Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a.

DNA nanostructure-based signal amplifiers offer new tools for imaging intracellular miRNA. However, the inadequate kinetics and susceptibility to enzymatic hydrolysis of these amplifiers, combined with a deficient cofactor concentration within the intracellular environment, significantly undermine their operational efficiency. In this study, we address these challenges by encapsulating a localized target strand displacement assembly (L-SD) and a toehold-exchange endogenous-powered component (R-mRNA) within a framework nucleic acid (FNA) structure─20 bp cubic DNA nanocage (termed RL-cube). This design enables the construction of an endogenous-powered and spatial-confinement DNA nanomachine for ratiometric fluorescence imaging of intracellular miRNA Let-7a. The R-mRNA is designed to be specifically triggered by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), an abundant cellular enzyme, and concurrently releases a component that can recycle the target Let-7a. Meanwhile, L-SD reacts with Let-7a to release a stem-loop beacon, generating a FRET signal. The spatial confinement provided by the framework, combined with the ample intracellular supply of GAPDH, imparts remarkable sensitivity (7.57 pM), selectivity, stability, biocompatibility, and attractive dynamic performance (2240-fold local concentration, approximately four times reaction rate, and a response time of approximately 7 min) to the nanomachine-based biosensor. Consequently, this study introduces a potent sensing approach for detecting nucleic acid biomarkers with significant potential for application in clinical diagnostics and therapeutics.

"Blade of Polarized Water Molecule" Is the Key to Hydrolase Catalysis Regulation.

Hydrolysis catalyzed by aspartic proteases is a crucial reaction in many biological processes. However, anchoring water molecules and unifying multiple catalytic pathways remain significant challenges. Consequently, molecular design often compromises by focusing on enhancing substrate specificity. Using our self-developed polarizable point charge (PPC) force field, we determined the significant role of polarization in the hydrolase of pepsin for the first time. To be stably anchored in the active site, the water should be intensely polarized with a charge higher than -0.94e. Induced by this polarization, the pepsin was shown to support three general base/general acid pathways, with a preference for the gemdiol-intermediate-based pathway. Consequently, we proposed the "Blade of Polarized Water Molecule" model for rational enzyme design, highlighting that the polarization of both the attacking water and the attacked carbonyl is crucial for enhancing hydrolysis. Mutants D290Q and S172P showed activity enhancements of 191.23% and 324.70%, respectively. The improved polarization of water, carbonyl, and relevant nucleophilic attack distances in the mutants reaffirmed the crucial role of polarization in improving hydrolysis. This study provides a new perspective on hydrolase analysis and modification.

Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation.

The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.

Framework Nucleic Acid-Based Spatial-Confinement Amplifier for miRNA Imaging in Living Cells.

Real-time in situ monitoring of miRNAs in living cells is often appealed to signal amplifiers to tackle their low abundance challenges. However, the poor kinetics of amplifiers and potential interferences from the complex intracellular environment hamper its widespread applications in vivo. Herein, we report a framework nucleic acid (FNA)-based nonenzymatic spatial-confinement amplifier for rapid and reliable intracellular miRNA imaging. The amplifier consists of a localized catalytic hairpin assembly (L-CHA) reactor encapsulated in the inner cavity of an FNA (a 20 bp cube). The L-CHA reactor is certainly confined to the internal frame by integrating two probes (H1 and H2) of the L-CHA within a DNA strand and harnessing it to the opposite angles of the cube. We find that the stability of the amplifier is remarkably improved due to the protection of the FNA. More importantly, the spatial-confinement effect of the FNA can endow the confined L-CHA amplifier with enhanced local concentrations of reagents (5000-fold), thereby accelerating the reaction rate and improving the dynamic performance (up to 14.34-fold). With these advantages, the proposed amplifier can enable accurate and effective monitoring of miRNA expression levels in living cells and poses great potential in medical diagnostics and biomedical research.

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis.

