Impact of residual antibiotics on microbial decomposition of livestock manures in Eutric Regosol: Implications for sustainable nutrient recycling and soil carbon sequestration.

The land application of livestock manure has been widely acknowledged as a beneficial approach for nutrient recycling and environmental protection. However, the impact of residual antibiotics, a common contaminant of manure, on the degradation of organic compounds and nutrient release in Eutric Regosol is not well understood. Here, we studied, how oxytetracycline (OTC) and ciprofloxacin (CIP) affect the decomposition, microbial community structure, extracellular enzyme activities and nutrient release from cattle and pig manure using litterbag incubation experiments. Results showed that OTC and CIP greatly inhibited livestock manure decomposition, causing a decreased rate of carbon (28%-87%), nitrogen (15%-44%) and phosphorus (26%-43%) release. The relative abundance of gram-negative (G-) bacteria was reduced by 4.0%-13% while fungi increased by 7.0%-71% during a 28-day incubation period. Co-occurrence network analysis showed that antibiotic exposure disrupted microbial interactions, particularly among G- bacteria, G+ bacteria, and actinomycetes. These changes in microbial community structure and function resulted in decreased activity of urease, ß-1,4-N-acetyl-glucosaminidase, alkaline protease, chitinase, and catalase, causing reduced decomposition and nutrient release in cattle and pig manures. These findings advance our understanding of decomposition and nutrient recycling from manure-contaminated antibiotics, which will help facilitate sustainable agricultural production and soil carbon sequestration.

Metabolomics analysis of bioactive compositions of Michelia macclurei Dany and its antioxidant and enzyme inhibitory activities.

BACKGROUND: Michelia macclurei Dandy is a traditional Chinese medicinal plant, but little is understood about the bioactive compositions and biological potential of its different parts, limiting their applications. This study aims to identify the bioactive compositions and analyze differences in accumulation patterns from different parts of Michelia macclurei (heartwood, sapwood, bark, root, leaf, and fruit) using metabolomics. It also seeks to explore their biological potential and analyze the relationship between the bioactive compositions and biological potential. RESULTS: A total of 63 volatile metabolites (VMs) were identified by gas chromatography-mass spectrometry (GC-MS) in six parts, and the VMs in each part were dominated by sesquiterpenes and their derivatives (71.40-88.32%). Six parts of Michelia macclurei contained structurally diverse non-volatile metabolites (NVMs) with a total of 207 bioactive compounds, including 92 alkaloids, 30 flavonoids, 19 lignans, and 18 organic acids, utilizing ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis. Multivariate statistical analysis showed that the accumulation patterns of bioactive compositions differed significantly among the different parts, and the 25 VMs and 72 NVMs could be considered potential markers for distinguishing the different parts of Michelia macclurei. The excellent antioxidant and enzyme inhibitory capacity of extracts of all six parts was indicated by in vitro bioactivity assays. Pearson's correlation analysis showed that the bioactive compositions in the six parts were significantly correlated with antioxidant and enzyme inhibitory activities. CONCLUSION: This study offers helpful information on the distribution of bioactive compositions in different parts of Michelia macclurei and confirms the excellent antioxidant, and enzyme inhibitory potential of its extracts, which could provide scientific evidence for its potential applications in the pharmaceutical industry, cosmetics, and functional foods. © 2024 Society of Chemical Industry.

Intracellular Construction of Organelle-like Compartments Facilitates Metabolic Flux in Escherichia coli.

The formation of well-designed synthetic compartments or membraneless organelles for applications in synthetic biology and cellular engineering has aroused enormous interest. However, establishing stable and robust intracellular compartments in bacteria remains a challenge. Here, we use the structured DIX domains derived from Wnt signaling pathway components, more specifically, Dvl2 and Axin1, as building blocks to generate intracellular synthetic compartments in Escherichia coli. Moreover, the aggregation behaviors and physical properties of the DIX-based compartments can be tailored by genetically embedding a specific dimeric domain into the DIX domains. Then, a pair of interacting motifs, consisting of the aforementioned dimeric domain and its corresponding binding ligand, was incorporated to modify the client recruitment pattern of the synthetic compartments. As a proof of concept, the human milk oligosaccharide lacto-N-tetraose (LNT) biosynthesis pathway was selected as a model metabolic pathway. The fermentation results demonstrated that the co-compartmentalization of sequential pathway enzymes into intracellular compartments created by DIX domain, or by the DIX domain in conjunction with interacting motifs, prominently enhanced the metabolic flux and increased LNT production. These synthetic protein compartments may provide a feasible and effective tool to develop versatile organelle-like compartments in bacteria for applications in cellular engineering and synthetic biology.

