Mechanism-based traps enable protease and hydrolase substrate discovery.

Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets1. However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond2; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs. 3,4). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref. 5) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.

Synthetic lethal connectivity and graph transformer improve synthetic lethality prediction.

Synthetic lethality (SL) has shown great promise for the discovery of novel targets in cancer. CRISPR double-knockout (CDKO) technologies can only screen several hundred genes and their combinations, but not genome-wide. Therefore, good SL prediction models are highly needed for genes and gene pairs selection in CDKO experiments. However, lack of scalable SL properties prevents generalizability of SL interactions to out-of-sample data, thereby hindering modeling efforts. In this paper, we recognize that SL connectivity is a scalable and generalizable SL property. We develop a novel two-step multilayer encoder for individual sample-specific SL prediction model (MLEC-iSL), which predicts SL connectivity first and SL interactions subsequently. MLEC-iSL has three encoders, namely, gene, graph, and transformer encoders. MLEC-iSL achieves high SL prediction performance in K562 (AUPR, 0.73; AUC, 0.72) and Jurkat (AUPR, 0.73; AUC, 0.71) cells, while no existing methods exceed 0.62 AUPR and AUC. The prediction performance of MLEC-iSL is validated in a CDKO experiment in 22Rv1 cells, yielding a 46.8% SL rate among 987 selected gene pairs. The screen also reveals SL dependency between apoptosis and mitosis cell death pathways.

STW-MD: a novel spatio-temporal weighting and multi-step decision tree method for considering spatial heterogeneity in brain gene expression data.

Gene expression during brain development or abnormal development is a biological process that is highly dynamic in spatio and temporal. Previous studies have mainly focused on individual brain regions or a certain developmental stage. Our motivation is to address this gap by incorporating spatio-temporal information to gain a more complete understanding of brain development or abnormal brain development, such as Alzheimer's disease (AD), and to identify potential determinants of response. In this study, we propose a novel two-step framework based on spatial-temporal information weighting and multi-step decision trees. This framework can effectively exploit the spatial similarity and temporal dependence between different stages and different brain regions, and facilitate differential gene analysis in brain regions with high heterogeneity. We focus on two datasets: the AD dataset, which includes gene expression data from early, middle and late stages, and the brain development dataset, spanning fetal development to adulthood. Our findings highlight the advantages of the proposed framework in discovering gene classes and elucidating their impact on brain development and AD progression across diverse brain regions and stages. These findings align with existing studies and provide insights into the processes of normal and abnormal brain development.

The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity.

Proper transcription regulation by key transcription factors, such as IRF3, is critical for anti-viral defense. Dynamics of enhancer activity play important roles in many biological processes, and epigenomic analysis is used to determine the involved enhancers and transcription factors. To determine new transcription factors in anti-DNA-virus response, we have performed H3K27ac ChIP-Seq and identified three transcription factors, NR2F6, MEF2D and MAFF, in promoting HSV-1 replication. NR2F6 promotes HSV-1 replication and gene expression in vitro and in vivo, but not dependent on cGAS/STING pathway. NR2F6 binds to the promoter of MAP3K5 and activates AP-1/c-Jun pathway, which is critical for DNA virus replication. On the other hand, NR2F6 is transcriptionally repressed by c-Jun and forms a negative feedback loop. Meanwhile, cGAS/STING innate immunity signaling represses NR2F6 through STAT3. Taken together, we have identified new transcription factors and revealed the underlying mechanisms involved in the network between DNA viruses and host cells.

Sustainable Copolymer Synthesis from Carbon Dioxide and Butadiene.

Carbon dioxide (CO2) has long been recognized as an ideal C1 feedstock comonomer for producing sustainable materials because it is renewable, abundant, and cost-effective. However, activating CO2 presents a significant challenge because it is highly oxidized and stable. A CO2/butadiene-derived δ-valerolactone (EVP), generated via palladium-catalyzed telomerization between CO2 and butadiene, has emerged as an attractive intermediate for producing sustainable copolymers from CO2 and butadiene. Owing to the presence of two active carbon-carbon double bonds and a lactone unit, EVP serves as a versatile intermediate for creating sustainable copolymers with a CO2 content of up to 29 wt % (33 mol %). In this Review, advances in the synthesis of copolymers from CO2 and butadiene with divergent structures through various polymerization protocols have been summarized. Achievements made in homo- and copolymerization of EVP or its derivatives are comprehensively reviewed, while the postmodification of the obtained copolymers to access new polymers are also discussed. Meanwhile, potential applications of the obtained copolymers are also discussed. The literature references were sorted into sections based on polymerization strategies and mechanisms, facilitating readers in gaining a comprehensive view of the present chemistry landscape and inspiring innovative approaches to synthesizing novel CO2-derived copolymers.