COVID-19 has emerged as the most serious international pandemic in early 2020 and the lack of comprehensive knowledge in the recognition and transmission mechanisms of this virus hinders the development of suitable therapeutic strategies. The specific recognition during the binding of the spike glycoprotein (S protein) of coronavirus to the angiotensin-converting enzyme 2 (ACE2) in the host cell is widely considered the first step of infection. However, detailed insights on the underlying mechanism of dynamic recognition and binding of these two proteins remain unknown. In this work, molecular dynamics simulation and binding free energy calculation were carried out to systematically compare and analyze the receptor-binding domain (RBD) of six coronavirus' S proteins. We found that affinity and stability of the RBD from SARS-CoV-2 under the binding state with ACE2 are stronger than those of other coronaviruses. The solvent-accessible surface area (SASA) and binding free energy of different RBD subunits indicate an "anchor-locker" recognition mechanism involved in the binding of the S protein to ACE2. Loop 2 (Y473-F490) acts as an anchor for ACE2 recognition, and Loop 3 (G496-V503) locks ACE2 at the other nonanchoring end. Then, the charged or long-chain residues in the ß-sheet 1 (N450-F456) region reinforce this binding. The proposed binding mechanism was supported by umbrella sampling simulation of the dissociation process. The current computational study provides important theoretical insights for the development of new vaccines against SARS-CoV-2.

Integrating Target-Triggered Aptamer-Capped HRP@Metal-Organic Frameworks with a Colorimeter Readout for On-Site Sensitive Detection of Antibiotics.

Colorimetric analytical strategies exhibit great promise in developing on-site detection methods for antibiotics, while substantial recent research efforts remain problematic due to dissatisfactory sensitivity. Taking this into account, we develop a novel colorimetric sensor for in-field detection of antibiotics by using aptamer (Apt)-capped and horseradish peroxidise (HRP)-embedded zeolitic metal azolate framework-7 (MAF-7) (Apt/HRP@MAF-7) as target recognition and signal transduction, respectively. With the substrate 3,3',5,5'-tetramethylbenzidine (TMB)-impregnated chip attached on the lid, the assay can be conveniently operated in a tube and reliably quantified by a handheld colorimeter. Hydrophilic MAF-7 can not only prevent HRP aggregation but also enhance HRP activity, which would benefit its detection sensitivity. Besides, the catalytic activity of HRP@MAF-7 can be sealed through assembling with Apt and controllably released based on the bioresponsivity via forming target-Apt complexes. Consequently, a significant color signal can be observed owing to the oxidation of colorless TMB to its blue-green oxidized form oxTMB. As a proof-of-concept, portable detection of streptomycin was favorably achieved with excellent sensitivity, which is superior to most reported methods and commercial kits. The developed strategy affords a new design pattern for developing on-site antibiotics assays and immensely extends the application of enzyme embedded metal-organic framework composites.

Cloning, expression and structural stability of a cold-adapted ß-galactosidase from Rahnella sp. R3.

A novel gene was isolated for the first time from a psychrophilic gram-negative bacterium Rahnella sp. R3. The gene encoded a cold-adapted ß-galactosidase (R-ß-Gal). Recombinant R-ß-Gal was expressed in Escherichia coli BL21 (DE3), purified and characterized. R-ß-gal belongs to the glycosyl hydrolase family 42. Circular dichroism spectrometry of the structural stability of R-ß-Gal with respect to temperature indicated that the secondary structures of the enzyme were stable to 45°C. In solution, the enzyme was a homo-trimer and was active at temperatures as low as 4°C. The enzyme did not require the presence of metal ions to be active, but Mg(2+), Mn(2+), and Ca(2+) enhanced its activity slightly, whereas Fe(3+), Zn(2+) and Al(3+) appeared to inactive it. The purified enzyme displayed K(m) values of 6.5 mM for ONPG and 2.2mM for lactose at 4°C. These values were lower than the corresponding K(m)s reported for other cold-adapted ß-Gals.

Wireless Bioelectronics for In Vivo Pressure Monitoring with Mechanically-Compliant Hydrogel Biointerfaces.

