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1. Fast-acting chemical tools to delineate causality in transcriptional control

Author:
Jaeger, Martin G.; Winter, Georg E.
Source:
Molecular cell 2021 v.81 no.8 pp. 1617-1630
ISSN:
1097-2765
Subject:
active sites,   etc   ; genes; transcription (genetics);     Show all 3 Subjects
Abstract:
... Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in ...
DOI:
10.1016/j.molcel.2021.02.015

2. Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node

Author:
Hubrich, Florian; Müller, Michael; Andexer, Jennifer N.
Source:
Chemical communications 2021 v.57 no.20 pp. 2441-2463
ISSN:
1364-548X
Subject:
active sites,   etc   ; chorismic acid; metabolism;     Show all 3 Subjects
Abstract:
... Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochori ...
DOI:
10.1039/d0cc08078k

3. Spectroscopic discernibility of dopants and axial ligands in pyridinic FeN₄ environments relevant to single-atom catalysts

Author:
Gallenkamp, Charlotte; Kramm, Ulrike I.; Krewald, Vera
Source:
Chemical communications 2021 v.57 no.7 pp. 859-862
ISSN:
1364-548X
Subject:
active sites,   etc   ; electrochemistry; ligands; spectroscopy;     Show all 4 Subjects
Abstract:
... Single-atom catalysts (SACs) activate small molecules, e.g. the oxygen reduction reaction is catalysed by FeNC materials. Because the nature of active site(s) in this type of SAC is unclear, spectroscopic and computational insights are needed to clarify the atomistic composition and electronic structure. Using quantum chemistry, we show that key features of [Fe{phen₂A₂}L]ⁿ⁺ complexes (A = CH, N wi ...
DOI:
10.1039/d0cc06237e

4. A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody

Author:
De Raffele, Daria; Martí, Sergio; Moliner, Vicent
Source:
Chemical communications 2021 v.57 no.43 pp. 5306-5309
ISSN:
1364-548X
Subject:
active sites,   etc   ; ; Gibbs free energy; antibodies; enzymes;     Show all 5 Subjects
Abstract:
... The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods. The amino acids involved in the reaction have been identified, as well as their specific role played in the active site and in the flexibility of the loops. Finally, the comparison with a de novo enzyme RA95.5-8F provides ...
DOI:
10.1039/d1cc01081f

5. Aminoglycoside antibiotics can inhibit or activate twister ribozyme cleavage

Author:
Zhang, Jun; Liu, Getong; Sun, Wenxia; Chen, Dongrong; Murchie, Alastair I.H.
Source:
TheFEBS journal 2021 v.288 no.5 pp. 1586-1598
ISSN:
1742-464X
Subject:
active sites,   etc   ; ; acylation; guanine; kinetics; ribozymes; sisomicin;     Show all 7 Subjects
Abstract:
... Interactions between aminoglycoside antibiotics and the twister ribozyme were investigated in this study. An initial screen of 17 RNA‐binding antibiotics showed that a number of aminoglycosides inhibit the ribozyme, while a subset of aminoglycosides enhances twister cleavage. Initial kinetic analysis of the twister ribozyme showed a sevenfold inhibition of ribozyme cleavage by paromomycin and a fi ...
DOI:
10.1111/febs.15517

6. A general strategy to prepare atomically dispersed biomimetic catalysts based on host–guest chemistry

Author:
Han, Xiao; Chen, Zheng; Chen, Wenxing; Lv, Chunlin; Ji, Yongjun; Li, Jing; Cheong, Weng-Chon; Lei, Xiaojuan; Peng, Qing; Chen, Chen; Wang, Dingsheng; Lian, Chao; Li, Yadong
Source:
Chemical communications 2021 v.57 no.15 pp. 1895-1898
ISSN:
1364-548X
Subject:
active sites,   etc   ; activation energy; biomimetics; enzymes;     Show all 4 Subjects
Abstract:
... Herein, we report a general strategy based on host–guest interactions to fabricate atomically dispersed biomimetic catalysts, which were evaluated by diboration of phenylacetylene. The structure and function of these mimics are quite similar to those of enzymes, namely, the atomically dispersed metal serves as an active site, the external macromolecular structure plays a role as an enzyme catalyti ...
DOI:
10.1039/d0cc07119f

