The A_(2A)adenosine receptor(A_(2A)AR)has attracted attention as an emerging immunotherapeutic target with several antagonists being evaluated in clinical trials.However,A_(2A)AR antagonists show limited efficacy as m...The A_(2A)adenosine receptor(A_(2A)AR)has attracted attention as an emerging immunotherapeutic target with several antagonists being evaluated in clinical trials.However,A_(2A)AR antagonists show limited efficacy as monotherapies.Herein,we communicate our design and synthesis of a novel series of A_(2A)AR/histone deacetylase(HDAC)bifunctional inhibitors,based on the core structure of the A_(2A)AR antagonist The new compounds were designed using a pharmacophore-merging strategy and features a tri-substituted pyrimidine core.The binding affinity for A_(2A)AR and inhibitory activity against HDACs of all the new compounds were tested.A number of compounds exhibited nanomolar or subnanomolar activity against both targets and some showed equally potent antiproliferative activity against MC38,CT26 and HCT116 colon cancer lines compared to HDAC inhibitors SAHA and MGCD-0103 in vitro.The binding poses of compound 5a in both A_(2A)AR and HDAC1 were predicted by molecular docking studies.Collectively,these results suggest these tri-substituted pyrimidine derivatives are promising leads for developing A_(2A)AR/HDAC dual-acting compounds as novel antitumor agents.展开更多
Energy metabolism is fundamental for life.It encompasses the utilization of carbohydrates,lipids,and proteins for internal processes,while aberrant energy metabolism is implicated in many diseases.In the present study...Energy metabolism is fundamental for life.It encompasses the utilization of carbohydrates,lipids,and proteins for internal processes,while aberrant energy metabolism is implicated in many diseases.In the present study,using three-dimensional(3D)printing from polycarbonate via fused deposition modeling,we propose a multi-nuclear radiofrequency(RF)coil design with integrated 1H birdcage and interchangeable X-nuclei(^(2)H,^(13)C,^(23)Na,and^(31)P)single-loop coils for magnetic resonance imaging(MRI)/magnetic resonance spectroscopy(MRS).The single-loop coil for each nucleus attaches to an arc bracket that slides unrestrictedly along the birdcage coil inner surface,enabling convenient switching among various nuclei and animal handling.Compared to a commercial 1H birdcage coil,the proposed 1H birdcage coil exhibited superior signal-excitation homogeneity and imaging signal-to-noise ratio(SNR).For X-nuclei study,prominent peaks in spectroscopy for phantom solutions showed excellent SNR,and the static and dynamic peaks of in vivo spectroscopy validated the efficacy of the coil design in structural imaging and energy metabolism detection simultaneously.展开更多
Intracellular compartmentation is a key strategy for the functioning of a cell.In 2010,several studies revealed that the metabolic enzyme CTP synthase(CTPS)can form filamentous structures termed cytoophidia in prokary...Intracellular compartmentation is a key strategy for the functioning of a cell.In 2010,several studies revealed that the metabolic enzyme CTP synthase(CTPS)can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells.However,recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells.In this study,using negative staining and cryo-electron microscopy,we demonstrate that Drosophila CTPS,whether in substrate-bound or product-bound form,can form filaments.Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species.We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.展开更多
Compartmentation of enzymes via filamentation has arisen as a mechanism for the regulation of metabolism.In 2010,three groups independently reported that CTP synthase(CTPS)can assemble into a filamentous structure ter...Compartmentation of enzymes via filamentation has arisen as a mechanism for the regulation of metabolism.In 2010,three groups independently reported that CTP synthase(CTPS)can assemble into a filamentous structure termed the cytoophidium.In searching for CTPS-interacting proteins,here we perform a yeast two-hybrid screening of Drosophila proteins and identify a putative CTPS-interacting protein,△~1-pyrroline-5-carboxylate synthase(P5CS).Using the Drosophila follicle cell as the in vivo model,we confirm that P5CS forms cytoophidia,which are associated with CTPS cytoophidia.Overexpression of P5CS increases the length of CTPS cytoophidia.Conversely,filamentation of CTPS affects the morphology of P5CS cytoophid ia.Finally,in vitro analyses confirm the filament-fo rming property of P5CS.Our work links CTPS with P5CS,two enzymes involved in the rate-limiting steps in pyrimidine and proline biosynthesis,respectively.展开更多
Cryo-electron tomography（cryo-ET） is a cutting-edge technology providing three-dimensional in situ ultra-structural information of macromolecular machineries, organelles, and eukaryotic cells in their native environ...Cryo-electron tomography（cryo-ET） is a cutting-edge technology providing three-dimensional in situ ultra-structural information of macromolecular machineries, organelles, and eukaryotic cells in their native environment at an unprecedented level of detail. Cryo-ET enables the direct observation of dynamic macromolecular architectures of bio-samples in their naturally occurring physiological state, without any harmful artifacts introduced by heavy metal staining, dehydration, and chemical fixation, which occur in traditional transmission electron microscopy. Over decades, cryo-ET has been providing insights into numerous aspects of cellular biology by revealing the pristinely preserved ultra-structures of different cellular components comprising the crowded and complex environment of the cell, thus, bridging the gap between cellular biology and structural biophysics. In this paper, we review the fundamentals of this technique, its recent advances in optics, detection devices, and computational algorithms. The enhancement of our understanding of structural cellular biology by combining these improvements, when integrated with other methods, such as cryo-focused ion beam milling,correlative light and electron microscopy, is discussed via a few examples from research groups worldwide. We also believe that cryo-ET applications in cell biology continue to provide fundamental insights into the field, revolutionizing structural biology itself.展开更多
