Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants.

Human ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins and perform diverse functions. Many of them are associated with multidrug resistance that often results in cancer treatment with poor outcomes. Here, we present the structural bioinformatics study of six human ABC membrane transporters with experimentally determined cryo-electron microscopy (CryoEM) structures including ABCB7, ABCC8, ABCD1, ABCD4, ABCG1, ABCG5, and their AlphaFold2-predicted water-soluble QTY variants. In the native structures, there are hydrophobic amino acids such as leucine (L), isoleucine (I), valine (V), and phenylalanine (F) in the transmembrane alpha helices. These hydrophobic amino acids are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y). Therefore, these QTY variants become water soluble. We also present the superposed structures of native ABC transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with root mean square deviations between 1.064 and 3.413 Å despite significant (41.90-54.33%) changes to the protein sequence of the transmembrane domains. We also show the differences in hydrophobicity patches between the native ABC transporters and their QTY variants. We explain the rationale behind why the QTY membrane protein variants become water soluble. Our structural bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices and will likely further stimulate designs of water-soluble multispan transmembrane proteins and other aggregated proteins. The water-soluble ABC transporters may be useful as soluble antigens to generate therapeutic monoclonal antibodies for combating multidrug resistance in clinics.

Genome-Wide Identification of the WRKY Gene Family and Functional Characterization of CpWRKY5 in Cucurbita pepo.

The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I-III), with Group II further divided into five subgroups (IIa-IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.

Advancements and challenges of digital twins in industry.

Digital twins, which are considered an effective approach to realize the fusion between virtual and physical spaces, have attracted a substantial amount of attention in the past decade. With their rapid development in recent years, digital twins have been applied in various fields, particularly in industry. However, there are still some gaps to be filled and some limitations to be addressed. Here we provide a brief overview of digital twin advancements in industry and highlight the main pitfalls to avoid and challenges to overcome, to improve the maturity of digital twins and facilitate large-scale industrial applications in the future.

Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups.

Lactobacillus kefir alcohol dehydrogenase (LkADH) and ketoreductase from Chryseobacterium sp. CA49 (ChKRED12) exhibit different chemoselectivity and stereoselectivity toward a substrate with both keto and aldehyde carbonyl groups. LkADH selectively reduces the keto carbonyl group while retaining the aldehyde carbonyl group, producing optically pure R-alcohols. In contrast, ChKRED12 selectively reduces the aldehyde group and exhibits low reactivity toward ketone carbonyls. This study investigated the structural basis for these differences and the role of specific residues in the active site. Molecular dynamics (MD) simulations and quantum chemical calculations were used to investigate the interactions between the substrate and the enzymes and the essential cause of this phenomenon. The present study has revealed that LkADH and ChKRED12 exhibit significant differences in the structure of their respective active pockets, which is a crucial determinant of their distinct chemoselectivity toward the same substrate. Moreover, residues N89, N113, and E144 within LkADH as well as Q151 and D190 within ChKRED12 have been identified as key contributors to substrate stabilization within the active pocket through electrostatic interactions and van der Waals forces, followed by hydride transfer utilizing the coenzyme NADPH. Furthermore, the enantioselectivity mechanism of LkADH has been elucidated using quantum chemical methods. Overall, these findings not only provide fundamental insights into the underlying reasons for the observed differences in selectivity but also offer a detailed mechanistic understanding of the catalytic reaction.

Bioinspired Artificial Intelligence Applications 2023.

With rapid development of Artificial Intelligence (AI), researchers have found many bioinspired AI applications, such as bioinspired images and speech processing, which can increase accuracy [...].

A robust yeast chassis: comprehensive characterization of a fast-growing Saccharomyces cerevisiae.

Robust chassis are critical to facilitate advances in synthetic biology. This study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast growth rate is, in part, due to the efficient electron transport chain and key growth factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we used it to construct l-lactic acid producers for high lactate production. The development of genetically malleable yeast strains that grow faster than currently used strains may significantly enhance the uses of S. cerevisiae in biotechnology.IMPORTANCEYeast is known as an outstanding starting strain for constructing microbial cell factories. However, its growth rate restricts its application. A yeast strain XP, which grows fast in high concentrations of sugar and acidic environments, is revealed to demonstrate the potential in industrial applications. A toolbox was also built for its genetic manipulation including gene insertion, deletion, and ploidy transformation. The knowledge of its metabolism, which could guide the designing of genetic experiments, was generated with multi-omics analyses. This novel strain along with its toolbox was then tested by constructing an l-lactic acid efficient producer, which is conducive to the development of degradable plastics. This study highlights the remarkable competence of nonconventional yeast for applications in biotechnology.

Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy.

G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response.

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

Metabolic engineering of Geobacillus thermoglucosidasius for polymer-grade lactic acid production at high temperature.

The production and application of biodegradable polylactic acid are still severely hindered by the cost of its polymer-grade lactic acid monomers. High-temperature biomanufacturing has emerged as an increasingly attractive approach to enable low-cost and high-efficiency bulk chemical production. In this study, thermophilic Geobacillus thermoglucosidasius was reprogrammed to obtain optically pure l-lactic acid- and d-lactic acid-producing strains, G. thermoglucosidasius GTD17 and GTD7, by using rational metabolic engineering strategies including pathway construction, by-product elimination, and production enhancing. Moreover, semi-rational adaptive evolution was carried out to further improve their lactic acid synthesis performance. The final strains GTD17-55 and GTD7-144 produce 151.1 g/L of l-lactic acid and 153.1 g/L of d-lactic acid at 60 °C, respectively. In consideration of the high temperature, productive performance of these strains is superior compared to the state-of-the-art industrial strains. This study lays the foundation for the low-cost and efficient production of biodegradable plastic polylactic acid.

pH-Responsive Protein Conformation Transistor.

Analogous to electronic transistors, transistor-like responsive materials undergo sharp structural transitions in response to a very narrow range of microenvironment signals. This kind of material is typically limited to synthetic polymer-derived nanoscale assembly or disassembly and has profound implications for modern high-tech applications. Herein, we evolve this system from synthetic polymers to biopolymers and extend the corresponding assembly scale from the nanoscale to meso/macro-scale. We develop unique protein nanocrystals with core-shell structures through a two-step nucleation process. The protein nanocrystals exhibit exceptional transistor-like pH-responsive mesoscale assembly through the formation of inter-particle ß-sheet linkers. This allows ultrasensitive cross-linking behavior, such as self-coacervation at a water/water interface, ultrafast gelation in seconds, and ultrasensitive swelling for detection of basic vapors at extremely low concentrations. This breakthrough has great promise for broader applications such as drug encapsulation and delivery, biosensing, cytomimetic materials, and microfluidic chemistry.

QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study.

Therapeutic monoclonal antibodies are the most rapidly growing class of molecular medicine, and they are beneficial to the treatment of a broad spectrum of human diseases. However, the aggregation of antibodies during the process of manufacture, distribution, and storage poses significant challenges, potentially compromising efficacy and inducing adverse immune responses. We previously conceived a QTY (glutamine, threonine, tyrosine) code, a simple tool for enhancing protein water-solubility by systematically pairwise replacing hydrophobic residues L (leucine), V (valine)/I (isoleucine), and F (phenylalanine). The QTY code offers a promising alternative to traditional methods of controlling aggregation in integral transmembrane proteins. In this study, we designed variants of four antibodies applying the QTY code, changing only the ß-sheets. Through the structure-based aggregation analysis, we found that these QTY antibody variants demonstrated significantly decreased aggregation propensity compared to their wild-type counter parts. Our results of molecular dynamics simulations showed that the design by QTY code is capable of maintaining the antigen-binding affinity and structural stability. Our structural informatic and computational study suggests that the QTY code offers a significant potential in mitigating antibody aggregation.

Correction: Interface-mediated protein aggregation.

Correction for 'Interface-mediated protein aggregation' by Fei Tao et al., Chem. Commun., 2023, https://doi.org/10.1039/d3cc04311h.

High-Performance Production of N-Acetyl-d-Neuraminic Acid with Whole Cells of Fast-Growing Vibrio natriegens via a Thermal Strategy.

High performance is the core objective that biotechnologists pursue, of which low efficiency, low titer, and side products are the chief obstacles. Here, a thermal strategy is proposed for simultaneously addressing the obstacles of whole-cell catalysis that is widely applied in the food industry. The strategy, by combining fast-growing Vibrio natriegens, thermophilic enzymes, and high-temperature whole-cell catalysis, was successfully applied for the high-performance production of N-acetyl-d-neuraminic acid (Neu5Ac) that plays essential roles in the fields of food (infant formulas), healthcare, and medicine. By using this strategy, we realized the highest Neu5Ac titer and productivity of 126.1 g/L and up to 71.6 g/(L h), respectively, 7.2-fold higher than the productivity of Escherichia coli. The major byproduct acetic acid was also eliminated via quenching complex metabolic side reactions enabled by temperature elevation. This study offers a broadly applicable strategy for producing chemicals relevant to the food industry, providing insights for its future development.

