Molecular recognition of bioreceptors and enzymes relies on orthogonal interactions with small molecules within their cavity. To date, Chinese scientists have developed three types of strategies for introducing active...Molecular recognition of bioreceptors and enzymes relies on orthogonal interactions with small molecules within their cavity. To date, Chinese scientists have developed three types of strategies for introducing active sites inside the cavity of macrocyclic arenes to better mimic molecular recognition of bioreceptors and enzymes.The editorial aims to enlighten scientists in this field when they develop novel macrocycles for molecular recognition, supramolecular assembly, and applications.展开更多
Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,...Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,structure-and sequence-based features to predict nucleotide-level binding sites with high accuracy.RLsite leverages energy-based threedimensional representations,obtained from atomic probe interactions using a pre-trained ITScore-NL potential,and models their contextual features through a 3D convolutional neural network(3D-CNN)augmented with self-attention.In parallel,structure-based features,including network properties,Laplacian norm,and solvent-accessible surface area,together with sequence-based evolutionary constraint scores,are mapped along the RNA sequence and used as sequential descriptors.These descriptors are modeled using a bidirectional long short-term memory(BiLSTM)network enhanced with multihead self-attention.By effectively fusing these complementary modalities,RLsite achieves robust and precise binding site prediction.Extensive evaluations across four diverse RNA-ligand benchmark datasets demonstrate that RLsite consistently outperforms state-of-the-art methods in terms of precision,recall,Matthews correlation coefficient(MCC),area under the curve(AUC),and overall robustness.Notably,on a particularly challenging test set composed of RNA structures containing junctions,RLsite surpasses the second-best method by 7.3%in precision,3.4%in recall,7.5%in MCC,and 10.8%in AUC,highlighting its potential as a powerful tool for RNA-targeted molecular design.展开更多
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple t...Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.展开更多
In this paper a new continuous variable called core-ratio is defined to describe the probability for a residue to be in a binding site, thereby replacing the previous binary description of the interface residue using ...In this paper a new continuous variable called core-ratio is defined to describe the probability for a residue to be in a binding site, thereby replacing the previous binary description of the interface residue using 0 and 1. So we can use the support vector machine regression method to fit the core-ratio value and predict the protein binding sites. We also design a new group of physical and chemical descriptors to characterize the binding sites. The new descriptors are more effective, with an averaging procedure used. Our test shows that much better prediction results can be obtained by the support vector regression （SVR） method than by the support vector classification method.展开更多
Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein...Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein-protein interactions occur on comparatively fiat regions whereas protein-ligand bindings involve crevices. In the search for such sites various approaches have been designed and developed each of which is algorithmically unique. The use of grid units or voxels has been demonstrated in early studies with relatively good results obtained. We present here an approximated approach comprising of the use of voxels and computer vision methods in the search for ligand-binding areas. Each test protein is modelled and analysed in 2D with all corresponding residues graphically presented for successfully identified sites. The study was carried out on 2 sets of proteins： FK506-bound proteins and heme-bound proteins with promising results obtained for all test cases.展开更多
BACKGROUND Despite overt insulin resistance,adipocytes of genetically obese Zucker rats accumulate the excess of calorie intake in the form of lipids.AIM To investigate whether factors can replace or reinforce insulin...BACKGROUND Despite overt insulin resistance,adipocytes of genetically obese Zucker rats accumulate the excess of calorie intake in the form of lipids.AIM To investigate whether factors can replace or reinforce insulin lipogenic action by exploring glucose uptake activation by hydrogen peroxide,since it is produced by monoamine oxidase(MAO)and semicarbazide-sensitive amine oxidase(SSAO)in adipocytes.METHODS 3H-2-deoxyglucose uptake(2-DG)was determined in adipocytes from obese and lean rats in response to insulin or MAO and SSAO substrates such as tyramine and benzylamine.14C-tyramine oxidation and binding of imidazolinic radioligands[3H-Idazoxan,3H-(2-benzofuranyl)-2-imidazoline]were studied in adipocytes,the liver,and muscle.The influence of in vivo administration of tyramine+vanadium on glucose handling