Recent electronics-tissues biointefacing technology has offered unprecedented opportunities for long-term disease diagnosis and treatment. It remains a grand challenge to robustly anchor the pressure sensing bioelectronics onto specific organs, since the periodically-varying stress generated by normal biological processes may pose high risk of interfacial failures. Here, a general yet reliable approach is reported to achieve the robust hydrogel interface between wireless pressure sensor and biological tissues/organs, featuring highly desirable mechanical compliance and swelling resistance, despite the direct contact with biofluids and dynamic conditions. The sensor is operated wirelessly through inductive coupling, characterizing minimal hysteresis, fast response times, excellent stability, and robustness, thus allowing for easy handling and eliminating the necessity for surgical extraction after a functional period. The operation of the wireless sensor has been demonstrated with a custom-made pressure sensing model and in vivo intracranial pressure monitoring in rats. This technology may be advantageous in real-time post-operative monitoring of various biological inner pressures after the reconstructive surgery, thus guaranteeing the timely treatment of lethal diseases.

Self-Growing Hydrogel Bioadhesives for Chronic Wound Management.

Hydrogel bioadhesives have emerged as a promising alternative to wound dressings for chronic wound management. However, many existing bioadhesives do not meet the functional requirements for efficient wound management through dynamically mechanical modulation, due to the reduced wound contractibility, frequent wound recurrence, incapability to actively adapt to external microenvironment variation, especially for those gradually-expanded chronic wounds. Here, a self-growing hydrogel bioadhesive (sGHB) patch that exhibits instant adhesion to biological tissues but also a gradual increase in mechanical strength and interfacial adhesive strength within a 120-h application is presented. The gradually increased mechanics of the sGHB patch could effectively mitigate the stress concentration at the wound edge, and also resist the wound expansion at various stages, thus mechanically contracting the chronic wounds in a programmable manner. The self-growing hydrogel patch demonstrated enhanced wound healing efficacy in a mouse diabetic wound model, by regulating the inflammatory response, promoting the faster re-epithelialization and angiogenesis through mechanical modulation. Such kind of self-growing hydrogel bioadhesives have potential clinical utility for a variety of wound management where dynamic mechanical modulation is indispensable.

Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides.

Chronic diseases, such as hypertension, cause great harm to human health. Conventional drugs have promising therapeutic effects, but also cause significant side effects. Food-sourced angiotensin-converting enzyme (ACE) inhibitory peptides are an excellent therapeutic alternative to pharmaceuticals, as they have fewer side effects. However, there is no systematic and effective screening method for ACE inhibitory peptides, and the lack of understanding of the sequence characteristics and molecular mechanism of these inhibitory peptides poses a major obstacle to the development of ACE inhibitory peptides. Through systematically calculating the binding effects of 160,000 tetrapeptides with ACE by molecular docking, we found that peptides with Tyr, Phe, His, Arg, and especially Trp were the characteristic amino acids of ACE inhibitory peptides. The tetrapeptides of WWNW, WRQF, WFRV, YYWK, WWDW, and WWTY rank in the top 10 peptides exhibiting significantly high ACE inhibiting behaviors, with IC50 values between 19.98 ± 8.19 µM and 36.76 ± 1.32 µM. Salt bridges, π-π stacking, π-cations, and hydrogen bonds contributed to the high binding characteristics of the inhibitors and ACE. Introducing eight Trp into rabbit skeletal muscle protein (no Trp in wide sequence) endowed the protein with a more than 90% ACE inhibition rate, further suggesting that meat with a high content of Trp could have potential utility in hypertension regulation. This study provides a clear direction for the development and screening of ACE inhibitory peptides.

A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction.

Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-ß1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.

Recent advances on applications and biotechnological production of D-psicose.