Optimization and characterization of aqueous enzyme-assisted solvent extraction of apricot kernel oil.

Abstract: Aqueous enzyme-assisted solvent extraction (AE-SE) of oil from apricot (Prunus armeniaca L.) kernel was investigated in this study and the operational parameters were optimized. After preliminary screening, a cocktail of enzymes (Celluclast 1.5 L and Alcalase Pure 2.4 L [60:40, v/v)] of 1% (v/w) was chosen. The extraction process parameters: temperature (40-60 °C), time (1-5 h), and pH (4-9) were optimized using Box-Behnken design to achieve the highest oil yield (%) and antioxidant activity (DPPH, %). Under optimized conditions, i.e., temperature 40 °C, time 2.5 h, and pH 8.28, the highest oil yield and DPPH were 47.93% and 67.31%, respectively. The gas chromatography analysis disclosed that apricot kernel oil extracted by solvent extraction and AE-SE have similar fatty acid compositions, and the oil is rich in unsaturated fatty acids. The physicochemical analysis showed AE-SE method produces high-quality oil and can be substituted as green technology for industrial oil extraction purposes.

Molecular Cloning of the Extracellular Lipases of Bacillus Amyloliquefaciens Isolated from Agrifood Wastes.

Background: The lipase enzyme (EC: 3.1.1.3) is one of the most important catalysts in food, dairy, detergent, and textile industries. Objective: This study was performed to identify, isolate and characterize of lipase producing bacterial strain from agrifood wastes and to identify and characterize of their lipase genes. Materials and Methods: In the present study, two lipase-producing isolates were identified from the effluent of Golbahar meat products and Soveyda vegetable oil factories using in silico and in vitro approaches. Results: The results of morphological, biochemical, and molecular characterizations showed that both lipase-producing isolates belong to the Bacillus amyloliquefaciens species. Phylogenetic analysis confirmed the results of phenotypic, biochemical, and molecular characterizations. The results showed differences between LipA and LipB in the Golbahar and Soveyda isolates. Three different amino acids (residues 14, 100, and 165) were observed in LipA and one different amino acid (residue 102) was detected in LipB extracellular lipases. The protein molecular weight of the two extracted lipases ranged from 20 to 25 kDa. The identified extracellular lipases also had different physicochemical features. The maximum lipase activity of the Golbahar and Soveyda isolates was observed at 45 °C and at the pH of 8, but the Golbahar isolates exhibited higher lipase activity compared to the Soveyda isolates. The Golbahar and Soveyda isolates exhibited different activities in the presence of some ions, inhibitors, denaturing agents, and organic solvents and the Golbahar isolates showed better lipase activity than the Soveyda isolates. Conclusions: In this study, two extracellular lipase-producing isolates of B. amyloliquefaciens were identified from different food industries, and their characteristics were investigated. The results of various investigations showed that the lipases produced by the Golbahar isolate have better characteristics than the lipases of the Soveyda isolate. The Golbahar lipases have a suitable temperature and pH activity range and maintain their activity in the presence of some ions, inhibitors, denaturing agents, and organic solvents. After further investigation, the Golbahar isolate lipase can be used in various industries. In addition, this lipase can be used enzyme engineering processes and its activity can be arbitrarily changed by targeted mutations. The results of this study can increase our knowledge of extracellular lipases and may turn out to have industrial applications.

A comparative study of anti-ADAMTS-13 antibody dynamics in immune-mediated thrombotic thrombocytopenic purpura.

