Molecular Modification Research Articles

Perspective on Agricultural Industrialization: Modification Strategies for Enhancing the Catalytic Capacity of Keratinase.

Keratinases is a special hydrolytic enzyme produced by microorganisms, which has the ability to catalyze the degradation of keratin. Currently, keratinases show great potential for application in many agricultural and industrial fields, such as biofermented feed, leather tanning, hair removal, and fertilizer production. However, these potentials have not yet been fully unleashed on an industrial scale. This paper reviews the sources, properties, and catalytic mechanisms of keratinases. Strategies for the molecular modification of keratinases are summarized and discussed in terms of improving the substrate specificity, thermostability, and pH tolerance of keratinases. The modification strategies are also enriched by the introduction of immobilized enzymes and directed evolution. In addition, the selection of modification strategies when facing specific industrial applications is discussed and prospects are provided. We believe that this review serves as a reference for the future quest to extend the application of keratinases from the laboratory to industry.

Computational Protein Design - Where it goes?

Proteins have been playing a critical role in the regulation of diverse biological processes related to human life. With the increasing demand, functional proteins are sparse in this immense sequence space. Therefore, protein design has become an important task in various fields, including medicine, food, energy, materials, etc. Directed evolution has recently led to significant achievements. Molecular modification of proteins through directed evolution technology has significantly advanced the fields of enzyme engineering, metabolic engineering, medicine, and beyond. However, it is impossible to identify desirable sequences from a large number of synthetic sequences alone. As a result, computational methods, including data-driven machine learning and physics-based molecular modeling, have been introduced to protein engineering to produce more functional proteins. This review focuses on recent advances in computational protein design, highlighting the applicability of different approaches as well as their limitations.

Improving Catalytic Efficiency of L-Arabinose Isomerase from Lactobacillus plantarum CY6 towards D-Galactose by Molecular Modification.

L-Arabinose isomerase (L-AI) has been commonly used as an efficient biocatalyst to produce D-tagatose via the isomerization of D-galactose. However, it remains a significant challenge to efficiently synthesize D-tagatose using the native (wild type) L-AI at an industrial scale. Hence, it is extremely urgent to redesign L-AI to improve its catalytic efficiency towards D-galactose, and herein a structure-based molecular modification of Lactobacillus plantarum CY6 L-AI (LpAI) was performed. Among the engineered LpAI, both F118M and F279I mutants showed an increased D-galactose isomerization activity. Particularly, the specific activity of double mutant F118M/F279I towards D-galactose was increased by 210.1% compared to that of the wild type LpAI (WT). Besides the catalytic activity, the substrate preference of F118M/F279I was also largely changed from L-arabinose to D-galactose. In the enzymatic production of D-tagatose, the yield and conversion ratio of F118M/F279I were increased by 81.2% and 79.6%, respectively, compared to that of WT. Furthermore, the D-tagatose production of whole cells expressing F118M/F279I displayed about 2-fold higher than that of WT cell. These results revealed that the designed site-directed mutagenesis is useful for improving the catalytic efficiency of LpAI towards D-galactose.

A coarse-grained Poisson–Nernst–Planck model for polyelectrolyte-modified nanofluidic diodes

Abstract Polyelectrolyte (PE)-modified synthetic nanopores have gained substantial research attention because molecular modification promotes ion gating and rectification. However, theoretical research on PE-modified nanopores is relatively scarce because it is difficult to establish an elaborate model for PEs, and it accordingly causes a trade-off between the computational resources needed and the accuracy. Therefore, an appropriate simulation method for the PE-modified nanopore is in high demand and still an enormous challenge. Herein, we report the simulation result of ion transport through PE-modified nanopores through a coarse-grained Poisson–Nernst–Planck method. By modeling the stuffed PE molecules as PE particles in a well-established continuum model, adequate computational accuracy can be achieved with acceptable computational cost. Based on this model, we study the ion transport in PE-modified nanofluidic diodes and reveal the PE around ion selectivity, which can explain the previous experimental works. Intriguingly, we found that the ion enrichment state in the nanofluidic diode is sensitive to steric hindrance and charge distribution near the heterojunction region. This property is critical for the ion transport behavior in the PE-modified nanofluidic diodes. Based on this property, we predict a heterogeneous structure that can realize the single molecule response to charged analytes. These findings provide insights for understanding the ion transport in PE-modified nanofluidic systems and bring inspiration to the design and optimization of high-performance chemical sensors.

