Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• , indicating that the missing methyl group significantly influences the folding mode of the substrate in InsB2. It remains unclear why AdrI was unable to accept 1, but it is possible that the C-4 methyl group of (6R,10′R)-epoxyfarnesyl-DMOA methyl ester plays a critical role in substrate recognition by AdrI

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• activity, while for the wildtype no GGPP conversion is observed. These findings will assist in future protein engineering for improved activity and functional switches in other microbial terpene synthases. Highly conserved residues in the active site of SdS for Mg2+ complexation, substrate recognition and

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• overcome the bottleneck of poor substrate-recognition of longer oligosaccharides by glycosynthases [204]. Still, the polymer was obtained with a wide range of DP between 6–100. Shorter Xyl chains with up to 12 units were reported using a retaining xylanase from Cellulomonas fimi [202]. Well-defined xylan

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• substrate recognition follows a less specific rule, the reaction pattern uses an asterisk to denote parts of the acceptor that are of indeterminate length. The glossary in Table 2, footnote b, shows some of the assumptions implicit to the model, such as the configuration of the donors. From this information

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• behind the substrate recognition and catalytic reactivity for a long time. Hence, there is a wealth of knowledge on the type of interaction of small peptide sequences with specific partners. Researchers designed several artificial peptide-based receptors for molecular recognition purposes [10][11][12][13

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• probes is that they not only contained the ligand responsible for the substrate recognition but an additional ligand that allowed controlling the number of active residues on the surface. This structural feature allowed us to assess how the degree of surface functionalization affects the sensitivity, and

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• these two methyl groups are critical for the preorganization of GFPP in the biosynthetic pathways leading to sesterfisherol and quiannulatene. Keywords: biosynthesis; carbocation; DFT; substrate recognition; terpene cyclase; Introduction Terpene synthases are thought to have four main roles: (i

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• structural effect of this functional unit was explored. Herein we report on the synthesis and properties of the 6’-diF-bc4,3-thymidine analog (Figure 1), and the biophysical properties of oligonucleotides containing this modification. Moreover, we investigated the substrate recognition of the 6’-diF-bc4,3-T

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• with catalysis and/or substrate recognition, rather than in a canonical interbacterial or host–pathogen lectin–carbohydrate adhesion role. As described above, only limited data exists concerning expression, subcellular localization and physiological functions of mycobacterial lectins and

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• proteolytic activity [79]. Its active center contains an extended binding region consisting of several subsites, at least four or five subsites on the N-terminal side of the scissile bond (S1 to S4/S5) and three subsites C-terminal to the scissile bond (S1’ to S3’) [81][82][83]. The “bottom” of substrate

• recognition site is predominantly hydrophobic and there is evidence that not the sequence of the substrate is of importance in the recognition but only the volume of the side chains [84]. Substitution of Ala in position P2 with Ile and Leu leads to a greater or comparable amount of degradation after 120 min

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• dynamics, plasticity of GTs and conformation changes that allow for substrate recognition and catalysis [37]. In plants, GTs are also involved in the biosynthesis of hemicellulose. Xyloglucan is one of the main hemicellulose components in the cell walls of dicots. Its biosynthesis involves different GTs

Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces

• Enjuro Harunari,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2017, 13, 441–450, doi:10.3762/bjoc.13.47

• isobutyl CoA (bafilomycin: LAAHS [33], α-lipomycin: LAAHS [34], tautomycin: LAAHS [35]). Meanwhile, it is known that the substrate recognition is not strict for the loading module of avermectin (VPAHS) [36] and myxalamide (VAVHS) [37] which accept both isobutyl-CoA and 2-methylbutyl-CoA. In addition, genes

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• only 5-phenyl- and 5-tert-butyl-6-azauracils displayed very low substrate activity. The role of structural peculiarities and electronic properties in the substrate recognition by E. coli nucleoside phosphorylases is discussed. Keywords: enzymatic glycosylation; PM3 and ab initio calculations

• binding and activation at the catalytic sites of UP and TP. Whereas the substrate recognition of 4-thiouracil by the latter enzyme depends strongly on the electronic structure and/or the van der Waals radius of the substituent at C-4, UP is less sensitive to these differences, in particular, to

• and the respective 3N(H) and 2C(=O) functions of substrate (open form) and its activation (catalytically competent closed form) are proposed, wherein there is no prevailing factor determining the substrate recognition (as opposed to E. coli UP), giving an impetus to the sp3 → sp2 transformation of the