Background: Thrombotic thrombocytopenic purpura, particularly its immune-mediated variant (iTTP), necessitates accurate diagnostic approaches for effective management. Objectives: To compare a chemiluminescence immunoassay (CLIA) and an enzyme-linked immunosorbent assay (ELISA) for testing ADAMTS-13 activity and detecting anti-ADAMTS-13 autoantibodies (AAbs) in patients with iTTP. Methods: This study involved 31 paired samples from 12 iTTP patients. ADAMTS-13 activity was measured using the HemosIL AcuStar (Instrumentation Laboratory, CLIA) and Technozym (Technoclone) activity assay (ELISA). The presence of AAbs was assessed using Technozym ADAMTS-13-INH assay (ELISA) and HemosIL AcuStar activity (CLIA) within a Bethesda assay following mixing with normal pool plasma. von Willebrand factor (VWF) multimers were analyzed using the HYDRASYS-2 SCAN system and the HYDRAGEL 5- or 11-VW Multimer kits (Sebia). VWF activity levels were measured with the HemosIL AcuStar VWF:GPIbR on the ACL AcuStar Analyzer (IL). Results: For ADAMTS-13 activity, a strong linear relationship and no bias between CLIA and ELISA were confirmed (slope = 1.01 [0.91, 1.11], intercept = 0.00 [-0.47, 0]). However, significant discrepancies were found in AAb detection during remission phases with ADAMTS-13 activity between 10% and 50%, with CLIA and ELISA showing significant divergence (P < .001, Cohen's g = 0.34). Consistently, VWF multimers and activity levels exhibited significantly different values between remission samples with ADAMTS-13 activity below 50% and above 50%. In longitudinal analysis of patients with multiple iTTP relapses, positivity to CLIA appears to precede ELISA in predicting exacerbations. Conclusion: While CLIA and ELISA might be interchangeable for assessing ADAMTS-13 activity, they are not equivalent for detecting AAbs, particularly in patients in clinical remission with ADAMTS-13 activity between 10% and 50%.

Characterization of lignin degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid (PDC).

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is CHMS dehydrogenase, which acts on the substrate 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS). We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

Unveiling Generally-ignored Co-substrate Effect of Catalase-inherent Peroxidase Mimic for Self-verifiable Detection of High-concentration Hydrogen Peroxide.

One nanoparticle possessing both peroxidase (POD) and catalase (CAT) activities is a prevalent co-substrate nanozyme system, distinct from the extensively researched cascade nanozyme system. During the sensing of hydrogen peroxide by POD, the impact of CAT is actually ignored in most studies. In this study, the CAT effect on hydrogen peroxide detection is thoroughly investigated based on POD catalysis by finely tuning the relative activity of POD and CAT. It is discovered that the CAT effect can be changed by delaying the injection of chromogenic substrate after adding hydrogen peroxide and that the linear range grows with the delayed time. Then, a theoretical mechanism showed that the time-delay mediated CAT effect magnification does not change the Vmax, but it causes Km to linearly increase with delayed time, consistent with the experiment results. Furthermore, the detection of high concentrations of hydrogen peroxide is successfully realized in contact lens care solutions by utilizing time-delay-mediated POD/CAT nanozyme. On the other hand, its linear range-tunable characteristic is used to produce multiple standard curves, then enabled self-verifying hydrogen peroxide detection. Overall, this work investigates the role of CAT in CAT-inherent POD nanozymes both theoretically and experimentally, and confirms POD/CAT nanozyme's priority in developing high-performance sensors.

Sequential Targeted Enzyme-Instructed Self-Assembly Supramolecular Nanofibers to Attenuate Intervertebral Disc Degeneration.

As an age-related disease, intervertebral disc degeneration is closely related to inflammation and aging. Inflammatory cytokines and cellular senescence collectively contribute to the degradation of intervertebral disc. Blocking this synergy reduces disc extracellular matrix damage caused by inflammation and aging. In this study, drug-loaded nanofibers with sequential targeting functions are constructed through intelligent response, hydrophilicity, and in situ self-assembly empowerment of flurbiprofen. The peptide precursor responds to the cleavage of overexpressed MMP-2 in the degenerative intervertebral disc microenvironment (intracellular and extracellular), resulting in the formation of self-assembled nanofibers that enable the on-demand release of flurbiprofen and COX-2 response. In vitro, Comp. 1 (Flurbiprofen-GFFYPLGLAGEEEERGD) reduces the expression of inflammation-related genes and proteins and the polarization of M1 macrophages by competitively inhibiting COX-2 and increases the expression of extracellular matrix proteins COL-2 and aggrecan. Additionally, it can reduce the expression of Senescence-Associated Secretory Phenotype and DNA damage in aged nucleus pulposus cells and promote the recovery of proliferation and cell cycle. In vivo, drug-loaded nanofibers delay intervertebral disc degeneration by inhibiting inflammation and preventing the accumulation of senescent cells. Therefore, the sequentially targeted self-assembled drug-loaded nanofibers can delay intervertebral disc degeneration by blocking the synergistic effect of inflammatory cytokines and cellular senescence.