SLKB: synthetic lethality knowledge base.

Emerging CRISPR-Cas9 technology permits synthetic lethality (SL) screening of large number of gene pairs from gene combination double knockout (CDKO) experiments. However, the poor integration and annotation of CDKO SL data in current SL databases limit their utility, and diverse methods of calculating SL scores prohibit their comparison. To overcome these shortcomings, we have developed SL knowledge base (SLKB) that incorporates data of 11 CDKO experiments in 22 cell lines, 16,059 SL gene pairs and 264,424 non-SL gene pairs. Additionally, within SLKB, we have implemented five SL calculation methods: median score with and without background control normalization (Median-B/NB), sgRNA-derived score (sgRNA-B/NB), Horlbeck score, GEMINI score and MAGeCK score. The five scores have demonstrated a mere 1.21% overlap among their top 10% SL gene pairs, reflecting high diversity. Users can browse SL networks and assess the impact of scoring methods using Venn diagrams. The SL network generated from all data in SLKB shows a greater likelihood of SL gene pair connectivity with other SL gene pairs than non-SL pairs. Comparison of SL networks between two cell lines demonstrated greater likelihood to share SL hub genes than SL gene pairs. SLKB website and pipeline can be freely accessed at https://slkb.osubmi.org and https://slkb.docs.osubmi.org/, respectively.

Polyethylene Materials with Tunable Degradability by Incorporating In-Chain Mechanophores.

Polyolefins are recognized as fundamental plastic materials that are manufactured in the largest quantities among all synthetic polymers. The chemical inertness of the saturated hydrocarbon chains is crucial for storing and using polyolefin plastics, but poses significant environmental challenges related to plastic pollution. Here, we report a versatile approach to creating polyethylene materials with tunable degradability by incorporating in-chain mechanophores. Through palladium-catalyzed coordination/insertion copolymerization of ethylene with cyclobutene-fused comonomers, several cyclobutane-fused mechanophores were successfully incorporated with varied insertion ratios (0.35-26 mol %). The resulting polyethylene materials with in-chain mechanophores exhibit both high thermal stability and remarkable acid resistance. Upon mechanochemical activation by ultrasonication or ball-milling, degradable functional units (imide and ester groups) are introduced into the main polymer chain. The synergy of mechanochemical activation and acid hydrolysis facilitates the efficient degradation of high molecular weight polyethylene materials into telechelic oligomers.

SCD1 sustains brown fat sympathetic innervation and thermogenesis during the long-term cold exposure.

Brown fat adipose tissue (BAT) is a therapeutic potential target to improve obesity, diabetes and cold acclimation in mammals. During the long-term cold exposure, the hyperplastic sympathetic network is crucial for BAT the maintain the highly thermogenic status. It has been proved that the sympathetic nervous drives the thermogenic activity of BAT via the release of norepinephrine. However, it is still unclear that how the thermogenic BAT affects the remodeling of the hyperplastic sympathetic network, especially during the long-term cold exposure. Here, we showed that following long-term cold exposure, SCD1-mediated monounsaturated fatty acid biosynthesis pathway was enriched, and the ratios of monounsaturated/saturated fatty acids were significantly up-regulated in BAT. And SCD1-deficiency in BAT decreased the capacity of cold acclimation, and suppressed long-term cold mediated BAT thermogenic activation. Furthermore, by using thermoneutral exposure and sympathetic nerve excision models, we disclosed that SCD1-deficiency in BAT affected the thermogenic activity, depended on sympathetic nerve. In mechanism, SCD1-deficiency resulted in the unbalanced ratio of palmitic acid (PA)/palmitoleic acid (PO), with obviously higher level of PA and lower level of PO. And PO supplement efficiently reversed the inhibitory role of SCD1-deficiency on BAT thermogenesis and the hyperplastic sympathetic network. Thus, our data provided insight into the role of SCD1-mediated monounsaturated fatty acids metabolism to the interaction between thermogenic activity BAT and hyperplastic sympathetic networks, and illustrated the critical role of monounsaturated fatty acids biosynthetic pathway in cold acclimation during the long-term cold exposure.