Screening and Characterization of an α-Amylase Inhibitor from Carya cathayensis Sarg. Peel.

Inhibiting α-amylase can lower postprandial blood glucose levels and delay glucose absorption, offering an effective approach for the development of antidiabetic diets. In this study, an active constituent with inhibitory activity against α-amylase was isolated and purified by bioassay-guided fractionation from Carya cathayensis Sarg. peel (CCSP). The active constituent was identified by NMR and Q-Exactive Orbitrap Mass Spectrometry as 5-O-p-coumaroylquinic acid (5-CQA). 5-CQA possessed strong inhibitory activity against α-amylase, with an IC50 value of 69.39 µM. In addition, the results of the kinetic study indicated that 5-CQA was a potent, reversible, noncompetitive inhibitor against α-amylase. The findings indicate that 5-CQA derived from CCSP has potential as a novel inhibitor against α-amylase, which can help mitigate postprandial blood sugar spikes, making it suitable for inclusion in antidiabetic diets.

Genomic Insights on the Carbon-Negative Workhorse: Systematical Comparative Genomic Analysis on 56 Synechococcus Strains.

Synechococcus, a type of ancient photosynthetic cyanobacteria, is crucial in modern carbon-negative synthetic biology due to its potential for producing bioenergy and high-value products. With its high biomass, fast growth rate, and established genetic manipulation tools, Synechococcus has become a research focus in recent years. Abundant germplasm resources have been accumulated from various habitats, including temperature and salinity conditions relevant to industrialization. In this study, a comprehensive analysis of complete genomes of the 56 Synechococcus strains currently available in public databases was performed, clarifying genetic relationships, the adaptability of Synechococcus to the environment, and its reflection at the genomic level. This was carried out via pan-genome analysis and a detailed comparison of the functional gene groups. The results revealed an open-genome pattern, with 275 core genes and variable genome sizes within these strains. The KEGG annotation and orthology composition comparisons unveiled that the cold and thermophile strains have 32 and 84 unique KO functional units in their shared core gene functional units, respectively. Each KO functional unit reflects unique gene families and pathways. In terms of salt tolerance and comparative genomics, there are 65 unique KO functional units in freshwater-adapted strains and 154 in strictly marine strains. By delving into these aspects, our understanding of the metabolic potential of Synechococcus was deepened, promoting the development and industrial application of cyanobacterial biotechnology.

Dynamic Dimerization of Chemokine Receptors and Potential Inhibitory Role of Their Truncated Isoforms Revealed through Combinatorial Prediction.

Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the oligomerization patterns of many chemokine receptors remain poorly understood. Furthermore, several chemokine receptors have highly truncated isoforms whose functional role is not yet clear. Here, we computationally show homo- and heterodimerization patterns of four human chemokine receptors, namely CXCR2, CXCR7, CCR2, and CCR7, along with their interaction patterns with their respective truncated isoforms. By combining the neural network-based AlphaFold2 and physics-based protein-protein docking tool ClusPro, we predicted 15 groups of complex structures and assessed the binding affinities in the context of atomistic molecular dynamics simulations. Our results are in agreement with previous experimental observations and support the dynamic and diverse nature of chemokine receptor dimerization, suggesting possible patterns of higher-order oligomerization. Additionally, we uncover the strong potential of truncated isoforms to block homo- and heterodimerization of chemokine receptors, also in a dynamic manner. Our study provides insights into the dimerization patterns of chemokine receptors and the functional significance of their truncated isoforms.

Interface-mediated protein aggregation.

The aggregation of proteins at interfaces has significant roles and can also lead to dysfunction of different physiological processes. The interfacial effects on the assembly and aggregation of biopolymers are not only crucial for a comprehensive understanding of protein biological functions, but also hold great potential for advancing the state-of-the-art applications of biopolymer materials. Recently, there has been remarkable progress in a collaborative context, as we strive to gain control over complex interfacial assembly structures of biopolymers. These biopolymer structures range from the nanoscale to mesoscale and even macroscale, and are attained through the rational design of interactions between biological building blocks and surfaces/interfaces. This review spotlights the recent advancements in interface-mediated assembly and properties of biopolymer materials. Initially, we introduce the solid-liquid interface (SIL)-mediated biopolymer assembly that includes the inorganic crystalline template effect and protein self-adoptive deposition through phase transition. Next, we display the advancement of biopolymer assembly instigated by the air-water interface (AWI) that acts as an energy conversion station. Lastly, we discuss succinctly the assembly of biopolymers at the liquid-liquid interface (LLI) along with their applications. It is our hope that this overview will stimulate the integration and progression of the science of interfacial assembled biopolymer materials and surfaces/interfaces.