How does CHD4 slide nucleosomes?

Chromatin remodelling enzymes reposition nucleosomes throughout the genome to regulate the rate of transcription and other processes. These enzymes have been studied intensively since the 1990s, and yet the mechanism by which they operate has only very recently come into focus, following advances in cryoelectron microscopy and single-molecule biophysics. CHD4 is an essential and ubiquitous chromatin remodelling enzyme that until recently has received less attention than remodellers such as Snf2 and CHD1. Here we review what recent work in the field has taught us about how CHD4 reshapes the genome. Cryoelectron microscopy and single-molecule studies demonstrate that CHD4 shares a central remodelling mechanism with most other chromatin remodellers. At the same time, differences between CHD4 and other chromatin remodellers result from the actions of auxiliary domains that regulate remodeller activity by for example: (1) making differential interactions with nucleosomal epitopes such as the acidic patch and the N-terminal tail of histone H4, and (2) inducing the formation of distinct multi-protein remodelling complexes (e.g. NuRD vs ChAHP). Thus, although we have learned much about remodeller activity, there is still clearly much more waiting to be revealed.

Exploring Acyl Thiotriazinoindole Based Pharmacophores: Design, Synthesis, and SAR Studies with Molecular Docking and Biological Activity Profiling against Urease, α-amylase, α-glucosidase, Antimicrobial, and Antioxidant Targets.

A diminutive chemical library of acyl thiotriazinoindole (ATTI) based bioactive scaffolds was synthesized, instigated by taking the economical starting material Isatin, through a series of five steps. Isatin was first nitrated followed by the attachment of pentyl moiety via nucleophilic substitution reaction. The obtained compound was reacted with thiosemicarbazide to obtain thiosemicarbazone derivative, which was eventually cyclized using basic conditions in water as solvent. Finally, the reported series was obtained through reaction of nitrated thiotriazinoindole moiety with differently substituted phenacyl bromides. The synthesized compounds were characterized using NMR spectroscopy and elemental analysis. Finally, the synthesized motifs were scrutinized for their potential to impede urease, α-glucosidase, DPPH, and α-amylase. Compound 5 h with para cyano group manifested the most pivotal biological activity among all, displaying IC50 values of 29.7 ± 0.8, 20.5 ± 0.5 and 36.8 ± 3.9 µM against urease, α-glucosidase, and DPPH assay, respectively. Simultaneously, for α-amylase compound 5 g possessing a p-CH3 at phenyl ring unfolded as most active, with calculated IC50 values 90.3 ± 1.1 µM. The scaffolds were additionally gauged for their antifungal and antibacterial activity. Among the tested strains, 5d having bromo as substituent exhibited the most potent antibacterial activity, while it also demonstrated the highest potency against Aspergillus fumigatus. Other derivatives 5b, 5e, 5i, and 5j also exhibited dual inhibition against both antibacterial and antifungal strains. The interaction pattern of derivatives clearly displayed their SAR, and their docking scores were correlated with their IC50 values. In molecular docking studies, the importance of interactions like hydrogen bonding was further asserted. The electronic factors of various substituents engendered variety of interactions between the ligands and targets implying their importance in the structures of the synthesized heterocyclic scaffolds. To conclude, the synthesized compounds had satisfactory biological activity against various important targets. Further studies are therefore encouraged by attachment of different substitutions in the structure at various positions to enhance the activity of these compounds.

Preparation and characterization of kelp polysaccharide and its research on anti-influenza a virus activity.