Analysis of 12 kinds of cytokines in seminal plasma by flow cytometry and their correlations with routine semen parameters.

OBJECTIVE: To investigate the levels of 12 kinds of cytokines in seminal plasma and their correlations with routine semen parameters. METHODS: The remaining seminal plasma samples of 134 patients undergoing routine semen examination were collected for detecting cytokines. The parameters for sperm concentration, percentage of progressively motile sperm (PR), and motility were analyzed by a computer-assisted sperm analysis (CASA) system. According to the results of sperm concentration, PR and motility, 134 patients were divided into the normal routine semen parameters group, oligoasthenospermia group and azoospermia group. The levels of 12 kinds of cytokines in seminal plasma, including interleukin (IL)-1ß, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12P70, IL-17, interferin (IFN)-α, IFN-γ, and tumor necrosis factor (TNF)-α, were detected by flow cytometry. Two seminal plasma samples were detected for 10 times, respectively, to calculate the coefficients of variation (CV) of each cytokine. The linear range of each cytokine was measured using the standard, and the correlation coefficient (r) was calculated. RESULTS: The r2 of 12 kinds of cytokines detected by flow cytometry were all greater than 0.99. The reproducibility of 2 seminal plasma samples showed that the CVs of all cytokines were lower than 15 % except for TNF-α in sample 1 (15.15 %). Seminal plasma IL-6 levels were negatively correlated with semen volume (P < 0.01). Seminal plasma IL-5 levels were positively correlated with sperm concentration (P < 0.01). Seminal plasma IL-8 levels were negatively correlated with sperm motility (P < 0.01). Seminal plasma IL-8, IL-17 and IL-12P70 levels were negatively correlated with sperm PR (P < 0.05). In addition to the significant negative correlation between IL-5 and IL-17 (P < 0.05), there was a significant positive correlation between the majority of other cytokines. The levels of seminal plasma IL-17 and IL-12P70 in the oligoasthenospermia group and IL-1ß and IL-12P70 in the azoospermia group were significantly higher than those in the normal routine semen parameters group (P ≤ 0.05), while the levels of IL-10 in the azoospermia group were significantly lower than that in the normal routine semen parameters group (P < 0.05). CONCLUSION: There are certain correlations between seminal plasma cytokines and routine semen parameters and strong correlations between different seminal plasma cytokines, suggesting that the imbalance between seminal plasma cytokines may affect sperm quality. However, it still needs to be further confirmed by large samples and multi-center clinical studies and related basic researches.

A gain-of-function mutation in BnaIAA13 disrupts vascular tissue and lateral root development in Brassica napus.

Rapeseed (Brassica napus) is an important oilseed crop worldwide. Plant vascular tissues are responsible for material transport and provide mechanical support. The lateral roots (LRs) absorb sufficient water and nutrients. The genetic basis of vascular tissues and LRs development in rapeseed remains unknown. This study characterized an EMS-mutagenized rapeseed mutant, T16, which showed dwarf stature, reduced LRs, and leaf wilting. Scanning electron microscopy observations showed that the internode-cell shortened. Observations of the tissue sections revealed defects in the development of vascular bundles in the stems and petioles. Genetic analysis revealed that the phenotypes of T16 were controlled by a single semi-dominant nuclear gene. Map-based cloning and genetic complementarity confirmed that BnaA03.IAA13 is the functional gene, a G-to-A mutation in second exon changed the glycine at the 79th position to glutamic acid, disrupting the conserved degron motif VGWPP. Transcriptome analysis in roots and stems showed that auxin and cytokinin signaling pathways were disordered in T16. Evolutionary analysis showed that AUXIN/INDOLE-3-ACETIC ACID was conserved during plant evolution. The heterozygote of T16 significantly reduced the plant height while maintaining other agronomic traits. Our findings provide novel insights into the regulatory mechanisms of vascular tissues and LRs development, and provide a new germplasm resource for rapeseed breeding.