A Review of Macrocycles Applied in Electrochemical Energy Storge and Conversion.

Macrocycles composed of diverse aromatic or nonaromatic structures, such as cyclodextrins (CDs), calixarenes (CAs), cucurbiturils (CBs), and pillararenes (PAs), have garnered significant attention due to their inherent advantages of possessing cavity structures, unique functional groups, and facile modification. Due to these distinctive features enabling them to facilitate ion insertion and extraction, form crosslinked porous structures, offer multiple redox-active sites, and engage in host-guest interactions, macrocycles have made huge contributions to electrochemical energy storage and conversion (EES/EEC). Here, we have summarized the recent advancements and challenges in the utilization of CDs, CAs, CBs, and PAs as well as other novel macrocycles applied in EES/EEC devices. The molecular structure, properties, and modification strategies are discussed along with the corresponding energy density, specific capacity, and cycling life properties in detail. Finally, crucial limitations and future research directions pertaining to these macrocycles in electrochemical energy storage and conversion are addressed. It is hoped that this review is able to inspire interest and enthusiasm in researchers to investigate macrocycles and promote their applications in EES/EEC.

Enhanced Efficiency and Stability of Wide‐Bandgap Perovskite Solar Cells Via Molecular Modification with Piperazinium Salt

AbstractWide‐bandgap (WBG) perovskite solar cell (PSC) plays a pivotal role as the top subcell in all‐perovskite tandem solar cells (TSCs), facilitating the absorption of high‐energy photons and affording a large open‐circuit voltage (VOC). Nonetheless, the stability and efficiency of WBG PSCs are constrained by light‐induced halide segregation and non‐radiative recombination losses. In this study, this work presents an approach of utilizing 2‐methylpiperazinium bromide (2‐MePBr) via interfacial engineering to realize high‐efficiency WBG (1.77 eV) PSCs. The C─NH─C functional group in 2‐MePBr, serving as an electron donor, can interact with under‐coordinated lead defects at the perovskite surface. Consequently, the treatment with 2‐MePBr mitigates interfacial non‐radiative recombination, enhances charge transport, inhibits ion migration, and thus delivers an improved power conversion efficiency (PCE) of 19.30% with a VOC of 1.29 V, and a fill factor of 83.08%. Notably, the WBG PSCs manifest enhanced stability, preserving 80% of the initial PCE after 337 h of continuous operation under 1 sun illumination at the maximum power point. Furthermore, the all‐perovskite TSCs based on this WBG subcell achieve a PCE of 27.47%, showing its promising application in perovskite‐based tandem solar cells.

Calculations of Stopping Power, Straggling and Range Projected of FeKr<sup>+</sup>

The present work consists of the simulation of the interaction of a beam of Kr<sup>+</sup> ions with a solid iron target by the software SRIM (Stopping and Range of Ions In Matter). Our goal is to calculate different parameters related to sputtering and ion implantation in a target, such as the spatial distribution of implanted ions, the distributions of electronic and nuclear energy losses as a function of penetration depth and sputtering efficiency, as well as the damage created inside the target. The sputter induced photon spectroscopy technique was used to study the luminescence spectra of the species sputtered from Iron powder, during 5 keV Kr<sup>+</sup> ions bombardment in vacuum better than 107 torr. The optical spectra recorded between 350 and 470 nm exhibit discrete lines which are attributed to neutral excited atoms of Iron (Fe). The experiments are also performed under 105 torr ultra-pure oxygen partial pressure. To ensure the maximum efficiency of molecular modification process, energy of irradiation was decided by using of SRIM software. Based on SRIM simulation of Iron ions interaction with Krypton, the areas on which effect of high energy ions will maximum were predicted. A comparative analysis of molecular before and after irradiation was carried out by scanning electron microscopy. The maximum change in Krypton morphology, in the form of destruction of walls, was appeared at a distance of about μm from the start point of Fe<sup>+</sup> ions track inside the molecular. A substantiation of reason of wall degradation in this area was proposed.