The beneficial effects of kelp polysaccharide (KPS) have recently attracted attention. In this study, KPS was extracted from kelp using the enzyme hydrolysis combined with freeze-drying, namely, KPS-EF. The structural characterization showed that KPS-EF was a highly sulfated macromolecule with the Mw of 764.2 kDa and the sulfate content of 23.49 %. The antiviral activity of KPS-EF in vitro was verified, and the IC50 value of KPS against the PR8 virus was 0.58 mg/mL. Intranasal administration of KPS-EF significantly inhibited death and weight loss in IAV-infected mice and alleviated virus-induced pneumonia symptoms, meanwhile, KPS-EF (10 mg/kg/day) significantly decreased the production levels of chemokines (CXCL1, RANTES) and inflammatory cytokines (IL-6, TNF-α) in lungs (p < 0.05). KPS-EF could downregulate the activity of viral neuraminidase (NA) primarily in the late stage of viral adsorption with an IC50 value of 0.29 mg/mL. This study provides a theoretical basis for the using KPS as a supplement to NA inhibitors or anti-influenza drugs.

Recent developments in enzymatic preparation, physicochemical properties, bioactivity, and application of resistant starch type III from staple food grains.

Resistant starch (RS) was classified into five types and referred to the starch that cannot be digested and absorbed by the small intestine of healthy human beings. Among them, RS3 has received a lot of attention from researchers because of its good functional properties and greater application prospects. Meanwhile, the enzymatic method is widely used in the preparation of RS3 because of its high efficiency and environmental protection. α-Amylase and pullulanase as the main enzymes can effectively improve the yield of RS3. The physical properties of RS3 have an excellent potential for application in improving food crispness, texture and producing low glycemic index (GI) foods. It is more valuable because it has biological activities such as inducing apoptosis in tumor cells, lowering intestinal pH, and regulating blood glucose, etc. This paper summarized the current research progress of RS3 from different staple food grains, including current applications of enzymes commonly used in the preparation of RS3, physical properties and biological activities of RS3, and the application of RS3 in different areas to provide a theoretical basis for future research on RS3 as well as further development and applications based on the market requirement.

Probing the nucleobase selectivity of RNA polymerases with dual-coding substrates.

Formycin A (FOR) and Pyrazofurin A (PYR) are nucleoside analogues with antiviral and antitumor properties. They are known to interfere with nucleic acid metabolism, but their direct effect on transcription is less understood. We explored how RNA polymerases (RNAPs) from bacteria, mitochondria, and viruses utilize FOR, PYR, and oxidized purine nucleotides. All tested polymerases incorporated FOR in place of adenine and PYR in place of uridine. FOR also exhibited surprising dual-coding behavior, functioning as a cytosine substitute, particularly for viral RNAP. In contrast, 8-oxoadenine and 8-oxoguanine were incorporated in place of uridine in addition to their canonical Watson-Crick codings. Our data suggest that the interconversion of canonical anti- and alternative syn-conformers underlies dual-coding abilities of FOR and oxidized purines. Structurally distinct RNAPs displayed varying abilities to utilize syn-conformers during transcription. By examining base pairings that led to substrate incorporation and the entire spectrum of geometrically compatible pairings, we have gained new insights into the nucleobase selection processes employed by structurally diverse RNAPs. These insights may pave the way for advancements in antiviral therapies.

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: deciphering of performance, metabolic pathways and microbial communities.

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.

High efficiency removal of antibiotic resistance gene with designer zinc-finger protein.

The use of agricultural biomass-based fertilizers, and the release of feces into the environment leads to last-lasting pollution of antibiotic resistance genes that cannot be removed from waters via traditional methods, resulting in significant health threats. To solve this issue, an antibiotic resistance gene removal method was proposed and tested that used sequence-specific DNA-binding designer zinc finger proteins, which target an 18-bp DNA sequence for specific antibiotic resistance gene binding and removal. Targeting the sulfonamide-resistant sul1 gene, sul1-binding zinc-finger protein was designed, overexpressed, and purified. This protein showed specific binding with sul1 over tetA that do not have the targeted sequence. This protein was further immobilized on agarose-based resins to prepare a sul1-removal column. When loaded with 10 mg protein, this column can remove over 99 % sul1 in water, suggesting high efficiency. This work presents a new method attempting to eliminate environmental and health threats posed by antibiotic resistance genes.