In protein engineering,while computational models are increasingly used to predict mutation effects,their evaluations primarily rely on high-throughput deep mutational scanning(DMS)experiments that use surrogate reado...In protein engineering,while computational models are increasingly used to predict mutation effects,their evaluations primarily rely on high-throughput deep mutational scanning(DMS)experiments that use surrogate readouts,which may not adequately capture the complex biochemical properties of interest.Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties,and this is particularly true for the real industrial application scenario.Therefore,the desired testing datasets,will be small-size(∼10–100)experimental data for each protein,and involve as many proteins as possible and as many properties as possible,which is,however,lacking.Here,we present VenusMutHub,a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases,spanning 527 proteins across diverse functional properties including stability,activity,binding affinity,and selectivity.These datasets feature direct biochemical measurements rather than surrogate readouts,providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions.We evaluate 23 computational models across various methodological paradigms,such as sequence-based,structure-informed and evolutionary approaches.This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.展开更多
Disrupted bone morphogenetic protein type 2 receptor(BMPR2)signaling in endothelial cells drives pulmonary arterial hypertension(PAH).However,targeted recovery of this signaling pathway by lipid nanoparticles(LNPs)has...Disrupted bone morphogenetic protein type 2 receptor(BMPR2)signaling in endothelial cells drives pulmonary arterial hypertension(PAH).However,targeted recovery of this signaling pathway by lipid nanoparticles(LNPs)has not been explored as a therapy.Here,we employed Design of Experiments to optimize the delivery efficiency of LNPs targeting pulmonary endothelial cells developed by our laboratory,resulting in a remarkable 35-fold increase in a simplified three-component formulation without helper lipids.Administration of BMPR2 mRNA LNPs effectively reversed established PAH in two experimental rat models(monocrotaline or SU5416-hypoxia)by reversing pulmonary vascular remodeling.Specifically,BMPR2 mRNA LNPs replenished the expression of BMPR2 protein and subsequently activated downstream pathways,as confirmed by elevated levels of p-SMAD1/5/9 and ID1 proteins.The relief of pulmonary arterial occlusion was demonstrated by thinned pulmonary arterial media and decreased proportion of full muscularized vessels.Alleviation of right ventricular hypertrophy was indicated by declined Fulton index,the cross-sectional area of right ventricular cardiomyocytes as well as collagen deposition.Effective recovery of right ventricular function was evidenced by increased pulmonary artery flow acceleration time/pulmonary artery flow ejection time ratio.These findings underscore the potential of restoring BMPR2 signaling through pulmonary endothelial cell-specific LNPs for treating PAH.展开更多
Psychedelics,encompassing both classical and non-classical categories,are psychoactive substances known for inducing hallucinations as well as a range of cognitive and emotional effects[1].Archeological studies have d...Psychedelics,encompassing both classical and non-classical categories,are psychoactive substances known for inducing hallucinations as well as a range of cognitive and emotional effects[1].Archeological studies have demonstrated that both classical psychedelics and non-classical psychedelics have been used for medical purposes for centuries.Moreover,accumulating evidence supports the idea that psychedelics can regulate mood disturbances and psychiatric disorders.展开更多
Dear Editor,G protein-coupled receptors(GPCRs)play a vital role in regulating almost every aspect of human physiology,making up more than one-third of marketed drug targets(Santos et al.,2017).GPCRs orchestrate their ...Dear Editor,G protein-coupled receptors(GPCRs)play a vital role in regulating almost every aspect of human physiology,making up more than one-third of marketed drug targets(Santos et al.,2017).GPCRs orchestrate their signalling through interactions with three distinct downstream protein families:G proteins,G protein-coupled receptor kinases(GRKs),and arrestins(Santos et al.,2017).While G protein-mediated signalling is initiated upon GPCR stimulation,activated GPCRs return to their basal levels through a GRK-and arrestin-regulated desensitization process(Santos et al.,2017).In addition to modulating receptor desensitization,β-arrestin also regulates downstream events that are distinct from classical G protein signalling(Ahn et al.,2020).展开更多
RNA helicases are involved in almost every aspect of RNA, from transcription to RNA decay. DExD/H-box hell- cases compdse the largest SF2 helicase superfamily, which are characterized by two conserved RecA-like domain...RNA helicases are involved in almost every aspect of RNA, from transcription to RNA decay. DExD/H-box hell- cases compdse the largest SF2 helicase superfamily, which are characterized by two conserved RecA-like domains. In recent years, an increasing number of unexpected functions of these proteins have been discovered. They play important roles not only in innate immune response but also in diseases like cancers and chronic hepatitis C. In this review, we summarize the recant literatures on one member of the SF2 superfamily, the DEAD- box protein DDX41. After bacterial or viral infection, DNA or cyclic-di-GMP is released to cells. After phosphorylation of Tyr414 by BTK kinase, DDX41 will act as a sensor to recognize the invaders, followed by induction of type I interferons （IFN）. After the immune response, DDX41 is degraded by the E3 ligase TRIM21, using Lys9 and Lys115 of DDX41 as the ubiquitination sites. Besides the roles in Innate immunity, DDX41 is also related to diseases. An increasing number of both inherited and acquired mutetions in DDX41 gane are identified from myelodysplastic syndrome and/or acute myeloid leukemia （MDS/AML） patients. The review focuses on DDX41, as well as its homolog Abstrakt in Drosophila, which is important for survlval at all stages throughout the life cycle of the fly.展开更多
As one of the most successful therapeutic target families,G protein-coupled receptors(GPCRs)have experienced a transformation from random ligand screening to knowledge-driven drug design.We are eye-witnessing tremendo...As one of the most successful therapeutic target families,G protein-coupled receptors(GPCRs)have experienced a transformation from random ligand screening to knowledge-driven drug design.We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace.This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.展开更多
