Rational multienzyme architecture design with iMARS.

Biocatalytic cascades with spatial proximity can orchestrate multistep pathways to form metabolic highways, which enhance the overall catalytic efficiency. However, the effect of spatial organization on catalytic activity is poorly understood, and multienzyme architectural engineering with predictable performance remains unrealized. Here, we developed a standardized framework, called iMARS, to rapidly design the optimal multienzyme architecture by integrating high-throughput activity tests and structural analysis.

Semi-rational design of an aromatic dioxygenase by substrate tunnel redirection.

Lignin valorization is crucial for achieving economic and sustainable biorefinery processes. However, the enzyme substrate preferences involved in lignin degradation remain poorly understood, and low activity toward specific substrates presents a significant challenge to the efficient utilization of lignin. In this study, we investigated the substrate promiscuity of Ado, a key enzyme involved in lignin valorization.

Intraoperative thermostatic nursing and failure mode and effects analysis enhance gastrectomies' care quality.

Background: Utilizing failure mode and effects analysis (FMEA) in operating room nursing provides valuable insights for the care of patients undergoing radical gastric cancer surgery

Aim: To evaluate the impact of FMEA on the risk of adverse events and nursing-care quality in patients undergoing radical surgery.

Methods: Among 230 patients receiving radical cancer surgery between May 2019 and May 2024, 115 were assigned to a control group that received standard intraoperative thermoregulation, while the observation group benefited from FMEA-modeled operating room care. Clinical indicators, stress responses, postoperative gastrointestinal function recovery, nursing quality, and the incidence of adverse events were compared between the two groups.

Novel Feruloyl Esterase for the Degradation of Polyethylene Terephthalate (PET) Screened from the Gut Microbiome of Plastic-Degrading Mealworms ( Larvae).

Mealworms () larvae can degrade both plastics and lignocellulose through synergistic biological activities of their gut microbiota because they share similarities in chemical and physical properties. Here, a total of 428 genes encoding lignocellulose-degrading enzymes were screened from the gut microbiome of larvae to identify poly(ethylene terephthalate) (PET)-degrading activities. Five genes were successfully expressed in , among which a feruloyl esterase-like enzyme named Fae-PETase demonstrated the highest PET degradation activity, converting PET into MHET (0.

A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine.

Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive.

New modifications of PBAT by a small amount of oxalic acid: Fast crystallization and enhanced degradation in all natural environments.

Biodegradable plastics are often mistakenly thought to be capable of degrading in any environment, but their slow degradation rate in the natural environment is still unsatisfactory. We synthetized a novel series of poly(butylene oxalate-co-adipate-co-terephthalate) (PBOAT) with unchanged melting point (135 °C), high elastic modulus (140 - 219 MPa) and elongation at break (478 - 769%). Fast isothermal crystallization with a semi-crystallization time < 20 s was demonstrated by the PBOAT.

Understanding base and backbone contributions of phosphorothioate DNA for molecular recognition with SBD proteins.

Bacterial DNA phosphorothioate (PT) modification provides a specific anchoring site for sulfur-binding proteins (SBDs). Besides, their recognition patterns include phosphate links and bases neighboring the PT-modified site, thereby bringing about genome sequence-dependent properties in PT-related epigenetics. Here, we analyze the contributions of the DNA backbone (phosphates and deoxyribose) and bases bound with two SBD proteins in and ( and ).

Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation.

Here, we present a protocol to examine asymmetric pairwise pre-reaction and transition states in enzymatic catalysis. We describe steps to set up the calculated systems, run umbrella sampling molecular dynamics simulation, and conduct quantum mechanics/molecular mechanics calculations. We also provide analytical scripts to yield potential of mean force of pre-reaction states and reaction barriers.

Theoretical Studies of Mutual Effects between 6-m-r Hemiketalization and 26-m-r Lactonization in Pimaricin Thioesterase.

Pimaricin is a small polyene macrolide antibiotic and has been broadly used as an antimycotic and antiprotozoal agent in both humans and foods. As a thioesterase in type-I polyketide synthase, pimTE controls the 26-m-r macrolide main chain release in pimaricin biosynthesis. In this work, we sought to determine whether the 6-m-r hemiketal formation was linked to pimTE-catalyzed 26-m-r lactonization.

Visually induced γ band rhythm in spatial summation beyond the receptive field in mouse primary visual cortex.