Improving linolenic acid content in rapeseed oil by overexpression of CsFAD2 and CsFAD3 genes.

With the increasing public attention to the health benefit of polyunsaturated fatty acids (PUFAs) and demand for linolenic acid (C18:3), it is of great significance to increase the C18:3 content in our meal. As an oil crop with high content of C18:3, Camelina sativa has three homologous copies of FAD2 and three homologous copies FAD3. In this study, we seed-specifically overexpressed two Camelina sativa fatty acid desaturase genes, CsFAD2 and CsFAD3, in rapeseed cultivar Zhongshuang 9. The results show that C18:3 content in CsFAD2 and CsFAD3 overexpressed seeds is increased from 8.62% in wild-type (WT) to 10.62-12.95% and 14.54-26.16%, respectively. We crossed CsFAD2 and CsFAD3 overexpression lines, and stable homozygous digenic crossed lines were obtained. The C18:3 content was increased from 8.62% in WT to 28.46-53.57% in crossed overexpression lines. In addition, we found that the overexpression of CsFAD2 and CsFAD3 had no effect on rapeseed growth, development, and other agronomic traits. In conclusion, we successfully generated rapeseed germplasms with high C18:3 content by simultaneously overexpressing CsFAD2 and CsFAD3, which provides a feasible way for breeding high C18:3 rapeseed cultivars. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01445-0.

Chemical synthesis of a 28 kDa full-length PET degrading enzyme ICCG by the removable backbone modification strategy.

Chemical protein synthesis offers a powerful way to access otherwise-difficult-to-obtain proteins such as mirror-image proteins. Although a large number of proteins have been chemically synthesized to date, the acquisition to proteins containing hydrophobic peptide fragments has proven challenging. Here, we describe an approach that combines the removable backbone modification strategy and the peptide hydrazide-based native chemical ligation for the chemical synthesis of a 28 kDa full-length PET degrading enzyme IGGC (a higher depolymerization efficiency of variant leaf-branch compost cutinase (LCC)) containing hydrophobic peptide segments. The synthetic ICCG exhibits the enzymatic activity and will be useful in establishing the corresponding mirror-image version of ICCG.

Effects of sustained viral response on lipid in Hepatitis C: a systematic review and meta-analysis.

BACKGROUND: Direct-acting Antiviral Agents (DAAs) influence serum lipids of patients with Hepatitis C virus (HCV). This paper presents an analysis of the relevant literature to investigate the effects of DAAs in treating hepatitis C to achieve a sustained viral response (SVR) on lipid parameters. METHODS: PubMed,Web of science, Embase and Central databases were searched, with a deadline of September 2023. Studies on the effects of sustained viral response on lipid parameters after DAAs treatment for hepatitis C were selected. The required information was extracted from the included studies, and then the Stata 12.0 was used to analyze the data quantitatively. RESULTS: Of 32 studies, the results showed that total cholesterol (TC) levels increased from the end of treatment (WMD = 20.144, 95%CI = 3.404, 36.884,P = 0.018) to one year after treatment (WMD = 24.900, 95%CI = 13.669, 36.131, P < 0.001). From the end of treatment (WMD = 17.728, 95%CI = 4.375, 31.082, P = 0.009) to one year after treatment (WMD = 18.528, 95%CI = 7.622, 29.433, P < 0.001), the levels of low-density lipoprotein (LDL) were also increased. High-density lipoprotein (HDL) levels were elevated from 4 weeks after treatment (WMD = 6.665, 95%CI = 3.906, 9.424, P < 0.001) to 24 weeks after treatment (WMD = 3.159,95% CI = 0.176, 6.142, P = 0.038). Triglyceride (TG) levels showed no significant change after the treatment. CONCLUSIONS: Hepatitis C patients who achieved SVR on DAAs showed the increase of lipid levels and the improvement of hepatic inflammation indicators AST and ALT. This may provide evidence-based medical evidence for the follow-up and monitoring of blood lipids and hyperlipidemia treatment. REGISTRATION: PROSPERO CRD42020180793.