7. Oxygen defect-stabilized heterogeneous single atom catalysts: preparation, properties and catalytic application

Author:
Zhang, Lei; Zhao, Xiufei; Yuan, Zhengqiu; Wu, Ming; Zhou, Hu
Source:
Journal of materials chemistry A 2021 v.9 no.7 pp. 3855-3879
ISSN:
2050-7496
Subject:
active sites,   etc   ; catalytic activity; chemoselectivity; energy; oxygen;     Show all 5 Subjects
Abstract:
... Single atom catalysts (SACs) show outstanding activity and selectivity in chemical catalysis owing to their unique electronic structure and unsaturated coordination environment, in which every dispersed metal species on the support can serve as catalytic centers to achieve maximum atomic utilization efficiency. However, fabricating SACs with high atomic dispersion is still challenging owing to the ...
DOI:
10.1039/d0ta10541d

8. Artificial maturation of [FeFe] hydrogenase in a redox polymer film

Author:
Felbek, Christina; Hardt, Steffen; Papini, Cecilia; Pramanik, Debajyoti; Artero, Vincent; Fontecave, Marc; Fourmond, Vincent; Plumeré, Nicolas; Léger, Christophe
Source:
Chemical communications 2021 v.57 no.14 pp. 1750-1753
ISSN:
1364-548X
Subject:
active sites,   etc   ; electrochemistry; electron transfer; enzymes; polymers;     Show all 5 Subjects
Abstract:
... We demonstrate that the insertion of the dinuclear active site of [FeFe] hydrogenase into the apo-enzyme can occur when the enzyme is embedded in a film of redox polymer, under conditions of mediated electron transfer. The maturation can be monitored by electrochemistry, and is as fast as under conditions of direct electron transfer. This new approach further clears the way to the implementation o ...
DOI:
10.1039/d0cc08168j

9. Defense and Offense Strategies: The Role of Aspartic Proteases in Plant–Pathogen Interactions

Author:
Figueiredo, Laura; Santos, Rita B.; Figueiredo, Andreia
Source:
Biology 2021 v.10 no.2
ISSN:
2079-7737
Subject:
active sites,   etc   ; abiotic stress; aspartic proteinases; proteolysis;     Show all 4 Subjects
Abstract:
... Plant aspartic proteases (APs; E.C.3.4.23) are a group of proteolytic enzymes widely distributed among different species characterized by the conserved sequence Asp-Gly-Thr at the active site. With a broad spectrum of biological roles, plant APs are suggested to undergo functional specialization and to be crucial in developmental processes, such as in both biotic and abiotic stress responses. Over ...
DOI:
10.3390/biology10020075

10. Catechols: a new class of carbonic anhydrase inhibitors

Author:
D'Ambrosio, Katia; Carradori, Simone; Cesa, Stefania; Angeli, Andrea; Monti, Simona M.; Supuran, Claudiu T.; De Simone, Giuseppina
Source:
Chemical communications 2020 v.56 no.85 pp. 13033-13036
ISSN:
1364-548X
Subject:
active sites,   etc   ; ; carbonate dehydratase;     Show all 3 Subjects
Abstract:
... To date, catechols have been only poorly investigated as carbonic anhydrase (CA) inhibitors. Here we report the first structural information on the CA inhibition mechanism of these molecules, showing that they adopt a peculiar binding mode to the enzyme active site which involves the zinc-bound water molecule and the “deep water”. ...
DOI:
10.1039/d0cc05172a

11. Insights into the co-doping effect of Fe3+ and Zr4+ on the anti-K performance of CeTiOx catalyst for NH3-SCR reaction

Author:
Kang, Keke; Yao, Xiaojiang; Huang, Yike; Cao, Jun; Rong, Jing; Zhao, Wanxia; Luo, Wen; Chen, Yang
Source:
Journal of hazardous materials 2021 v.416 pp. 125821
ISSN:
0304-3894
Subject:
active sites,   etc   ; acidity; catalysts; catalytic activity; coprecipitation; oxidation; surface area;     Show all 7 Subjects
Abstract:
... A novel K-resistant Fe³⁺ and Zr⁴⁺ co-doped CeTiOₓ catalyst was first prepared by co-precipitation method for the ammonia-selective catalytic reduction (NH₃-SCR) of NOₓ. On the premise of retaining the outstanding catalytic activity of CeTiOₓ catalyst, Fe³⁺ and Zr⁴⁺ co-doping efficiently improves its K-resistance with superior NOₓ conversion up to 84% after K-poisoning. Specially, the grain growth ...
DOI:
10.1016/j.jhazmat.2021.125821

12. Insights on the mechanism of Fe doped ZnO for tightly-bound extracellular polymeric substances tribo-catalytic degradation: The role of hydration layers at the interface