Lutein-Rich Beverage Alleviates Visual Fatigue in the Hyperglycemia Model of Sprague-Dawley Rats.

Asthenopia is a syndrome based on the symptoms of eye discomfort that has become a chronic disease that interferes with and harms people's physical and mental health. Lutein is an internationally recognized "eye nutrient", and studies have shown that it can protect the retina and relieve visual fatigue. In this study, lutein was extracted from marigold (Tagetes erecta L.) and saponified. The purified lutein concentration measured by HPLC was 50.12 mg/100 g. Then, purified lutein was modified to be water-soluble by nanoscale modification and microencapsulation technology. Water-soluble lutein was then mixed with a leaching solution of Chinese wolfberry and chrysanthemum to make a functional beverage. The effects of this beverage on hepatic antioxidant enzymes and the alleviation of visual fatigue in a rat model of diabetes were investigated for 4 weeks. Lutein intake of 0.72 (medium-lutein beverage group) and 1.44 mg/mL (high-lutein beverage group) relieved visual fatigue, ameliorated turbidity symptoms of impaired crystalline lenses, reduced hepatic MDA concentration, increased hepatic GSH concentration, and significantly increased the activities of the hepatic antioxidant enzymes SOD, CAT, GSH-Px, and GR in rats. These data suggest that a lutein-rich beverage is an effective and harmless way to increase the total anti-oxidation capacity of lenses and alleviate visual fatigue.

Controllable Fabrication of Vertical Graphene with Tunable Growth Nature by Remote Plasma-Enhanced Chemical Vapor Deposition.

As an important member of the graphene family, vertical graphene (VG) has broad applications like field emission, energy storage, and sensors owing to its fascinating physical and chemical properties. Among various fabrication methods for VG, plasma enhanced chemical vapor deposition (PECVD) is most employed because of the fast growth rate at relatively low temperature for the high-quality VG. However, to date, relations between growth manner of VG and growth parameters such as growth temperature, dosage of gaseous carbon source, and electric power to generate plasma are still less known, which in turn hinder the massive production of VG for further applications. In this study, the growth behavior of VG was studied as functions of temperature, plasma power, and gas composition (or chamber pressure). It was found that the growth behavior of VG is sensitive to the growth conditions mentioned above. Although conditions with high growth temperature, large flow rate of mixed gas of methane and carrier gases, and high plasma power may be helpful for the fast growth of VG, brunching of VG is simultaneously enhanced, which in turn decreases the vertical growth nature of VG. High-quality VG can be achieved by optimizing the growth parameters. It was revealed that the vertical growth nature of VG is governed by the electric field at the interfacial layer between VG and the substrate, for which its strength is influenced by the density of plasma. These findings are important for the general understanding of the VG growth and provided a feasible way for the controllable fabrication of VG using the remote PECVD method which is usually believed to be unsuitable for the fabrication of VG.

Optimization of green deep eutectic solvent (DES) extraction of Chenopodium quinoa Willd. husks saponins by response surface methodology and their antioxidant activities.

Quinoa saponins have outstanding activity, and there are an increasing number of extraction methods, but there are few research programs on green preparation technology. The extraction conditions of quinoa saponins with deep eutectic solvents (DESs) were optimized by single-factor experiments combined with response surface methodology. The antioxidant capacity of saponins extracted by DESs and traditional methods was evaluated by the DPPH clearance rate, iron ion chelation rate and potassium ferricyanide reducing power. The results show that the optimal DES is choline chloride: 1,2-propylene glycol (1 : 1), and its water content is 40%. The optimal extraction conditions were as follows: the solid-to-solvent ratio was 0.05 g mL-1, the extraction time was 89 min, and the extraction temperature was 75 °C. Under these conditions, the extraction of quinoa saponins by DES was more effective than the traditional extraction methods. The saponins extracted by DES and traditional methods were analyzed by UPLC-MS, and five main saponins were identified. Quantitative analysis by HPLC-UV showed that Q1 (m/z = 971) and Q2 (m/z = 809) had higher contents of saponins. In vitro antioxidant experiments showed that all DES saponin extracts showed good antioxidant capacity. This study provides new insight into the development and utilization of quinoa saponins.