Purification and characterization of a Rieske oxygenase and its NADH-regenerating partner proteins.

The Rieske non-heme iron oxygenases (Rieske oxygenases) comprise a class of metalloenzymes that are involved in the biosynthesis of complex natural products and the biodegradation of aromatic pollutants. Despite this desirable catalytic repertoire, industrial implementation of Rieske oxygenases has been hindered by the multicomponent nature of these enzymes and their requirement for expensive reducing equivalents in the form of a reduced nicotinamide adenine dinucleotide cosubstrate (NAD(P)H). Fortunately, however, some Rieske oxygenases co-occur with accessory proteins, that through a downstream reaction, recycle the needed NAD(P)H for catalysis. As these pathways and accessory proteins are attractive for bioremediation applications and enzyme engineering campaigns, herein, we describe methods for assembling Rieske oxygenase pathways in vitro. Further, using the TsaMBCD pathway as a model system, in this chapter, we provide enzymatic, spectroscopic, and crystallographic methods that can be adapted to explore both Rieske oxygenases and their co-occurring accessory proteins.

Photo-reduction facilitated stachydrine oxidative N-demethylation reaction: A case study of Rieske non-heme iron oxygenase Stc2 from Sinorhizobium meliloti.

Rieske-type non-heme iron oxygenases (ROs) are an important family of non-heme iron enzymes. They catalyze a diverse range of transformations in secondary metabolite biosynthesis and xenobiotic bioremediation. ROs typically shuttle electrons from NAD(P)H to the oxygenase component via reductase component(s). This chapter describes our recent biochemical characterization of stachydrine demethylase Stc2 from Sinorhizobium meliloti. In this work, the eosin Y/sodium sulfite pair serves as the photoreduction system to replace the NAD(P)H-reductase system. We describe Stc2 protein purification and quality control details as well as a flow-chemistry to separate the photo-reduction half-reaction and the oxidation half-reaction. Our study demonstrates that the eosin Y/sodium sulfite photo-reduction pair is a NAD(P)H-reductase surrogate for Stc2-catalysis in a flow-chemistry setting. Experimental protocols used in this light-driven Stc2 catalysis are likely to be applicable as a photo-reduction system for other redox enzymes.

Spectroscopic definition of ferrous active sites in non-heme iron enzymes.

Non-heme iron enzymes play key roles in antibiotic, neurotransmitter, and natural product biosynthesis, DNA repair, hypoxia regulation, and disease states. These enzymes had been refractory to traditional bioinorganic spectroscopic methods. Thus, we developed variable-temperature variable-field magnetic circular dichroism (VTVH MCD) spectroscopy to experimentally define the excited and ground ligand field states of non-heme ferrous enzymes (Solomon et al., 1995). This method provides detailed geometric and electronic structure insight and thus enables a molecular level understanding of catalytic mechanisms. Application of this method across the five classes of non-heme ferrous enzymes has defined that a general mechanistic strategy is utilized where O2 activation is controlled to occur only in the presence of all cosubstrates.

Theoretical Framework for Novel Catalytic Biomolecules Composed of Multiple Peptides.

Protein-based enzymes are among the most efficient catalysts on our planet. A common feature of protein enzymes is that all catalytic amino acids occupy a limited, narrow space and face each other. In this study, we created a theoretical novel biomimetic molecule containing different multiple catalytic peptides. Although single peptides are far less catalytically efficient than protein enzymes, Octopus-arms-mimicking biomolecules containing eight different peptides (Octopuzymes) can efficiently catalyze organic reactions. Since structural information for extant protein enzymes, predicted enzymes based on genome data, and artificially designed enzymes is available for designing Octopuzymes, they could in theory mimic all protein enzyme reactions on our planet. Moreover, besides L-amino acids, peptides can contain D-amino acids, non-natural amino acids, chemically modified amino acids, nucleotides, vitamins, and manmade catalysts, leading to a huge expansion of catalytic space compared with extant protein enzymes. Once a reaction catalyzed by an Octopuzyme is defined, it could be rapidly evolvable via multiple amino acid substitutions on the eight peptides of Octopuzymes.