Apical actin filaments are highly dynamic structures that are crucial for rapid pollen tube growth, but the mechanisms regulating their dynamics and spatial organization remain incompletely understood. We here identif...Apical actin filaments are highly dynamic structures that are crucial for rapid pollen tube growth, but the mechanisms regulating their dynamics and spatial organization remain incompletely understood. We here identify that AtAIP1-1 is important for regulating the turnover and organization of apical actin filaments in pollen tubes. AtAIP1-1 is distributed uniformly in the pollen tube and loss of function of AtAIP1-1 affects the organization of the actin cytoskeleton in the pollen tube. Specifically, actin filaments became disorganized within the apical region of aip1-1 pollen tubes. Consistent with the role of apical actin filaments in spatially restricting vesicles in pollen tubes, the apical region occupied by vesicles becomes enlarged in aip1-1 pollen tubes compared to WT. Using ADF1 as a representative actin-depolymerizing factor, we demonstrate that AtAIP1-1 enhances ADF1-mediated actin depolymerization and filament severing in vitro, although AtAIP1-1 alone does not have an obvious effect on actin assembly and disassembly. The dynamics of apical actin filaments are reduced in aip1-1 pollen tubes compared to WT. Our study suggests that AtAIP1-1 works together with ADF to act as a module in regulating the dynamics of apical actin filaments to facilitate the construction of the unique "apical actin structure" in the pollen tube.展开更多
Olfactory receptors are poorly annotated for most genome-sequenced chordates.To address this deficiency,we developed a nhmmer-based olfactory receptor annotation tool Genome2OR(https://github.com/To Hanwei/Genome2OR.g...Olfactory receptors are poorly annotated for most genome-sequenced chordates.To address this deficiency,we developed a nhmmer-based olfactory receptor annotation tool Genome2OR(https://github.com/To Hanwei/Genome2OR.git),and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January,2021.In total,765,248 olfactory receptor genes were annotated,with 404,426 functional genes and 360,822 pseudogenes,which represents a four-fold increase in the number of annotated olfactory receptors.Based on the annotation data,we built a database called Chordata Olfactory Receptor Database(CORD,https://cord.ihuman.shanghaitech.edu.cn)for archiving,analysing and disseminating the data.Beyond the primary data,we offer derivative information,including pictures of species,cross references to public databases,structural models,sequence similarity networks and sequence profiles in the CORD.Furthermore,we did brief analyses on these receptors,including building a huge protein sequence similarity network covering all receptors in the database,and clustering them into 20 communities,classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish.We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models.We believe the CORD can benefit the researchers and the general public who are interested in olfaction.展开更多
Fe-N-C electrocatalysts,comprising FeN_(4) single atom sites immobilized on N-doped carbon supports,offer excellent activity in the oxygen reduction reaction(ORR),especially in alkaline solution.Herein,we report a sim...Fe-N-C electrocatalysts,comprising FeN_(4) single atom sites immobilized on N-doped carbon supports,offer excellent activity in the oxygen reduction reaction(ORR),especially in alkaline solution.Herein,we report a simple synthetic strategy for improving the accessibility of FeN_(4) sites during ORR and simultaneously fine-tuning the microenvironment of FeN_(4) sites,thus enhancing the ORR activity.Our approach involved a simple one-step pyrolysis of a Fe-containing zeolitic imidazolate framework in the presence of NaCl,yielding a hierarchically porous Fe-N-C electrocatalyst containing tailored FeN_(4) sites with slightly elongated Fe-N bond distances and reduced Fe charge.The porous carbon structure improved mass transport during ORR,whilst the microenvironment optimized FeN_(4) sites benefitted the adsorption/desorption of ORR intermediates.Accordingly,the developed electrocatalyst,possessing a high FeN_(4) site density(9.9×10^(19) sites g^(-1))and turnover frequency(2.26 s^(-1)),delivered remarkable ORR performance with a low overpotential(a half-wave potential of 0.90 V vs.reversible hydrogen electrode)in 0.1 mol L^(-1) KOH.展开更多
Naturally occurring interleukin-2(IL-2)is a pleiotropic glycoprotein that regulates immune responses by controlling the differentia-tion and homeostasis of T cells.Non-glycosylated IL-2 has been used in clinical setti...Naturally occurring interleukin-2(IL-2)is a pleiotropic glycoprotein that regulates immune responses by controlling the differentia-tion and homeostasis of T cells.Non-glycosylated IL-2 has been used in clinical settings for three decades.However,the function of the O-glycan of native IL-2 remains elusive.Herein,to stress this issue,we report a highly efficient semi-synthesis of homogeneous glycosylated IL-2 with various glycoproteoforms on a multi-milligram scale.The glycopeptide fragment was prepared by chemical synthesis and then merged with recombinant fragment via a serine ligation to generate the desired glycoprotein in a single opera-tion.Biological evaluation of the homogenous glycoprotein library reveals that the activity of IL-2 in activating individual T cell subset is glycan dependent,thus highlighting the possibility of further improving current clinical medicine.展开更多
Human glycerol channel aquaporin 7(AQP7)conducts glycerol release from adipocyte and enters the cells in pancreatic islets,muscles,and kidney tubules,and thus regulates glycerol metabolism in those tissues.Compared wi...Human glycerol channel aquaporin 7(AQP7)conducts glycerol release from adipocyte and enters the cells in pancreatic islets,muscles,and kidney tubules,and thus regulates glycerol metabolism in those tissues.Compared with other human aquaglyceroporins,AQP7 shows a less conserved‘‘NPA”motif in the center cavity and a pair of aromatic residues at Ar/R selectivity filter.To understand the structural basis for the glycerol conductance,we crystallized the human AQP7 and determined the structure at 3.7Å.A substrate binding pocket was found near the Ar/R filter where a glycerol molecule is bound and stabilized by R229.Glycerol uptake assay on human AQP7 as well as AQP3 and AQP10 demonstrated strong glycerol transportation activities at the physiological condition.The human AQP7 structure,in combination with the molecular dynamics simulation thereon,reveals a fully closed conformation with its permeation pathway strictly confined by the Ar/R filter at the exoplasmic side and the gate at the cytoplasmic side,and the binding of glycerol at the Ar/R filter plays a critical role in controlling the glycerol flux by driving the dislocation of the residues at narrowest parts of glycerol pathway in AQP7.展开更多
Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-i...Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-inhibited. Structural comparisons revealed that within a homo- dimer of Uch37, each of the catalytic domains was blocking the other＇s ubiquitin （Ub）-binding site. This blockage likely prevented Ub from entering the active site of Uch37 and might form the basis of auto-inhibition. To understand the mode of auto-inhibition clearly and shed light on the activation mechanism of Uch37 by Rpn13, we investigated the Uch37-Rpn13 complex using a combi- nation of mutagenesis, biochemical, NMR, and small- angle X-ray scattering （SAXS） techniques. Our results also proved that Uch37 oligomerized in solution and had very low activity against the fluorogenic substrate ubi- quitin-7-amino-4-methylcoumarin （Ub-AMC） of de-ubiq- uitinating enzymes. Uch37AHb＇Hc＇KEKE, a truncation removal of the C-terminal extension region （residues 256- 329） converted oligomeric Uch37 into a monomeric form that exhibited iso-peptidase activity comparable to that of a truncation-containing the Uch37 catalytic domain only. We also demonstrated that Rpn13C （Rpn13 residues 270- 407） could disrupt the oligomerization of Uch37 by sequestering Uch37 and forming a Uch37-Rpn13 com- plex. Uch37 was activated in such a complex, exhibiting 12-fold-higher activity than Uch37 alone. Time-resolved SAXS （TR-SAXS） and FRET experiments supported the proposed mode of auto-inhibition and the activation mechanism of Uch37 by Rpn13. Rpn13 activated Uch37 by forming a 1：1 stoichiometric complex in which the active site of Uch37 was accessible to Ub.展开更多
Interferon gamma-inducible protein 16(IFI16)senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear(HIN)domains,HINa and HINb,through the cooperative assembly of IFI1...Interferon gamma-inducible protein 16(IFI16)senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear(HIN)domains,HINa and HINb,through the cooperative assembly of IFI16 filaments on double-stranded DNA(dsDNA).The role of HINa in sensing DNA is not clearly understood.Here,we describe the crystal structure of the HINa domain in complex with DNA at 2.55A°resolution and provide the first insight into the mode of DNA binding by the HINa domain.The structure reveals the presence of two oligosaccharide/nucleotide-binding(OB)folds with a unique DNA-binding surface.HINa uses loop L45 of the canonical OB2 fold to bind to the DNA backbone.The dsDNA is recognized as two single strands of DNA.Interestingly,deletion of HINb compromises the ability of IFI16 to induce IFN-b,while HINa mutants impaired in DNAbinding enhance the production of IFN-b.These results shed light on the roles of IFI16 HIN domains in DNA recognition and innate immune responses.展开更多
Dear Editor,Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)has caused the COVID-19 pandemic,with more than 528 million infections and 6.2 million deaths.To fight against this rapidly spreading pandemic,pro...Dear Editor,Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)has caused the COVID-19 pandemic,with more than 528 million infections and 6.2 million deaths.To fight against this rapidly spreading pandemic,prophylactic vaccines have been developed using different techniques,such as inactivated virus,messenger RNAs,recombinant proteins,and viral-vectored vaccines.However,rapidly spreading variants of SARS-CoV-2,such as alpha,beta,delta,and omicron variants,have been emerging.展开更多
MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct ...MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct catalytic triad,and yet did not catalyze either the hydrolysis of di-ubiquitin,crosslinking with C-terminally propargylated ubiquitin,or hydrolysis of ubiquitin-7-amino-4-methylcoumarin.After obtaining a crystal structure of the catalytic domain of YGL082 W,we identified an interesting difference between the catalytic center loop of YGL082 W and that of its human homolog MINDY-1.Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1,we hypothesized that Glu27(instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082 W may impair the conformational change and account for the lack of activity.This hypothesis was supported by homology modeling and molecular dynamics simulations,which showed that the Pro-to-Glu mutation(P136 E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1.Further experiments through site-directed mutation validated this hypothesis,showing that the P27 E mutation caused MIY1(a homologous active DUB from yeast) to lose activity.展开更多
基金Lingang Laboratory(No.LG-QS-202205-03)ShanghaiTech University and the Shanghai Municipal Government.
文摘The A_(2A)adenosine receptor(A_(2A)AR)has attracted attention as an emerging immunotherapeutic target with several antagonists being evaluated in clinical trials.However,A_(2A)AR antagonists show limited efficacy as monotherapies.Herein,we communicate our design and synthesis of a novel series of A_(2A)AR/histone deacetylase(HDAC)bifunctional inhibitors,based on the core structure of the A_(2A)AR antagonist The new compounds were designed using a pharmacophore-merging strategy and features a tri-substituted pyrimidine core.The binding affinity for A_(2A)AR and inhibitory activity against HDACs of all the new compounds were tested.A number of compounds exhibited nanomolar or subnanomolar activity against both targets and some showed equally potent antiproliferative activity against MC38,CT26 and HCT116 colon cancer lines compared to HDAC inhibitors SAHA and MGCD-0103 in vitro.The binding poses of compound 5a in both A_(2A)AR and HDAC1 were predicted by molecular docking studies.Collectively,these results suggest these tri-substituted pyrimidine derivatives are promising leads for developing A_(2A)AR/HDAC dual-acting compounds as novel antitumor agents.
基金This work was supported in part by the STI 2030-Major Projects(No.2021ZD0200401)the National Key Research and Development Program of China(No.2018YFA0701400)+3 种基金the National Natural Science Foundation of China(Nos.52277232,52293424,81701774,and 61771423)the Fundamental Research Funds for the Central Universities(Nos.226-2022-00136 and 226-2023-00125)the Zhejiang Provincial Natural Science Foundation of China(No.LR23E070001),the Key R&D Program of Jiangsu Province(No.BE2022049)the Key-Area R&D Program of Guangdong Province(No.2018B030333001),China.
文摘Energy metabolism is fundamental for life.It encompasses the utilization of carbohydrates,lipids,and proteins for internal processes,while aberrant energy metabolism is implicated in many diseases.In the present study,using three-dimensional(3D)printing from polycarbonate via fused deposition modeling,we propose a multi-nuclear radiofrequency(RF)coil design with integrated 1H birdcage and interchangeable X-nuclei(^(2)H,^(13)C,^(23)Na,and^(31)P)single-loop coils for magnetic resonance imaging(MRI)/magnetic resonance spectroscopy(MRS).The single-loop coil for each nucleus attaches to an arc bracket that slides unrestrictedly along the birdcage coil inner surface,enabling convenient switching among various nuclei and animal handling.Compared to a commercial 1H birdcage coil,the proposed 1H birdcage coil exhibited superior signal-excitation homogeneity and imaging signal-to-noise ratio(SNR).For X-nuclei study,prominent peaks in spectroscopy for phantom solutions showed excellent SNR,and the static and dynamic peaks of in vivo spectroscopy validated the efficacy of the coil design in structural imaging and energy metabolism detection simultaneously.