was assessed in lean and obese rats.RESULTS 2-DG uptake and lipogenesis stimulation by insulin were dampened in adipocytes from obese rats,when compared to their lean littermates.Tyramine and benzylamine activation of hexose uptake was vanadate-dependent and was also limited,while MAO was increased and SSAO decreased.These changes were adipocyte-specific and accompanied by a greater number of imidazoline I2 binding sites in the obese rat,when compared to the lean.In vitro,tyramine precluded the binding to I2 sites,while in vivo,its administration together with vanadium lowered fasting plasma levels of glucose and triacylglycerols in obese CONCLUSION The adipocytes from obese Zucker rats exhibit increased MAO activity and imidazoline binding site number.However,probably as a consequence of SSAO down-regulation,the glucose transport stimulation by tyramine is decreased as much as that of insulin in these insulin-resistant adipocytes.The adipocyte amine oxidases deserve more studies with respect to their putative contribution to the management of glucose and lipid handling.展开更多
Dear Editor,Bread wheat(Triticum aestivum L.,2n=42,AABBDD),one of the three major food crops,is crucial for global food security and human sustenance.Significant efforts have been made in breeding programs to modify y...Dear Editor,Bread wheat(Triticum aestivum L.,2n=42,AABBDD),one of the three major food crops,is crucial for global food security and human sustenance.Significant efforts have been made in breeding programs to modify yield-related traits to enhance wheat productivity,with grain size being one of the critical targets for achieving this objective.展开更多
The studies of novel inhibitors of DNA topoisomerase I(Topo I)have already be-come very promising in cancer chemotherapy.Identifying the new drug-binding residues is playing an important role in the design and optimiz...The studies of novel inhibitors of DNA topoisomerase I(Topo I)have already be-come very promising in cancer chemotherapy.Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors.The designed com-pounds may have novel scaffolds,thus will be helpful to overcome the toxicities of current camptothecin(CPT)drugs and may provide a solution to cross resistance with these drugs.Mul-tiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed.The Evolutionary Trace method was applied to iden-tify functionally important residues of human Topo I.It has been demonstrated that class-specific hydrophobic residues Ala351,Met428,Pro431 are located around the 7,9-position of CPT,indi-cating suitable substitution of hydrophobic group on CPT will increase antitumor activity.The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs.It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily,whose mutation will render CPT resistance.As our molecular docking studies demonstrated they did not make any direct interaction with CPT,they are important drug-binding site residues for future design of novel non-camptothecin lead compounds.This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds.展开更多
The plant actin depolymerizing factor （ADF） binds to both monomeric and filamentous actin, and is directly involved in the depolymerization of actin filaments. To better understand the actin binding sites of the Ara...The plant actin depolymerizing factor （ADF） binds to both monomeric and filamentous actin, and is directly involved in the depolymerization of actin filaments. To better understand the actin binding sites of the Arabidopsis thaliana L. AtADF1, we generated mutants of AtADF1 and investigated their functions in vitro and in vivo. Analysis of mutants harboring amino acid substitutions revealed that charged residues （Arg98 and Lys100） located at the α-helix 3 and forming an actin binding site together with the N-terminus are essential for both G- and F-actin binding. The basic residues on the β-strand 5 （K82/A） and the α-helix 4 （R135/A, R137/A） form another actin binding site that is important for F-actin binding. Using transient expression of CFP-tagged AtADF1 mutant proteins in onion （Allium cepa） peel epidermal cells and transgenic Arabidopsis thaliana L. plants overexpressing these mutants, we analyzed how these mutant proteins regulate actin organization and affect seedling growth. Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional, unless the affinity for actin monomers is also affected. The G-actin binding activity of the ADF plays an essential role in actin binding, depolymerization of actin polymers, and therefore in the control of actin organization.展开更多
Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the...Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the molecular basis of expression divergence remains unclear.Squamosa promoter-binding protein-like(SPL)transcription factors are critical for a wide array of biological processes.In this study,we constructed expression regulatory networks by combining DAP-seq for 40 SPLs,ATACseq,and RNA-seq.Our findings indicate that a group of low-affinity SPL binding regions(SBRs)were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif.The SBRs including the low-affinity ones are evolutionarily conserved,enriched GWAS signals related to important agricultural traits.However,those SBRs are highly diversified among the cis-regulatory regions(CREs)of syntenic genes,with less than 8%SBRs coexisting in triad genes,suggesting that CRE variations are critical for subgenome differentiations.Knocking out of Ta SPL7A/B/D and Ta SPL15A/B/D subfamily further proved that both high-and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes.Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.展开更多