A superior near infrared fluorescent probe for revealing the relationship between peroxynitrite and Alzheimer's disease

The typical neurodegenerative Alzheimer's disease (AD) poses an increasing threat to human health as the population ages. Though increasing attention has been drawn for the etiology of AD over decades, regretfully, the exact pathogenesis of AD is not fully elucidated. The elevated levels of ROS are among the major pathological alterations in AD. Among them, peroxynitrite (ONOO-) exhibits a greater impact compared to other reactive oxygen species and plays an important role in AD, but the role ONOO- plays in AD progression remains unclear. In this work, the near-infrared (NIR) fluorophore (benzopyran derivative) was optimized by molecular skeleton modification, and a fluorophore DCM-Cl-OH with better spectral properties was obtained. On this basis, a NIR fluorescence probe DCM-Cl-P with excellent detection performance was obtained. Based on the high selectivity and fast response of the probe to ONOO-, DCM-Cl-P was used to visual detection of ONOO- in living cells and zebrafish, and further demonstrated the excessive accumulation of ONOO- in AD model mice. More importantly, through analysis of the correlation between ONOO- and amyloid-β protein (Aβ), ONOO- and the aggregation of Aβ were closely related and mutually reinforcing was demonstrated and ONOO- underwent significant changes in the early stage of the change of Aβ aggregation, indicating that ONOO- may serve as an early marker of AD. These findings have greatly promoted the research on the intrinsic relationship between ONOO- and AD, and provides a powerful means for pathological research of AD.

Construction of Dual-Active Sites by Interfacing with Polyhydroxy Fullerene on Nickel Hydroxide Surfaces to Promote CO2 Deep Photoreduction to CH4.

Due to the complex series of elementary steps involved, achieving deep photoreduction of CO2 to multielectron products such as CH4 remains a challenging task. Therefore, it is crucial to strategically design catalysts that facilitate the controlled formation of the crucial intermediates and provide precise control over the reaction pathway. Herein, we present a pioneering approach by employing polyhydroxy fullerene (PHF) molecules to modify the surface of Ni(OH)2, creating stable and effective synergistic sites to enhance the formation of CH4 from CO2 under light irradiation. As a result, the optimized PHF-modified Ni(OH)2 cocatalyst achieves a CH4 production rate of 455 μmol g-1 h-1, with an electron-based selectivity of approximately 60%. The combination of in situ characterizations and theoretical calculations reveals that the hydroxyl species on the surface of PHF can participate in stabilizing crucial intermediates and facilitating water activation, thereby altering the reaction pathway to form CH4 instead of CO. This study provides a novel approach to regulating the selectivity of photocatalytic CO2 reduction by exploring molecular surface modification through interfacing with functionalized carbon clusters.

Highly efficient biosynthesis of 3′-sialyllactose in engineered Escherichia coli

3′-Sialyllactose (3′-SL), one of the abundant and important sialylated human milk oligosaccharides, is an emerging food ingredient used in infant formula milk. We previously developed an efficient route for 3′-SL biosynthesis in metabolically engineered Escherichia coli BL21(DE3). Here, several promising α2,3-sialyltransferases were re-evaluated from the byproduct synthesis perspective. The α2,3-sialyltransferase from Neisseria meningitidis MC58 (NST) with great potential and the least byproducts was selected for subsequent molecular modification. Computer-assisted mutation sites combined with a semi-rational modification were designed and performed. A combination of two mutation sites (P120H/N113D) of NST was finally confirmed as the best one, which significantly improved 3′-SL biosynthesis, with extracellular titers of 24.5 g/L at 5-L fed-batch cultivations. When NST-P120H/N113D was additionally integrated into the genome of host EZAK (E. coli BL21(DE3)ΔlacZΔnanAΔnanT), the final strain generated 32.1 g/L of extracellular 3′-SL in a 5-L fed-batch fermentation. Overall, we underscored the existence of by-products and improved 3′-SL production by engineering N. meningitidis α2,3-sialyltransferase.