基金supported by grants from the National Natural Science Foundation of China(No.31771490)to J.-L.L.
文摘Intracellular compartmentation is a key strategy for the functioning of a cell.In 2010,several studies revealed that the metabolic enzyme CTP synthase(CTPS)can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells.However,recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells.In this study,using negative staining and cryo-electron microscopy,we demonstrate that Drosophila CTPS,whether in substrate-bound or product-bound form,can form filaments.Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species.We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.
基金supported by ShanghaiTech University,the UK Medical Research Council(Grant No.MC_UU_12021/3 and MC_U137788471)National Natural Science Foundation of China(Grant No.31771490)。
文摘Compartmentation of enzymes via filamentation has arisen as a mechanism for the regulation of metabolism.In 2010,three groups independently reported that CTP synthase(CTPS)can assemble into a filamentous structure termed the cytoophidium.In searching for CTPS-interacting proteins,here we perform a yeast two-hybrid screening of Drosophila proteins and identify a putative CTPS-interacting protein,△~1-pyrroline-5-carboxylate synthase(P5CS).Using the Drosophila follicle cell as the in vivo model,we confirm that P5CS forms cytoophidia,which are associated with CTPS cytoophidia.Overexpression of P5CS increases the length of CTPS cytoophidia.Conversely,filamentation of CTPS affects the morphology of P5CS cytoophid ia.Finally,in vitro analyses confirm the filament-fo rming property of P5CS.Our work links CTPS with P5CS,two enzymes involved in the rate-limiting steps in pyrimidine and proline biosynthesis,respectively.
基金supported by the National Key Research and Development Program of China(Grant No.2017YFA0504800)the Pujiang Talent Program(Grant No.17PJ1406700)
文摘Cryo-electron tomography（cryo-ET） is a cutting-edge technology providing three-dimensional in situ ultra-structural information of macromolecular machineries, organelles, and eukaryotic cells in their native environment at an unprecedented level of detail. Cryo-ET enables the direct observation of dynamic macromolecular architectures of bio-samples in their naturally occurring physiological state, without any harmful artifacts introduced by heavy metal staining, dehydration, and chemical fixation, which occur in traditional transmission electron microscopy. Over decades, cryo-ET has been providing insights into numerous aspects of cellular biology by revealing the pristinely preserved ultra-structures of different cellular components comprising the crowded and complex environment of the cell, thus, bridging the gap between cellular biology and structural biophysics. In this paper, we review the fundamentals of this technique, its recent advances in optics, detection devices, and computational algorithms. The enhancement of our understanding of structural cellular biology by combining these improvements, when integrated with other methods, such as cryo-focused ion beam milling,correlative light and electron microscopy, is discussed via a few examples from research groups worldwide. We also believe that cryo-ET applications in cell biology continue to provide fundamental insights into the field, revolutionizing structural biology itself.
基金supported by Science and Technology Innovation Key R&D Program of Chongqing(CSTB2024TIAD-STX0032,China)the Computational Biology Key Program of Shanghai Science and Technology Commission(23JS1400600,China)+3 种基金Shanghai Jiao Tong University Scientific and Technological Innovation Funds(21X010200843,China)and Science and Technology Innovation Key R&D Program of Chongqing(CSTB2022TIAD-STX0017,China)the Postdoctoral Fellowship Program of CPSF under Grant Number GZC20241010the Student Innovation Center at Shanghai Jiao Tong University,and Shanghai Artificial Intelligence Laboratory.
文摘In protein engineering,while computational models are increasingly used to predict mutation effects,their evaluations primarily rely on high-throughput deep mutational scanning(DMS)experiments that use surrogate readouts,which may not adequately capture the complex biochemical properties of interest.Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties,and this is particularly true for the real industrial application scenario.Therefore,the desired testing datasets,will be small-size(∼10–100)experimental data for each protein,and involve as many proteins as possible and as many properties as possible,which is,however,lacking.Here,we present VenusMutHub,a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases,spanning 527 proteins across diverse functional properties including stability,activity,binding affinity,and selectivity.These datasets feature direct biochemical measurements rather than surrogate readouts,providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions.We evaluate 23 computational models across various methodological paradigms,such as sequence-based,structure-informed and evolutionary approaches.This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.
基金sponsored by Science and Technology Commission of Shanghai Municipality(YDZX20223100001002,China)the Natural Science Foundation of Shanghai(25ZR1401251)the ShanghaiTech University Startup Grant.
文摘Disrupted bone morphogenetic protein type 2 receptor(BMPR2)signaling in endothelial cells drives pulmonary arterial hypertension(PAH).However,targeted recovery of this signaling pathway by lipid nanoparticles(LNPs)has not been explored as a therapy.Here,we employed Design of Experiments to optimize the delivery efficiency of LNPs targeting pulmonary endothelial cells developed by our laboratory,resulting in a remarkable 35-fold increase in a simplified three-component formulation without helper lipids.Administration of BMPR2 mRNA LNPs effectively reversed established PAH in two experimental rat models(monocrotaline or SU5416-hypoxia)by reversing pulmonary vascular remodeling.Specifically,BMPR2 mRNA LNPs replenished the expression of BMPR2 protein and subsequently activated downstream pathways,as confirmed by elevated levels of p-SMAD1/5/9 and ID1 proteins.The relief of pulmonary arterial occlusion was demonstrated by thinned pulmonary arterial media and decreased proportion of full muscularized vessels.Alleviation of right ventricular hypertrophy was indicated by declined Fulton index,the cross-sectional area of right ventricular cardiomyocytes as well as collagen deposition.Effective recovery of right ventricular function was evidenced by increased pulmonary artery flow acceleration time/pulmonary artery flow ejection time ratio.These findings underscore the potential of restoring BMPR2 signaling through pulmonary endothelial cell-specific LNPs for treating PAH.