Recent studies in many kinds of mammals have established the existence of multiple γ rhythms in the cerebral cortex subserving different functions. In the primary visual cortex (V1), visually induced γ rhythms are dependent on stimulus features. However, experimental findings of γ power induced by varying the size of the drifting grating are inconsistent.

Chemical control over the conversion between bicyclic and polycyclic terpenes by fungal bifunctional terpene synthases.

Fungal bifunctional terpene synthases (BFTSs) reportedly associate with a series of new skeletons of di/sesterterpenes. However, the molecular mechanisms underlying the variabilities in the ring system of BFTS-catalyzed products are not well understood. In this study, we identified a key site, S89/L89, that controls the conversion between bicyclic and polycyclic terpene skeletons catalyzed by two BFTSs, BsPS and FoFS.

Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation.

Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 106 nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels.

Molecular recognition between bacterial phosphorothioate DNA and sulfur-binding domain (SBD): competition between the water cage and chalcogen-hydrophobic packet.

Bacterial DNA phosphorothioation (PT) physiologically and stereo-specifically replaces a non-bridging oxygen in a phosphate link with a sulfur atom, which can be recognized by a highly conserved sulfur-binding domain (SBD). Here we conducted thermodynamic integration (TI), molecular dynamics simulation, and quantum chemical calculations to decipher the specific molecular interactions between PT-DNA and SBD in type IV restriction enzyme ScoMcrA. The TI-calculated binding affinity of (5'-CCGGCCGG-3') is larger than that of (5'-CCGGCCGG-3') by about 7.

Acid-triggered, degradable and high strength-toughness copolyesters: Comprehensive experimental and theoretical study.

The popularization and widespread use of degradable polymers is hindered by their poor mechanical properties. It is of great importance to find a balance between degradation and mechanical properties. Herein, poly(butylene terephthalate) (PBT) modified by SPG diol from 10% to 40 mol% were synthesized through a two-step polycondensation reaction.

Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics.

Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway.

Phosphorothioate-DNA bacterial diet reduces the ROS levels in C. elegans while improving locomotion and longevity.

DNA phosphorothioation (PT) is widely distributed in the human gut microbiome. In this work, PT-diet effect on nematodes was studied with PT-bioengineering bacteria. We found that the ROS level decreased by about 20-50% and the age-related lipofuscin accumulation was reduced by 15-25%.

Evolutionary coupling-inspired engineering of alcohol dehydrogenase reveals the influence of distant sites on its catalytic efficiency for stereospecific synthesis of chiral alcohols.

Alcohol dehydrogenase (ADH) has attracted much attention due to its ability to catalyze the synthesis of important chiral alcohol pharmaceutical intermediates with high stereoselectivity. ADH protein engineering efforts have generally focused on reshaping the substrate-binding pocket. However, distant sites outside the pocket may also affect its activity, although the underlying molecular mechanism remains unclear.

Exploring the Molecular Basis of Substrate and Product Selectivities of Nocardicin Bifunctional Thioesterase.

D-amino acid introduction in peptides can enrich their biological activities and pharmacological properties as potential drugs. This achievement of stereochemical inversion usually owes to an epimerase or racemase. Interestingly, a unique bifunctional thioesterase (NocTE), which is incorporated in nonribosomal peptide synthetase (NRPS) NocA-NocB assembly line for the biosynthesis of monocyclic β-lactam antibiotic nocardicin A, can control the generation of D-products with high stereochemical purity.

Natural Syringyl Mediators Accelerate Laccase-Catalyzed β-O-4 Cleavage and Cα-Oxidation of a Guaiacyl Model Substrate via an Aggregation Mechanism.

Laccase-mediator systems (LMSs) have been intensively investigated in lignin degradation. Although only natural metabolites are available for fungal lignin degradation, mediator molecules from metabolites have received substantially less attention than artificial organic-synthetic compounds. It remains unclear which metabolites can accelerate laccase-catalyzed reactions and how those natural mediators influence lignin degradation.

Biosynthesis of Cyclophane-Containing Hirsutellone Family of Fungal Natural Products.

Hirsutellones are fungal natural products containing a macrocyclic cyclophane connected to a decahydrofluorene ring system. We have elucidated the biosynthetic pathway for pyrrocidine B () and GKK1032 A (). Two small hypothetical proteins, an oxidoreductase and a lipocalin-like protein, function cooperatively in the oxidative cyclization of the cyclophane, while an additional hypothetical protein in the pyrrocidine pathway catalyzes the specific cycloaddition to form the fused decahydrofluorene.