Response of lettuce seeds undergoing dormancy break and early senescence to plasma irradiation

This study reports the response of lettuce seeds undergoing dormancy breaking and early senescence to DBD plasma irradiation. A heat map of germination percentages at 12 h reveals that dormancy has broken at 39 days' storage, and that one minute of plasma irradiation enhances germination in dormant seeds. Plasma irradiation does not affect those seeds where dormancy has already broken. Early senescence via storage was estimated using ESR measurements and the molecular modification of quercetin. This study reveals that lettuce seed susceptibility to plasma irradiation depends on storage duration and conditions, with dormancy state as a critical variable modulating the impact of plasma irradiation.

A novel molecular structure design of liquid silicone rubber modified by ceramic precursors for high-performance flexible ablation

High ablation-resistant silicone rubber exhibits a significant role in the thermal protection of space vehicles. However, its limited by the low mechanical strength in practical heat protection applications. Herein, a novel molecular network structure is proposed, which links polycarboxysilane (PCS) rigid molecules onto polydimethylsiloxane molecular chains. The use of PCS rigid chains enhances the heat resistance while reducing the material's mass ablation rate. The addition of a small quantity of PCS (0.406 mmol) increases the tensile strength of the material by 10.4 % and augmentes the static ablation residual weight by 32.8 % compared with polydimethylsiloxane. Additionally, PCS molecular modification of polydimethylsiloxane is beneficial for maintaining the stability of the char layer after oxygen acetylene ablation, making the char layer denser, and improving the interface bonding between the ceramic layer, pyrolysis layer and matrix, ultimately improving the ablation performance of polydimethylsiloxane. This work provides a new approach for development of high-performance flexible ablative materials.

Research and application progress of microbial β-mannanases: a mini-review.

Mannan is a predominant constituent of cork hemicellulose and is widely distributed in various plant tissues. β-Mannanase is the principal mannan-degrading enzyme, which breaks down the β-1,4-linked mannosidic bonds in mannans in an endo-acting manner. Microorganisms are a valuable source of β-mannanase, which exhibits catalytic activity in a wide range of pH and temperature, making it highly versatile and applicable in pharmaceuticals, feed, paper pulping, biorefinery, and other industries. Here, the origin, classification, enzymatic properties, molecular modification, immobilization, and practical applications of microbial β-mannanases are reviewed, the future research directions for microbial β-mannanases are also outlined.

The Discovery of a Multidomain Mannanase Containing Dual-Catalytic Domain of the Same Activity: Biochemical Properties and Synergistic Effect.

In recent years, the wide application of mannan has driven the demand for the exploration of mannanase. As one of the main components of hemicellulose, mannan is an important polysaccharide that ruminants need to degrade and utilize, making rumen a rich source of mannanases. In this study, gene mining of mannanases was performed using bioinformatics, and potential dual-catalytic domain mannanases were heterologously expressed to analyze their properties. The hydrolysis pattern and enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). A dual-catalytic domain mannanase Man26/5 with the same function as the substrate was successfully mined from the genome of cattle rumen microbiota. Compared to the single-catalytic domain, its higher thermal stability (≤50 °C) and catalytic efficiency confirm the synergistic effect between the two catalytic domains. It exhibited a unique "crab-like" structure where the CBM located in the middle is responsible for binding, and the catalytic domains at both ends are responsible for cutting. The exploration of its multidomain structure and synergistic patterns could provide a reference for the artificial construction and molecular modification of enzymes.