Author:
Hu, Jinglu; Ma, Wei; Pan, Yuzhen; Cheng, Zihong; Yu, Shuangen; Gao, Jian; Zhang, Zhe; Wan, Chunxiang; Qiu, Chenxi
Source:
Chemosphere 2021 v.276 pp. 130170
ISSN:
0045-6535
Subject:
active sites,   etc   ; catalytic activity; fluorescence; pollution; polymers; zinc oxide;     Show all 6 Subjects
Abstract:
... The control of interfacial microbial pollution is of great significance for water safety. Herein, the tribo-catalysis ability of zinc oxide (ZnO) has been investigated, which can realize the control of tightly-bound extracellular polymeric substances (T-EPS) in water under dark environment. The DFT calculation proves the Fe doping introduces the impurity level and decreases the work function from ...
DOI:
10.1016/j.chemosphere.2021.130170

13. Advances in metal/ biochar catalysts for biomass hydro-upgrading: A review

Author:
Wang, Siqi; Li, Hao; Wu, Meng
Source:
Journal of cleaner production 2021 v.303 pp. 126825
ISSN:
0959-6526
Subject:
active sites,   etc   ; biochar; biomass; catalysts; catalytic activity; feedstocks; hydrogenation;     Show all 7 Subjects
Abstract:
... Catalytic hydrogenation of biomass feedstocks into clean fuels and chemicals by heterogeneous catalysis is one of the most important means to realize the utilization of biomass, which has a promising application prospect. This review summarizes the recent advances in the preparation of metal/biochar catalysts and the commonness and individuality of catalytic performance for hydrogenation of biomas ...
DOI:
10.1016/j.jclepro.2021.126825

14. Insight into the amorphous nickel-iron (oxy)hydroxide catalyst for efficient oxygen evolution reaction

Author:
Liao, Hanxiao; Tan, Pengfei; Dong, Rui; Jiang, Min; Hu, Xiaoyue; Lu, Lili; Wang, Yuan; Liu, Hongqin; Liu, Yong; Pan, Jun
Source:
Journal of colloid and interface science 2021 v.591 pp. 307-313
ISSN:
0021-9797
Subject:
active sites,   etc   ; adsorption; catalysts; electrochemistry; iron; nickel; oxygen production;     Show all 7 Subjects
Abstract:
... The specific roles of Ni and Fe in nickel-iron (oxy)hydroxide catalyst (NiFeOₓ(OH)y) are extensively discussed during oxygen evolution reaction (OER). However, there still remains controversy about whether Ni or Fe species as the dominate active site. In this work, we reported the NiFeOₓ(OH)y catalysts with varied atomic ratio of nickel and iron for OER to explore the dominate active site during O ...
DOI:
10.1016/j.jcis.2021.02.020

15. Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands

Author:
Woo, Sung Oh; Oh, Myungkeun; Alhalhooly, Lina; Farmakes, Jasmin; Rajapakse, Arith J.; Yang, Zhongyu; Collins, Philip G.; Choi, Yongki
Source:
TheJournal of physical chemistry 2021 v.125 no.22 pp. 5750-5756
ISSN:
1520-5207
Subject:
active sites,   etc   ; catalytic activity; chitin; hydrolysis; indoles; ligands; lysozyme; peptidoglycans;     Show all 8 Subjects
Abstract:
... Single-molecule measurements of protein dynamics help unveil the complex conformational changes and transitions that occur during ligand binding and catalytic processes. Using high-resolution single-molecule nanocircuit techniques, we have investigated differences in the conformational dynamics and transitions of lysozyme interacting with three ligands: peptidoglycan substrate, substrate-based chi ...
DOI:
10.1021/acs.jpcb.1c01589

16. Gatekeeping Ketosynthases Dictate Initiation of Assembly Line Biosynthesis of Pyrrolic Polyketides

Author:
Yi, Dongqi; Acharya, Atanu; Gumbart, James C.; Gutekunst, Will R.; Agarwal, Vinayak
Source:
Journal of the American Chemical Society 2021 v.143 no.20 pp. 7617-7622
ISSN:
1520-5126
Subject:
active sites,   etc   ; amino acids; biosynthesis; exercise; polyketide synthases; polyketides;     Show all 6 Subjects
Abstract:
... Assembly line biosynthesis of polyketide natural products involves checkpoints where identities of thiotemplated intermediates are verified before polyketide extension reactions are allowed to proceed. Determining what these checkpoints are and how they operate is critical for reprogramming polyketide assembly lines. Here we demonstrate that ketosynthase (KS) domains can perform this gatekeeping r ...
DOI:
10.1021/jacs.1c02371

