López de Los Santos Y, Doucet N, Déziel E, Castonguay A Tags: Chembiochem Source Type: research

Near-infrared probe based on novel fluorescence quenching mechanism for detection of cysteine in bioimaging.
Abstract The near-infrared (NIR) fluorescent probe is greatly significant for detecting cysteine (Cys) in biological systems. Herein, we reported a highly selective and sensitive NIR turn-on fluorescent probe ( BDP-NIR ) based on BODIPY with large Stokes shift (105 nm) for detecting Cys. The sensing mechanism based on the different thiols-induced S N Ar substitution-rearrangement reaction of the probe with Cys and Hcy/GSH, leading to the corresponding amino- and thiol-BODIPY dyes with distinct photo-physical properties was clarified. Besides, a novel mechanism of fluorescence quenching was demonstrated by density ...
Source: Chembiochem - June 18, 2020 Category: Biochemistry Authors: Tao Y, Ji X, Zhang J, Jin Y, Wang N, Si Y, Zhao W Tags: Chembiochem Source Type: research

Probing the interaction between HIV-1 protease and the homodimeric p66/p66' reverse transcriptase precursor by double electron-electron resonance EPR spectroscopy.
Abstract Following excision from the Gag-Pol polyprotein, HIV-1 reverse transcriptase is released as an asymmetric homodimer comprising two structurally dissimilar but amino acid sequence identical p66 subunits. Subsequent cleavage of the RNase H domain from only one of the subunits, denoted as p66', results in the formation of the mature p66/p51 enzyme in which catalytic activity resides in the p66 subunit and the p51 subunit (derived from p66') provides a supporting structural scaffold. Here we probe the interaction of the p66/p66' asymmetric reverse transcriptase precursor with HIV-1 protease by pulsed Q-band d...
Source: Chembiochem - June 18, 2020 Category: Biochemistry Authors: Schmidt T, Louis J, Clore GM Tags: Chembiochem Source Type: research

The Rieske Oxygenase SnoT Catalyzes 2''-Hydroxylation of l-Rhodosamine in Nogalamycin Biosynthesis.
auml; M Abstract Nogalamycin is an anthracycline anti-cancer agent that intercalates into the DNA double helix. The binding is facilitated by two carbohydrate units l-nogalose and l-nogalamine, which interact with the minor and major grooves of DNA, respectively. However, recent investigations have shown that nogalamycin biosynthesis proceeds through attachment of l-rhodosamine (2¢¢-deoxy-4¢¢-epi-l-nogalamine) to the aglycone. Here we demonstrate that the Rieske enzyme SnoT catalyzes 2¢¢-hydroxylation of l-rhodosamine as an initial post-glycosylation step. Furthermore, we establi...
Source: Chembiochem - June 17, 2020 Category: Biochemistry Authors: Wandi BN, Siitonen V, Palmu K, Metsä-Ketelä M Tags: Chembiochem Source Type: research