Discovery of the small molecular inhibitors against sclerostin loop3 as potential anti-osteoporosis agents by structural based virtual screening and molecular design

Sclerostin is a secreted glycoprotein that expresses predominantly in osteocytes and inhibits bone formation by antagonizing the Wnt/β-catenin signaling pathway, and the loop3 region of sclerostin has recently discovered as a novel therapeutic target for bone anabolic treatment without increasing cardiovascular risk. Herein, we used a structural based virtual screening to search for small molecular inhibitors selectively targeting sclerostin loop3. A novel natural product hit ZINC4228235 (THFA) was identified as the sclerostin loop3-selective inhibitor with a Kd value of 42.43 nM against sclerostin loop3. The simplification and derivation of THFA using molecular modeling-guided modification allowed the discovery of an effective and loop3-selective small molecular inhibitor, compound (4-(3-acetamidoprop-1-yn-1-yl)benzoyl)glycine (AACA), with improved binding affinity (Kd = 15.4 nM) compared to the hit THFA. Further in-vitro experiment revealed that compound AACA could attenuate the suppressive effect of transfected sclerostin on Wnt signaling and bone formation. These results make AACA as a potential candidate for development of anti-osteoporosis agents without increasing cardiovascular risk.

Molecular modification of low-dissolution soy protein isolates by anionic xanthan gum, neutral guar gum, or neutral konjac glucomannan to improve the protein dissolution and stabilize fish oil emulsion

Herein, the effects of anionic xanthan gum (XG), neutral guar gum (GG), and neutral konjac glucomannan (KGM) on the dissolution, physicochemical properties, and emulsion stabilization ability of soy protein isolate (SPI)-polysaccharide conjugates were studied. The SPI-polysaccharide conjugates had better water dissolution than the insoluble SPI. Compared with SPI, SPI-polysaccharide conjugates had lower β-sheet (39.6 %–56.4 % vs. 47.3 %) and α-helix (13.0 %–13.2 % vs. 22.6 %) percentages, and higher β-turn (23.8 %–26.5 % vs. 11.0 %) percentages. The creaming stability of SPI-polysaccharide conjugate-stabilized fish oil-loaded emulsions mainly depended on polysaccharide type: SPI-XG (Creaming index: 0) > SPI-GG (Creaming index: 8.1 %–21.2 %) > SPI-KGM (18.1 %–40.4 %). In addition, it also depended on the SPI preparation concentrations, glycation times, and glycation pH. The modification by anionic XG induced no obvious emulsion creaming even after 14-day storage, which suggested that anionic polysaccharide might be the best polysaccharide to modify SPI for emulsion stabilization. This work provided useful information to modify insoluble proteins by polysaccharides for potential application.

Improvement of thermostability and catalytic efficiency of xylanase from Myceliophthora thermophilar by N-terminal and C-terminal truncation.

Extracting xylanase from thermophilic filamentous fungi is a feasible way to obtain xylanase with good thermal stability. The transcriptomic data of Myceliophthora thermophilic destructive ATCC42464 were differentially expressed and enriched. By comparing the sequences of Mtxylan2 and more than 10 xylanases, the N-terminal and C-terminal of Mtxylan2 were truncated, and three mutants 28N, 28C and 28NC were constructed. GH11 xylan Mtxylan2 was identified by transcriptomic analysis, the specific enzyme activity of Mtxylan2 was 104.67 U/mg, and the optimal temperature was 65°C. Molecular modification of Mtxylan2 showed that the catalytic activity of the mutants was enhanced. Among them, the catalytic activity of 28C was increased by 9.3 times, the optimal temperature was increased by 5°C, and the residual enzyme activity remained above 80% after 30 min at 50-65°C, indicating that redundant C-terminal truncation can improve the thermal stability and catalytic performance of GH11 xylanase.

De Novo Biosynthesis of Difucosyllactose by Artificial Pathway Construction and α1,3/4-Fucosyltransferase Rational Design in Escherichia coli.