基金supported by the National Natural Science Foundation of China(32192410,32192414,32330043,T2350008,82325019,and 32241015)the Science and Technology Commission of Shanghai Municipality(23XD1423000 and 23ZR1480800)+1 种基金Shanghai Municipal Commission of Health(2022JC016)Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support(20181715)。
文摘Psychedelics,encompassing both classical and non-classical categories,are psychoactive substances known for inducing hallucinations as well as a range of cognitive and emotional effects[1].Archeological studies have demonstrated that both classical psychedelics and non-classical psychedelics have been used for medical purposes for centuries.Moreover,accumulating evidence supports the idea that psychedelics can regulate mood disturbances and psychiatric disorders.
基金supported by the National Key Research and Development Program of China grant 2022YFA1302903(T.H.)the National Natural Science Foundation of China grant 91953202(Z.-J.L.)+3 种基金the CAS Strategic Priority Research Program XDB37030104(Z.-J.L.)the National Science Fund for Distinguished Young Scholars 32022038(T.H.)the National Natural Science Foundation of China grants 32230026(Z.-J.L.)and 32271262(T.H.)Shanghai Frontiers Science Center for Bomacromolecules and Precision Medicine.
文摘Dear Editor,G protein-coupled receptors(GPCRs)play a vital role in regulating almost every aspect of human physiology,making up more than one-third of marketed drug targets(Santos et al.,2017).GPCRs orchestrate their signalling through interactions with three distinct downstream protein families:G proteins,G protein-coupled receptor kinases(GRKs),and arrestins(Santos et al.,2017).While G protein-mediated signalling is initiated upon GPCR stimulation,activated GPCRs return to their basal levels through a GRK-and arrestin-regulated desensitization process(Santos et al.,2017).In addition to modulating receptor desensitization,β-arrestin also regulates downstream events that are distinct from classical G protein signalling(Ahn et al.,2020).
基金ACKNOWLEDGMENTS This work was supported by the National Basic Research Program （973 Program） （No. 2014CB910400 and 2013CB911103）, the National Natural Science Foundation of China （Grants No. 31570875, 31330019, 81590761, 31560727 and 81501353）, the Beijing Nova Program （Grant No. Z141102001814020） to S.O., Youth Innovation Promotion Association CAS （Grant No. 2013065） to S.O., and the special project of Ebola virus research from the president foundation of Chinese Academy of Sciences.
文摘RNA helicases are involved in almost every aspect of RNA, from transcription to RNA decay. DExD/H-box hell- cases compdse the largest SF2 helicase superfamily, which are characterized by two conserved RecA-like domains. In recent years, an increasing number of unexpected functions of these proteins have been discovered. They play important roles not only in innate immune response but also in diseases like cancers and chronic hepatitis C. In this review, we summarize the recant literatures on one member of the SF2 superfamily, the DEAD- box protein DDX41. After bacterial or viral infection, DNA or cyclic-di-GMP is released to cells. After phosphorylation of Tyr414 by BTK kinase, DDX41 will act as a sensor to recognize the invaders, followed by induction of type I interferons （IFN）. After the immune response, DDX41 is degraded by the E3 ligase TRIM21, using Lys9 and Lys115 of DDX41 as the ubiquitination sites. Besides the roles in Innate immunity, DDX41 is also related to diseases. An increasing number of both inherited and acquired mutetions in DDX41 gane are identified from myelodysplastic syndrome and/or acute myeloid leukemia （MDS/AML） patients. The review focuses on DDX41, as well as its homolog Abstrakt in Drosophila, which is important for survlval at all stages throughout the life cycle of the fly.
基金The authors acknowledge funding support from the National Natural Science Foundation of China 81872915(to M.-W.W.),81773792(to D.Y.),81973373(to D.Y.),21704064(to Q.Z.),31971362(to W.S.),31971178(to S.Z.),and 31770796(to Y.J.)National Science&Technology Major Project of China-Key New Drug Creation and Manufacturing Program 2018ZX09735-001(to M.-W.W.),2018ZX09711002-002-005(to D.Y.),and 2018ZX09711002-002-002(to Y.J.)+4 种基金the National Key Basic Research Program of China 2018YFA0507000(to M.-W.W.,S.Z.,W.S.,and H.T.)Novo Nordisk-CAS Research Fund grant NNCAS-2017-1-CC(to D.Y.)The Belt and Road Master Fellowship program(to V.L.)UCAS Scholarship for International Students(to S.D.)and The CAS-TWAS President's Fellowship for International Doctoral Students(to E.Y.).
文摘As one of the most successful therapeutic target families,G protein-coupled receptors(GPCRs)have experienced a transformation from random ligand screening to knowledge-driven drug design.We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace.This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
基金supported by a grant from the National Natural Science Foundation of China(31671390)funding from the Tsinghua-Peking Joint Center for Life Sciences。
文摘Apical actin filaments are highly dynamic structures that are crucial for rapid pollen tube growth, but the mechanisms regulating their dynamics and spatial organization remain incompletely understood. We here identify that AtAIP1-1 is important for regulating the turnover and organization of apical actin filaments in pollen tubes. AtAIP1-1 is distributed uniformly in the pollen tube and loss of function of AtAIP1-1 affects the organization of the actin cytoskeleton in the pollen tube. Specifically, actin filaments became disorganized within the apical region of aip1-1 pollen tubes. Consistent with the role of apical actin filaments in spatially restricting vesicles in pollen tubes, the apical region occupied by vesicles becomes enlarged in aip1-1 pollen tubes compared to WT. Using ADF1 as a representative actin-depolymerizing factor, we demonstrate that AtAIP1-1 enhances ADF1-mediated actin depolymerization and filament severing in vitro, although AtAIP1-1 alone does not have an obvious effect on actin assembly and disassembly. The dynamics of apical actin filaments are reduced in aip1-1 pollen tubes compared to WT. Our study suggests that AtAIP1-1 works together with ADF to act as a module in regulating the dynamics of apical actin filaments to facilitate the construction of the unique "apical actin structure" in the pollen tube.