Radical polymerization by a supramolecular catalyst: cyclodextrin with a RAFT reagent

• Kohei Koyanagi,
• Yoshinori Takashima,
• Takashi Nakamura,
• Hiroyasu Yamaguchi and
• Akira Harada

Beilstein J. Org. Chem. 2016, 12, 2495–2502, doi:10.3762/bjoc.12.244

• distributed polymers. In the presence of 1,6-hexanediol (C6 diol) which works as a competitive molecule by being included in the α-CD cavity, the reaction yield was lower than that without C6 diol. Keywords: cyclodextrin; radical polymerization; RAFT polymerization; substrate recognition site; supramolecular

• catalyst; Introduction The folding of proteins in biological systems, the replication of DNA, and specific substrate recognition by enzymes play important roles in forming supramolecular structures, achieving functions, and maintaining life [1][2][3][4][5][6]. The crystal structures of RNA polymerase, DNA

• polymerase, and λ-exonuclease demonstrate that the cylindrical cavities of enzymes can effectively recognize substrates to produce biological polymers [1][2][3][4][5][6]. Cyclodextrins (CDs) have been widely used as substrate-recognition moieties in artificial enzymes [7][8][9][10][11][12][13][14][15], which

Versatile deprotonated NHC: C,N-bridged dinuclear iridium and rhodium complexes

• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 117–124, doi:10.3762/bjoc.12.13

• ], substrate recognition [29] and/or biological systems [30][31]. Among the synthetic methodologies to access to pNHC metal complexes [32][33][34][35][36][37][38][39][40], recently N-arylimine functionalized pNHC iridium complexes were obtained using excess of [Ir(cod)(µ-Cl)]2 [41], and next deprotonation of

Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

• Paul P. Kelly,
• Anja Eichler,
• Susanne Herter,
• David C. Kranz,
• Nicholas J. Turner and
• Sabine L. Flitsch

Beilstein J. Org. Chem. 2015, 11, 1713–1720, doi:10.3762/bjoc.11.186

• interactions [23], whereas Met184 is part of the P450cam substrate recognition site 2 (SRS 2) [24]. Accordingly, the entire P450cam active site was partitioned into seven residue pairs which were targeted in site-directed mutagenesis experiments in the manner of CASTing (Figure 1) [25]. NDT codon degeneracy

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

• Friederike Danneberg,
• Alice Ghidini,
• Plamena Dogandzhiyski,
• Elisabeth Kalden,
• Roger Strömberg and
• Michael W. Göbel

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• acids (PNA). RNA degradation occurs with similar rates and substrate specificities as in experiments with DNA conjugates we performed earlier. Although aggregation phenomena are observed in some cases, proper substrate recognition is not compromised. While our previous synthesis of 2-aminobenzimidazoles

The chemoenzymatic synthesis of clofarabine and related 2′-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases

• Ilja V. Fateev,
• Konstantin V. Antonov,
• Irina D. Konstantinova,
• Tatyana I. Muravyova,
• Frank Seela,
• Roman S. Esipov,
• Anatoly I. Miroshnikov and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2014, 10, 1657–1669, doi:10.3762/bjoc.10.173

• ab initio calculations in terms of the electronic structure (natural purines vs analogues) and stereochemical features (2FAra-1P vs Ara-1P) of the studied compounds to determine the substrate recognition by E. coli nucleoside phosphorylases. The second approach starts with the cascade one-pot

• electronic structure (natural purines vs analogues) and stereochemical features (2FAra-1P vs Ara-1P) of the studied compounds to determine the substrate recognition by E. coli nucleoside phosphorylases. Moreover, the cascade one-pot synthesis of clofarabine and related arabino-, xylo- and ribo-nucleosides (6

Synthesis of glycoconjugate fragments of mycobacterial phosphatidylinositol mannosides and lipomannan

• Benjamin Cao,
• Jonathan M. White and
• Spencer J. Williams

Beilstein J. Org. Chem. 2011, 7, 369–377, doi:10.3762/bjoc.7.47

• development of glycomimetic compounds. Homogeneous synthetic substructures have been used to deconvolute aspects of substrate recognition by biosynthetic enzymes and the structural determinants of host–pathogen interactions including antibody recognition and immune pattern-recognition systems such as the

• dendritic cell specific intercellular adhesion molecule-grabbing non-integrin (DC-SIGN) [8]. Thus, while total syntheses of many PIM structures have now been reported, the synthesis of substructures remains a worthwhile endeavor as these are useful to clarify fine details of enzymatic substrate recognition