17. Spectroscopic Definition of a Highly Reactive Site in Cu-CHA for Selective Methane Oxidation: Tuning a Mono-μ-Oxo Dicopper(II) Active Site for Reactivity

Author:
Rhoda, Hannah M.; Plessers, Dieter; Heyer, Alexander J.; Bols, Max L.; Schoonheydt, Robert A.; Sels, Bert F.; Solomon, Edward I.
Source:
Journal of the American Chemical Society 2021 v.143 no.19 pp. 7531-7540
ISSN:
1520-5126
Subject:
active sites,   etc   ; Raman spectroscopy; geometry; methane; methanol; oxidation; temperature; zeolites;     Show all 8 Subjects
Abstract:
... Using UV–vis and resonance Raman spectroscopy, we identify a [Cu₂O]²⁺ active site in O₂ and N₂O activated Cu-CHA that reacts with methane to form methanol at low temperature. The Cu–O–Cu angle (120°) is smaller than that for the [Cu₂O]²⁺ core on Cu-MFI (140°), and its coordination geometry to the zeolite lattice is different. Site-selective kinetics obtained by operando UV–vis show that the [Cu₂O] ...
DOI:
10.1021/jacs.1c02835

18. Readily useable bulk phenoxazine-based covalent organic framework cathode materials with superior kinetics and high redox potentials

Author:
Meng, Zhiying; Zhang, Ying; Dong, Mengqing; Zhang, Yue; Cui, Fengmin; Loh, Teck-Peng; Jin, Yinghua; Zhang, Wei; Yang, Haishen; Du, Ya
Source:
Journal of materials chemistry A 2021 v.9 no.17 pp. 10661-10665
ISSN:
2050-7496
Subject:
active sites,   etc   ; cathodes; electric power; electrical conductivity; electrolytes; energy; transportation;     Show all 7 Subjects
Abstract:
... Redox-active covalent organic frameworks (COFs) with dense redox sites are promising electrical energy storage materials with robust architectures, high surface areas, insolubility in electrolytes, and open pores for electrolyte transportation. However, low redox potentials and poor electrical conductivity of pristine COFs often result in low accessibilities of redox-active sites and slow redox ki ...
DOI:
10.1039/d0ta10785a

19. α-Glucosidase Inhibitors from Ageratina grandifolia

Author:
Gutiérrez-González, José A.; Pérez-Vásquez, Araceli; Torres-Colín, Rafael; Rangel-Grimaldo, Manuel; Rebollar-Ramos, Daniela; Mata, Rachel
Source:
Journal of natural products 2021 v.84 no.5 pp. 1573-1578
ISSN:
1520-6025
Subject:
active sites,   etc   ; ; Ageratina; acarbose; epoxides; flavonoids; fractionation; kinetics; probability; yeasts;     Show all 10 Subjects
Abstract:
... Fractionation of an aqueous extract from the aerial parts of Ageratina grandifolia yielded a new natural product, namely, 4-hydroxy-3-((S)-1′-angeloyloxy-(R)-2′,3′-epoxy-3′-methyl)butylacetophenone (1), along with eight known compounds, including three flavonoids (2–4) and five chromenes (5–9). NMR data interpretation and DFT-calculated chemical shifts combined with DP4+ statistical and J-DP4 prob ...
DOI:
10.1021/acs.jnatprod.1c00105

20. Angiotensin‐converting enzyme open for business: structural insights into the subdomain dynamics

Author:
Cozier, Gyles E.; Lubbe, Lizelle; Sturrock, Edward D.; Acharya, K. Ravi
Source:
TheFEBS journal 2021 v.288 no.7 pp. 2238-2256
ISSN:
1742-464X
Subject:
active sites,   etc   ; ; bradykinin; ligands; peptidyl-dipeptidase A; zinc;     Show all 6 Subjects
Abstract:
... Angiotensin‐1‐converting enzyme (ACE) is a key enzyme in the renin–angiotensin–aldosterone and kinin systems where it cleaves angiotensin I and bradykinin peptides, respectively. However, ACE also participates in numerous other physiological functions, can hydrolyse many peptide substrates and has various exo‐ and endopeptidase activities. ACE achieves this complexity by containing two homologous ...
DOI:
10.1111/febs.15601