Difucosyllactose (DFL) is a significant and plentiful oligosaccharide found in human breast milk. In this study, an artificial metabolic pathway of DFL was designed, focusing on the de novo biosynthesis of GDP-fucose from only glycerol. This was achieved by engineering Escherichia coli to endogenously overexpress genes manB, manC, gmd, and wcaG and heterologously overexpress a pair of fucosyltransferases to produce DFL from lactose. The introduction of α-1,2-fucosyltransferase from Helicobacter pylori (FucT2) along with α-1,3/4-fucosyltransferase (HP3/4FT) addressed rate-limiting challenges in enzymatic catalysis and allowed for highly efficient conversion of lactose into DFL. Based on these results, molecular modification of HP3/4FT was performed based on computer-assisted screening and structure-based rational design. The best-performing mutant, MH5, containing a combination of five mutated sites (F49K/Y131D/Y197N/E338D/R369A) of HP3/4FT was obtained. The best strain BLC09-58 harboring MH5 yielded 45.81 g/L of extracellular DFL in 5-L fed-batch cultures, which was the highest titer reported to date.

Single-cell transcriptomics reveals the intra-tumoral heterogeneity and SQSTM1/P62 and Wnt/β-catenin mediated epithelial to mesenchymal transition and stemness of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is characterized by the complex tumor microenvironment (TME) consisting of an abundance of mesenchymal stem cells (MSCs), which is known to facilitate epithelial-to-mesenchymal transition (EMT). The development of single-cell genomics is a powerful method for defining the intricate genetic landscapes of malignancies. In this study, we have employed single-cell RNA sequencing (scRNA-seq) to dissect the intra-tumoral heterogeneity and analyze the single-cell transcriptomic landscape to detect rare consequential cell subpopulations of significance. The scRNA-seq analysis of TNBC and Normal patient derived samples revealed that EMT markers and transcription factors were most upregulated in MSC population. Further, exploration of gene expression analysis among TNBC and Normal patient-derived MSCs ascertained the role of SQSTM1/P62 and Wnt/β-catenin in TNBC progression. Wnt/β-catenin and Wnt/PCP signaling pathways are prominent contributors of EMT, stemness, and cancer stem cell (CSC) properties of TNBC. SQSTM1/P62 cooperates with the components of the Wnt/PCP signaling pathway and is critically involved at the interface of autophagy and EMT.Moreover, siRNA targeting SQSTM1/P62 and inhibitor of Wnt/β-catenin (FH535) in conjunction was used to explore molecular modification of EMT and stemness markers. Although SQSTM1/P62 is not crucial for cell survival, cytotoxicity assay revealed synergistic interaction between the siRNA/inhibitor. Modulation of these important pathways helped in reduction of expression of genes and proteins contributing to CSC properties. Gene and protein expression analysis revealed the induction of EMT to MET. Moreover, co-treatment resulted in inactivation of non-canonical Wnt VANGL2-JNK signaling axis. The synergistic impact of inhibition of SQSTM1/P62 and Wnt/β-catenin signaling facilitates the development of a potential therapeutic regimen for TNBC.

Orientation of graphene nanosheets in suspension under an electric field: theoretical model and molecular dynamic simulations

Orientation regulation of nanoparticles in a suspension by an electric field is a powerful tool to tune its mechanical, thermal, optical, electrical properties etc. However, how molecular modification can affect the orientation of two-dimensional nanoparticles is still unclear. In this paper, the influence of molecular modification on the orientation of graphene nanosheets (GNS) in water was investigated through theoretical analyses and molecular dynamics (MD) simulations. Firstly, a new orientation angle model was proposed, which considers hydration effects, dipole moments and resistance torque. Then, MD simulations were conducted to investigate the effects of position, direction, type, and number of functional groups on the orientation of GNS. The trend observed in MD simulations is consistent with the proposed theoretical model. The results reveal that, under the combined influence of the dipole moment and hydration effects, the modification with hydrophilic functional groups can reduce the orientation angle from 21.31° to 8.34°, while the modification with hydrophobic functional groups increases it to 26.43°. Among the hydrophilic functional groups, orientation of hydroxylated GNS is the best. With an increase in the number of hydroxyl groups, orientation angle is decreased from 12.61° to 8.34°. This work can provide valuable guidance for the design of high-performance suspensions and composites, such as thermal smart materials with adjustable thermal conductivity and intelligent devices with tailored capabilities.