D-Psicose is a hexoketose monosaccharide sweetener, which is a C-3 epimer of D-fructose and is rarely found in nature. It has 70 % relative sweetness but 0.3 % energy of sucrose, and is suggested as an ideal sucrose substitute for food products. It shows important physiological functions, such as blood glucose suppressive effect, reactive oxygen species scavenging activity, and neuroprotective effect. It also improves the gelling behavior and produces good flavor during food process. This article presents a review of recent studies on the properties, physiological functions, and food application of D-psicose. In addition, the biochemical properties of D-tagatose 3-epimerase family enzymes and the D-psicose-producing enzyme are compared, and the biotechnological production of D-psicose from D-fructose is reviewed.

Umami polypeptide detection system targeting the human T1R1 receptor and its taste-presenting mechanism.

Umami is one of five basic tastes, the elucidation of its mechanism by the study of the interaction between umami polypeptides and hT1R1 umami receptors is of great significance. However, research on umami peptides targeting human T1R1 receptors is lacking, and the molecular mechanism remains elusive. Here, we successfully established a system to detect umami peptides targeting human T1R1 receptors by fluorescence spectroscopy, Surface Plasmon Resonance (SPR) and computational simulation. The sensory evaluation, calculated Kd value, and experimental affinity results between the four selected umami peptides (GRVSNCAA, KGDEESLA, KGGGGP, and TGDPEK) and glutamate were tested using this system, and all matched well. The maximum Ka value of GRVSNCAA was 479.55 M-1, and the minimum affinity of TGDPEK was 2.67 M-1. Computational simulations showed that the different peptide binding sites in the hT1R1 binding pocket occupied due to conformational changes are important factors for different taste thresholds, and that peptide hydrophobicity plays an important role in regulating affinity. Thus, our study enables rapid screening of high-intensity umami peptides and the development of T1R1 receptor-based umami detection sensors.

Framework nucleic acid programmed combinatorial delivery nanocarriers for parallel and multiplexed analysis.

Herein we report a framework nucleic acid programmed strategy to develop nanocarriers to precisely and independently package multiple homo- and heterogeneous cargos in vitro and in vivo, thereby enabling multiplexed analysis of aptamer-ligand complexes to distinguish normal people and patients with prostate enlargement via simple serum tests, as well as favorable imaging and discrimination of MCF-7, PC-3 and A549 cancer cells and normal QSG-7701 cells.

Enhancement of the Isomerization Activity and Thermostability of Cellobiose 2-Epimerase from Caldicellulosiruptor saccharolyticus by Exchange of a Flexible Loop.

Cellobiose 2-epimerase (CE) offers a promising enzymatic approach to produce lactulose. However, its application is limited by the unsatisfactory isomerization activity and thermostability. Our study attempted to optimize the catalytic performances of CEs by flexible loop exchange, for which four mutants were constructed using CsCE (CE from Caldicellulosiruptor saccharolyticus) as a template. As a result, all mutants maintained the same catalytic directions as the templates. Mutant RmC displayed a 2.2- and 1.34-fold increase in the isomerization activity and catalytic efficiency, respectively. According to the results of molecular dynamics (MD) simulations, it was revealed that the loop exchange in RmC enlarged the entrance of the active site for substrate binding and benefited proton transfer involved in the isomerization process. Besides, the t1/2 of mutant StC at 70 °C was increased from 29.07 to 38.29 h, owing to the abundance of rigid residues (proline) within the flexible loop of StC. Our work demonstrated that the isomerization activity and thermostability of CEs were closely related to the flexible loop surrounding the active site, which provides a new perspective to engineer CEs for higher lactulose production.

Insight into the potential factors influencing the catalytic direction in cellobiose 2-epimerase by crystallization and mutagenesis.