基金supported by the National Natural Science Foundation of China(32122024,31971178)the National Key Research and Development Programs of China(2018YFA0507000)ShanghaiTech University。
文摘Olfactory receptors are poorly annotated for most genome-sequenced chordates.To address this deficiency,we developed a nhmmer-based olfactory receptor annotation tool Genome2OR(https://github.com/To Hanwei/Genome2OR.git),and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January,2021.In total,765,248 olfactory receptor genes were annotated,with 404,426 functional genes and 360,822 pseudogenes,which represents a four-fold increase in the number of annotated olfactory receptors.Based on the annotation data,we built a database called Chordata Olfactory Receptor Database(CORD,https://cord.ihuman.shanghaitech.edu.cn)for archiving,analysing and disseminating the data.Beyond the primary data,we offer derivative information,including pictures of species,cross references to public databases,structural models,sequence similarity networks and sequence profiles in the CORD.Furthermore,we did brief analyses on these receptors,including building a huge protein sequence similarity network covering all receptors in the database,and clustering them into 20 communities,classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish.We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models.We believe the CORD can benefit the researchers and the general public who are interested in olfaction.
基金supported by a James Cook Research Fellowship,administered by the Royal Society Te Apārangifunding support from Greg and Kathryn Trounson,the Energy Education Trust of New Zealand,the Mac Diarmid Institute for Advanced Materials and Nanotechnology,the National Key Projects for Fundamental Research and Development of China(2017YFA0206904 and 2017YFA0206900)+1 种基金the National Natural Science Foundation of China(51825205 and 21871279)the Beijing Natural Science Foundation(2191002)。
文摘Fe-N-C electrocatalysts,comprising FeN_(4) single atom sites immobilized on N-doped carbon supports,offer excellent activity in the oxygen reduction reaction(ORR),especially in alkaline solution.Herein,we report a simple synthetic strategy for improving the accessibility of FeN_(4) sites during ORR and simultaneously fine-tuning the microenvironment of FeN_(4) sites,thus enhancing the ORR activity.Our approach involved a simple one-step pyrolysis of a Fe-containing zeolitic imidazolate framework in the presence of NaCl,yielding a hierarchically porous Fe-N-C electrocatalyst containing tailored FeN_(4) sites with slightly elongated Fe-N bond distances and reduced Fe charge.The porous carbon structure improved mass transport during ORR,whilst the microenvironment optimized FeN_(4) sites benefitted the adsorption/desorption of ORR intermediates.Accordingly,the developed electrocatalyst,possessing a high FeN_(4) site density(9.9×10^(19) sites g^(-1))and turnover frequency(2.26 s^(-1)),delivered remarkable ORR performance with a low overpotential(a half-wave potential of 0.90 V vs.reversible hydrogen electrode)in 0.1 mol L^(-1) KOH.
基金supported by the National Natural Science Foundation of China(22077080,21907064 and 22107068)Special Projects of the Central Government in Guidance of Local Science and Technology Development(2021Szvup077).
文摘Naturally occurring interleukin-2(IL-2)is a pleiotropic glycoprotein that regulates immune responses by controlling the differentia-tion and homeostasis of T cells.Non-glycosylated IL-2 has been used in clinical settings for three decades.However,the function of the O-glycan of native IL-2 remains elusive.Herein,to stress this issue,we report a highly efficient semi-synthesis of homogeneous glycosylated IL-2 with various glycoproteoforms on a multi-milligram scale.The glycopeptide fragment was prepared by chemical synthesis and then merged with recombinant fragment via a serine ligation to generate the desired glycoprotein in a single opera-tion.Biological evaluation of the homogenous glycoprotein library reveals that the activity of IL-2 in activating individual T cell subset is glycan dependent,thus highlighting the possibility of further improving current clinical medicine.
基金the National Key Research and Development Program of China(2018YFC1004704 and 2017YFC1001303)the National Natural Science Foundation of China(U1632132,31670849,and 91853206)+3 种基金the Shanghai Science and Technology Committee(20S11902000)the SHIPM-pi fund(JY201804)the SHIPM-sigma fund(2018JC002)from Shanghai Institute of Precision Medicine,Ninth People’s Hospital Shanghai Jiao Tong University School of Medicinethe Innovative Research Team of Highlevel Local Universities in Shanghai(SSMU-ZLCX20180600)。
文摘Human glycerol channel aquaporin 7(AQP7)conducts glycerol release from adipocyte and enters the cells in pancreatic islets,muscles,and kidney tubules,and thus regulates glycerol metabolism in those tissues.Compared with other human aquaglyceroporins,AQP7 shows a less conserved‘‘NPA”motif in the center cavity and a pair of aromatic residues at Ar/R selectivity filter.To understand the structural basis for the glycerol conductance,we crystallized the human AQP7 and determined the structure at 3.7Å.A substrate binding pocket was found near the Ar/R filter where a glycerol molecule is bound and stabilized by R229.Glycerol uptake assay on human AQP7 as well as AQP3 and AQP10 demonstrated strong glycerol transportation activities at the physiological condition.The human AQP7 structure,in combination with the molecular dynamics simulation thereon,reveals a fully closed conformation with its permeation pathway strictly confined by the Ar/R filter at the exoplasmic side and the gate at the cytoplasmic side,and the binding of glycerol at the Ar/R filter plays a critical role in controlling the glycerol flux by driving the dislocation of the residues at narrowest parts of glycerol pathway in AQP7.