Reclassification of Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 as a Later Heterotypic Synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953 using a Polyphasic Approach.

The taxonomic relationship between Streptomyces violarus and Streptomyces violaceus was reevaluated using a polyphasic taxonomic approach in this work. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Streptomyces violarus JCM 4534 T was closely related to Streptomyces arenae ISP 5293 T. However, phylogenetic analysis based on five house-keeping gene (atpD, gyrB, recA, rpoB and trpB) showed that the evolutionary neighbor of Streptomyces violarus JCM 4534 T was Streptomyces violaceus CGMCC 4.1456 T, suggesting that there was a close genetic relationship between these two strains. The average nucleotide identity and digital DNA-DNA hybridization values between them were 97.0 and 72.9%, respectively, greater than the 96.7 and 70% cut-off points recommended for delineating a Streptomyces species. This result indicated that they belonged to the same genomic species which was also verified by a comprehensive comparison of phenotypic and chemotaxonomic characteristics between Streptomyces violarus JCM 4534 T and Streptomyces violaceus CGMCC 4.1456 T. According to all these data and the rule of priority in nomenclature, it is proposed the Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 is a later heterotypic synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953. In addition, based on dDDH, Streptomyces violaceus and Streptomyces violarus are simultaneously designated as two different subspecies, i.e., Streptomyces violaceus subsp. violaceus and Streptomyces violaceus subsp. violarus.

Enhanced Cataluminescence Sensor Based on SiO2/MIL-53(Al) for Detecting Isobutylaldehyde.

A simple, rapid, and reliable method for detecting harmful gases is urgently required in environmental security fields. In this study, a highly effective cataluminescence sensor based on SiO2/MIL-53(Al) composites was developed to detect trace isobutylaldehyde. The sensor was designed using isobutylaldehyde to generate an interesting cataluminescence phenomenon in SiO2/MIL-53(Al). Under optimized conditions, a positive linear relationship was observed between the signal intensity of the cataluminescence and isobutylaldehyde concentration. The isobutylaldehyde concentration range of 1.55-310 ppm responded well to the sensing test, with an excellent correlation coefficient of 0.9996. The minimum detectable concentration signal-to-noise ratio (S/N = 3) was found to be 0.49 ppm. In addition, the sensor was effectively utilized for analyzing trace isobutylaldehyde; the analysis resulted in recoveries ranging from 83.4% to 105%, with relative standard deviations (RSDs) of 4.8% to 9.4%. Furthermore, the mechanism of cataluminescence between SiO2/MIL-53(Al) and isobutylaldehyde was explored using GC-MS analysis and density functional theory. We expect that this cataluminescence methodology will provide an approach for the environmental monitoring of isobutylaldehyde.

Mechanochemical Backbone Editing for Controlled Degradation of Vinyl Polymers.

The chemically inert nature of fully saturated hydrocarbon backbones endows vinyl polymers with desirable durability, but it also leads to their significant environmental persistence. Enhancing the sustainability of these materials requires a pivotal yet challenging shift: transforming the inert backbone into one that is degradable. Here, we present a versatile platform for mechanochemically editing the fully saturated backbone of vinyl polymers towards degradable polymer chains by integrating cyclobutene-fused succinimide (CBS) units along backbone through photo-iniferter reversible addition-fragmentation chain-transfer (RAFT) copolymerization. Significantly, the evenly insertion of CBS units does not compromise thermal or chemical stability but rather offers a means to adjust the properties of polymethylacrylate (PMA). Meanwhile, reactive acyclic imide units can be selectively introduced to the backbone through mechanochemical activation (pulse ultrasonication or ball-milling grinding) when required. Subsequent hydrolysis of the acyclic imide groups enables efficient degradation, yielding telechelic oligomers. This approach holds promise for inspiring the design and modification of more environmentally friendly vinyl polymers through backbone editing.

L-Glycosidase-Cleavable Natural Glycans Facilitate the Chemical Synthesis of Correctly Folded Disulfide-Bonded D-Proteins.