Cellobiose 2-epimerase (CE) is commonly recognized as an epimerase as most CEs mainly exhibit an epimerization activity towards disaccharides. In recent years, several CEs have been found to possess bifunctional epimerization and isomerization activities. They can convert lactose into lactulose, a high-value disaccharide that is widely used in the food and pharmaceutical industries. However, the factors that determine the catalytic direction in CEs are still not clear. In this study, the crystal structures of three newly discovered CEs, CsCE (a bifunctional CE from Caldicellulosiruptor saccharolyticus), StCE (a bifunctional CE from Spirochaeta thermophila DSM 6578) and BtCE (a monofunctional CE from Bacillus thermoamylovorans B4166), were determined at 1.54, 2.05 and 1.80 Šresolution, respectively, in order to search for structural clues to their monofunctional/bifunctional properties. A comparative analysis of the hydrogen-bond networks in the active pockets of diverse CEs, YihS and mannose isomerase suggested that the histidine corresponding to His188 in CsCE is uniquely required to catalyse isomerization. By alignment of the apo and ligand-bound structures of diverse CEs, it was found that bifunctional CEs tend to have more flexible loops and a larger entrance around the active site, and that the flexible loop 148-181 in CsCE displays obvious conformational changes during ligand binding. It was speculated that the reconstructed molecular interactions of the flexible loop during ligand binding helped to motivate the ligands to stretch in a manner beneficial for isomerization. Further site-directed mutagenesis analysis of the flexible loop in CsCE indicated that the residue composition of the flexible loop did not greatly impact epimerization but affects isomerization. In particular, V177D and I178D mutants showed a 50% and 80% increase in isomerization activity over the wild type. This study provides new information about the structural characteristics involved in the catalytic properties of CEs, which can be used to guide future molecular modifications.

Phenylboronic Acid Functionalized Adsorbents for Selective and Reversible Adsorption of Lactulose from Syrup Mixtures.

Boronate affinity materials have been widely used for enrichment of cis-diol molecules. In this work, phenylboronic acid functionalized adsorbents were prepared via a simple and efficient procedure grafting phenylboronic acid groups onto amino macroporous resins. Elemental analysis has confirmed the successful functionalization of AR-1M and AR-2M with approximately 2.17% and 0.73% weight percentage of boron. Comparatively, AR-1M possessed higher lactulose adsorption capacity ( qe-Lu, 84.78 ± 0.95 mg/g dry resin) under neutral conditions (pH = 7), while the introduced glutaraldehyde spacer arms on AR-2M resulted in excellent adsorption selectivity (α ≈ 23), high adsorption efficiency (π ≈ 22%), and fast adsorption/desorption rate. The purity of lactulose (PuDLu) through pH-driven adsorption (pH 7-8) and desorption (pH 1.5) can be effectively improved depending on the ratio of lactulose to lactose. When lactulose/lactose ≥ 1:1, PuDLu ≈ 95% was achieved. No significant drop in qe-Lu (>90%) was observed after ten-consecutive repeats. Results demonstrated that the newly developed method may achieve satisfactory performance in lactulose purification.

Preparation and Characterization of Sugar-Assisted Cross-Linked Enzyme Aggregates (CLEAs) of Recombinant Cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus ( CsCE).

High-efficiency lactulose-producing enzyme of Caldicellulosiruptor saccharolyticus cellobiose 2-epimerase (WT- CsCE) was immobilized in the form of cross-linked enzyme aggregates (CLEAs). Conditions for enzyme aggregation and cross-linking were optimized, and a sugar-assisted strategy with less damage to enzyme secondary structures was developed to improve the activity yield of CLEAs up to approximately 65%. The resulting CLEAs with multiple-layer network structures exhibited an enlarged optimal temperature range (70-80 °C) and maintained higher activity at 50-90 °C. Besides, CLEAs retained more than 95% of their initial activity after 10 successive batches at 60 °C, demonstrating superior reusability. Moreover, CLEAs displayed an equivalent or higher catalytic ability to free WT- CsCE in lactulose biosynthesis, and the final sugar ratios were similar, lactulose 58.8-61.7%, epilactose 9.3-10.2%, and lactose 27.8-30%, with a constant isomerization selectivity of 0.84-0.87 regardless of enzymes used and temperature applied. The proposed strategy is the first trial for enzymatic synthesis of lactulose catalyzed by CLEAs of WT- CsCE.