基金This work was supported by the National Basic Research Program （973 Program） （Nos. 2014CB910400 and 2013CB911103）, the Ministry of Health of China （Grant No. 2013ZX10004-602）, National Key Technology Research and Development Program of the Ministry of Science and Technology of China （Grant No. 2014BAI07B02） and the National Natural Science Foundation of China （Grant Nos. 31330019, 31200559）. We would like to thank Dr. Li-Qin Li from the Institute of High Energy Physics, CAS and Professor Robert E. Cohen for the gen- erous gift of the hUch37 （C88A） plasmid and Xiaoxia Yu and Yu- anyuan Chen at the Protein Science Core Facility of IBP for their technical help with the AUC and SPR experiments. The authors would also like to thank the staff at beamline BL13.3.1 at ALS for their technical support with the SAXS data collection. BL13.3.1 is supported in part by the DOE program Inte- grated Diffraction Analysis Technologies （IDAT） and the DOE pro- gram Molecular Assemblies Genes and Genomics Integrated Efficiently （MAGGIE） under Contract Number DE-AC02-05CH11231 with the DOE. The ALS is supported by the Director, Office of Sci- ence, Office of Basic Energy Sciences of the DOE under Contract No. DE-AC02-05CH11231. Use of the Advanced Photon Source, an Office of the Science User Facility operated for the U.S. Department of Energy （DOE） Office of Science by Argonne National Laboratory, was supported by the U.S. DOE under Contract No. DE-AC02- 06CHl1357. BioCAT was supported by grants from the National Center for Research Resources （2P41RR008630-17） and the National Institute of General Medical Sciences （9 P41 GM103622- 17） from the National Institutes of Health. The authors would like to thank the staff at 121D and 181D for the setup support.
文摘Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-inhibited. Structural comparisons revealed that within a homo- dimer of Uch37, each of the catalytic domains was blocking the other＇s ubiquitin （Ub）-binding site. This blockage likely prevented Ub from entering the active site of Uch37 and might form the basis of auto-inhibition. To understand the mode of auto-inhibition clearly and shed light on the activation mechanism of Uch37 by Rpn13, we investigated the Uch37-Rpn13 complex using a combi- nation of mutagenesis, biochemical, NMR, and small- angle X-ray scattering （SAXS） techniques. Our results also proved that Uch37 oligomerized in solution and had very low activity against the fluorogenic substrate ubi- quitin-7-amino-4-methylcoumarin （Ub-AMC） of de-ubiq- uitinating enzymes. Uch37AHb＇Hc＇KEKE, a truncation removal of the C-terminal extension region （residues 256- 329） converted oligomeric Uch37 into a monomeric form that exhibited iso-peptidase activity comparable to that of a truncation-containing the Uch37 catalytic domain only. We also demonstrated that Rpn13C （Rpn13 residues 270- 407） could disrupt the oligomerization of Uch37 by sequestering Uch37 and forming a Uch37-Rpn13 com- plex. Uch37 was activated in such a complex, exhibiting 12-fold-higher activity than Uch37 alone. Time-resolved SAXS （TR-SAXS） and FRET experiments supported the proposed mode of auto-inhibition and the activation mechanism of Uch37 by Rpn13. Rpn13 activated Uch37 by forming a 1：1 stoichiometric complex in which the active site of Uch37 was accessible to Ub.
基金supported by the National Natural Science Foundation of China(grant no.31570875,31330019,31200559,and 81590761)the Ministry of Science and Technology of China(grant no.2014CB910400 and 2013CB911103)+2 种基金the National Science and Technology Major Project of China(grant no.2013ZX10004-602)the Beijing Nova Program(grant no.Z141102001814020)Youth Innovation Promotion Association CAS,and the special project of Ebola virus research from the president foundation of Chinese Academy of Sciences.
文摘Interferon gamma-inducible protein 16(IFI16)senses DNA in the cytoplasm and the nucleus by using two tandem hematopoietic interferon-inducible nuclear(HIN)domains,HINa and HINb,through the cooperative assembly of IFI16 filaments on double-stranded DNA(dsDNA).The role of HINa in sensing DNA is not clearly understood.Here,we describe the crystal structure of the HINa domain in complex with DNA at 2.55A°resolution and provide the first insight into the mode of DNA binding by the HINa domain.The structure reveals the presence of two oligosaccharide/nucleotide-binding(OB)folds with a unique DNA-binding surface.HINa uses loop L45 of the canonical OB2 fold to bind to the DNA backbone.The dsDNA is recognized as two single strands of DNA.Interestingly,deletion of HINb compromises the ability of IFI16 to induce IFN-b,while HINa mutants impaired in DNAbinding enhance the production of IFN-b.These results shed light on the roles of IFI16 HIN domains in DNA recognition and innate immune responses.
基金supported by Science and Technology Commission of Shanghai Municipality(YDZX20223100001002)Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine at ShanghaiTech University,Shanghai Local College Capacity Building Project(22010502700)+1 种基金grants from the National Key Research and Development Program of China(2017YFC1001301(G.Z.),2019YFA0111000(H.W.))National Natural Science Foundation of China(31871487(C.L.)).
文摘Dear Editor,Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)has caused the COVID-19 pandemic,with more than 528 million infections and 6.2 million deaths.To fight against this rapidly spreading pandemic,prophylactic vaccines have been developed using different techniques,such as inactivated virus,messenger RNAs,recombinant proteins,and viral-vectored vaccines.However,rapidly spreading variants of SARS-CoV-2,such as alpha,beta,delta,and omicron variants,have been emerging.
基金supported by the National Key Research and Development Program of China(2017YFA0505200)the National Natural Science Foundation of China(21532004,91753205,81621002,21621003)Shanghai Tech University
文摘MINDY-1 is a recently discovered new family of deubiquitinating enzymes(DUB),but one of its yeast homologs,YGL082 W,does not show any DUB activity in vitro.Sequence alignment shows that YGL082 W possesses the correct catalytic triad,and yet did not catalyze either the hydrolysis of di-ubiquitin,crosslinking with C-terminally propargylated ubiquitin,or hydrolysis of ubiquitin-7-amino-4-methylcoumarin.After obtaining a crystal structure of the catalytic domain of YGL082 W,we identified an interesting difference between the catalytic center loop of YGL082 W and that of its human homolog MINDY-1.Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1,we hypothesized that Glu27(instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082 W may impair the conformational change and account for the lack of activity.This hypothesis was supported by homology modeling and molecular dynamics simulations,which showed that the Pro-to-Glu mutation(P136 E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1.Further experiments through site-directed mutation validated this hypothesis,showing that the P27 E mutation caused MIY1(a homologous active DUB from yeast) to lose activity.