D-peptide ligands can be screened for therapeutic potency and enzymatic stability using synthetic mirror-image proteins (D-proteins), but efficient acquisition of these D-proteins can be hampered by the need to accomplish their in vitro folding, which often requires the formation of correctly linked disulfide bonds. Here, we report the finding that temporary installation of natural O-linked-ß-N-acetyl-D-glucosamine (O-GlcNAc) groups onto selected D-serine or D-threonine residues of the synthetic disulfide-bonded D-proteins can facilitate their folding in vitro, and that the natural glycosyl groups can be completely removed from the folded D-proteins to afford the desired chirally inverted D-protein targets using naturally occurring O-GlcNAcase. This approach enabled the efficient chemical syntheses of several important but difficult-to-fold D-proteins incorporating disulfide bonds including the mirror-image tumor necrosis factor alpha (D-TNFα) homotrimer and the mirror-image receptor-binding domain of the Omicron spike protein (D-RBD). Our work establishes the use of O-GlcNAc to facilitate D-protein synthesis and folding and proves that D-proteins bearing O-GlcNAc can be good substrates for naturally occurring O-GlcNAcase.

Hydrogenation of CO2 to Light Olefins over ZnZrOx /SSZ-13.

Converting CO2 to olefins is an ideal route to achieve carbon neutrality. However, selective hydrogenation to light olefins, especially single-component olefin, while reducing CH4 formation remains a great challenge. Herein, we developed ZnZrOx /SSZ-13 tandem catalyst for the highly selective hydrogenation of CO2 to light olefins. This catalyst shows C2 = -C4 = and propylene selectivity up to 89.4 % and 52 %, respectively, while CH4 is suppressed down to 2 %, and there is no obvious deactivation. It is demonstrated that the isolated moderate Brønsted acid sites (BAS) of SSZ-13 promotes the rapid conversion of intermediate species derived from ZnZrOx , thereby enhancing the kinetic coupling of the reactions and inhibit the formation of alkanes and improve the light olefins selectivity. Besides, the weaker BAS of SSZ-13 promote the conversion of intermediates into aromatics with 4-6 methyl groups, which is conducive to the aromatics cycle. Accordingly, more propene can be obtained by elevating the Si/Al ratio of SSZ-13. This provides an efficient strategy for CO2 hydrogenation to light olefins with high selectivity.

An Enzyme-Cleavable Solubilizing-Tag Facilitates the Chemical Synthesis of Mirror-Image Proteins.

Mirror-image proteins (D-proteins) are useful in biomedical research for purposes such as mirror-image screening for D-peptide drug discovery, but the chemical synthesis of many D-proteins is often low yielding due to the poor solubility or aggregation of their constituent peptide segments. Here, we report a Lys-C protease-cleavable solubilizing tag and its use to synthesize difficult-to-obtain D-proteins. Our tag is easily installed onto multiple amino acids such as DLys, DSer, DThr, and/or the N-terminal amino acid of hydrophobic D-peptides, is impervious to various reaction conditions, such as peptide synthesis, ligation, desulfurization, and transition metal-mediated deprotection, and yet can be completely removed by Lys-C protease under denaturing conditions to give the desired D-protein. The efficacy and practicality of the new method were exemplified in the synthesis of two challenging D-proteins: D-enantiomers of programmed cell death protein 1 IgV domain and SARS-CoV-2 envelope protein, in high yield. This work demonstrates that the enzymatic cleavage of solubilizing tags under denaturing conditions is feasible, thus paving the way for the production of more D-proteins.

Capturing Covalent Catalytic Intermediates by Enzyme Mutants: Recent Advances in Methodologies and Applications.

Covalent catalytic intermediates provide valuable information for revealing the catalytic mechanism, probing the enzyme activity and identifying substrate specificity. However, naturally formed covalent intermediates are too rapidly degraded for general biological studies. In order to capture transient covalent intermediates, a variety of chemical strategies have been developed over decades to extend the half-life of the enzyme-substrate intermediates (or close analogues) required for the downstream structural and functional studies. This review summarizes three general mechanism-based strategies for trapping covalent catalytic intermediates. In particular, enzyme mutant-based approaches, especially the introduction of genetically encoded 2,3-diaminopropionic acid to replace the catalytic cysteine/serine in proteases for acyl-enzyme intermediate trapping are described. In addition, the applications of trapped intermediates in structural, functional and protein labeling studies are presented, and the potential new directions of using enzyme substrate traps are discussed at the end of the review.