Nucleotide-binding and oligomerization domain 2(NOD2),a member of the NOD protein family,plays an important role in innate immunity.In response to pathogen attack,NOD2 stimulates cytokine and defensin production by ac...Nucleotide-binding and oligomerization domain 2(NOD2),a member of the NOD protein family,plays an important role in innate immunity.In response to pathogen attack,NOD2 stimulates cytokine and defensin production by activating nuclear factor(NF)-kB,a key transcription factor responsible for mediating downstream reactions.However,the mechanism linking NOD2 regulation and NF-kB activation is poorly understood.Using bioinformatics,we found a completely preserved canonical NF-kB binding site in the NOD2 core promoter(216 to 225 bp)in both humans and chimpanzees.The functional role of this NF-kB binding site was investigated using the enhanced green fluorescent protein(EGFP)reporter system,site-directed mutagenesis,the NF-kB activation inhibitor(JSH-23)and the chromatin immunoprecipitation(ChIP)assay.The results show that the NF-kB binding site is critical for regulation of the NOD2 gene.Either deletion of the NF-kB binding elements within the NOD2 promoter or treatment with an NF-kB activation inhibitor could lead to a significant loss of NOD2 promoter activity as detected by reporter gene assay.The canonical NF-kB binding site was bound by NF-kB as determined by the ChIP method.Based on these results,we suggest a positive feedback regulation between NF-kB and NOD2,which may represent an efficient mechanism in response to pathogen invasion.展开更多
Bone Morphogenetic proteins(BMPs)like BMP2 and BMP7 have shown great potential in the treatment of severe bone defects.In recent in vitro studies,BMP9 revealed the highest osteogenic potential compared to other BMPs,p...Bone Morphogenetic proteins(BMPs)like BMP2 and BMP7 have shown great potential in the treatment of severe bone defects.In recent in vitro studies,BMP9 revealed the highest osteogenic potential compared to other BMPs,possibly due to its unique signaling pathways that differs from other osteogenic BMPs.However,in vivo the bone forming capacity of BMP9-adsorbed scaffolds is not superior to BMP2 or BMP7.In silico analysis of the BMP9 protein sequence revealed that BMP9,in contrast to other osteogenic BMPs such as BMP2,completely lacks so-called heparin binding motifs that enable extracellular matrix(ECM)interactions which in general might be essential for the BMPs’osteogenic function.Therefore,we genetically engineered a new BMP9 variant by adding BMP2-derived heparin binding motifs to the N-terminal segment of BMP9′s mature part.The resulting protein(BMP9 HB)showed higher heparin binding affinity than BMP2,similar osteogenic activity in vitro and comparable binding affinities to BMPR-II and ALK1 compared to BMP9.However,remarkable differences were observed when BMP9 HB was adsorbed to collagen scaffolds and implanted subcutaneously in the dorsum of rats,showing a consistent and significant increase in bone volume and density compared to BMP2 and BMP9.Even at 10-fold lower BMP9 HB doses bone tissue formation was observed.This innovative approach of significantly enhancing the osteogenic properties of BMP9 simply by addition of ECM binding motifs,could constitute a valuable replacement to the commonly used BMPs.The possibility to use lower protein doses demonstrates BMP9 HB’s high translational potential.展开更多
Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of th...Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases.Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.展开更多
With a view to finding out precisely how small peptides recognize a particular binding site of DNA, we have accomplished DNA binding studies of two peptides, H-Tyr-Arg-OH (YR) and H-Gly-Gly-His-OH (GGH) by using measu...With a view to finding out precisely how small peptides recognize a particular binding site of DNA, we have accomplished DNA binding studies of two peptides, H-Tyr-Arg-OH (YR) and H-Gly-Gly-His-OH (GGH) by using measurements in comparison with the binding between DNA and Hoechst 33258. The inhibition mode by YR and GGH to DNA binding of Hoechst 33258 was analyzed by Lineweaver-Burk plot which shows the plot of typical competitive inhibition at concentration of Hoechst 33258 from 3.66 ( 10-9 mol / L to 1.09 ( 10-8 mol / L. And it is concluded that YR binds to DNA in its minor groove (AT rich regions) with a binding constant K = 1.02 ( 108 (mol / L)-1. The GGH(s specificity is reduced at high concentration because it can also bind GC base pair.展开更多
Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a nov...Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//www.fi-pk.com/trfast.html.展开更多
Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory funct...Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.展开更多
Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear.Ethambutol(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,n...Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear.Ethambutol(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance problems.Genomic studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB resistance.EmbR-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B proteins.However,the EmbR binding site on PknH was unknown.We conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding site.Hydrogen bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA domain.Also,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation status.The discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding affinity.This approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.展开更多
Upon addition of Tb^(3+) to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb^(3+), but with much different intensity, upon excitation in the aromatic region of bases. ...Upon addition of Tb^(3+) to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb^(3+), but with much different intensity, upon excitation in the aromatic region of bases. The result suggested that nucleotides with at least one carbonyl group in nucleotide bases are better enhancers to the fluorescence of Tb3+. The complexes of ATP, GDP and GTP with T5^(3+) are synthesized as two types of models. Guanine tpye nucleotides with one carbonyl group in the bases are the best enhancers, while adenine type nucleotides with no carbonyl group in the bases are poorest enhancers to the fluorescence of Tb^(3+). Comparing the IR spectra of ATP, GTP, GDP and their Tb^(3+) complexes suggested that C-6 carbonyl group in GTP and GDP may be involved in complex formation, which may be responsible for the effective energy transfer. This is further supported by comparing the UV spectra of ATP, Poly(A), GTP, and Poly(G) with their Tb^(3+) complexes in water solution.展开更多
Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensabl...Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensable tool in the design and discovery of novel drugs by facilitating the analysis of biological datasets and aiding in the identification of potential therapeutic targets.With the rise of antibiotic resistance among bacterial species,the demand for new drug development has intensified.However,the process of drug discovery remains labor-intensive,costly,and time-consuming.The identification of new drugs involves multiple critical stages,including target identification,structural analysis of the target protein,selection of potential drug candidates,safety and efficacy assessments,drug optimization,and ultimately,validation.Bioinformatics contributes significantly to each of these phases.For instance,through the analysis of protein sequences and genetic data,researchers can pinpoint potential drug targets.Once a target protein is identified,bioinformatics tools enable detailed structural analysis of the protein.Upon locating the potential ligand-binding site,large compound databases can be screened to discover viable drug candidates.Simulations further aid in examining the interaction between the target protein and biomolecules,providing valuable insights into the drug’s safety and efficacy.Moreover,bioinformatics-driven drug optimization helps improve both safety and effectiveness.Recent advances,such as pharmacophore modeling and molecular docking techniques,have accelerated the screening process,narrowing thousands of candidate molecules down to a select few with promising therapeutic potential.In this study,bioinformatics was leveraged within the framework of network pharmacology to design and discover new drugs.展开更多
In this work,we employed a ring-opening strategy to develop a series of novel N-benzyl arylamide derivatives as tubulin polymerization inhibitors.Notably,13n(MY-1388)exhibited remarkable antiproliferative potency on f...In this work,we employed a ring-opening strategy to develop a series of novel N-benzyl arylamide derivatives as tubulin polymerization inhibitors.Notably,13n(MY-1388)exhibited remarkable antiproliferative potency on fifteen human cancer cell lines,with half maximal inhibitory concentration(IC_(50))values ranging from 8 nmol/L to 48 nmol/L.Furthermore,13n effectively suppressed tubulin polymerization by targeting the colchicine-binding site(IC_(50)=0.62μmol/L).13n also exhibited significant inhibition of cell colony formation,as well as displayed potent effects on inducing G2/M phase cell cycle arrest and promoting apoptosis.Importantly,13n exhibited enhanced and adequate liver microsomal stability in human and rat liver microsomes,and also exhibited a moderate half-life(T_(1/2)=0.938 h)in vivo.Meanwhile,13n demonstrated effective antitumor effects in vivo in suppressing tumor growth in the MGC-803xenograft model(tumor growth inhibition(TGI)value was 76.4%at the dosage of 30 mg kg^(-1)day^(-1))with a good safety profile.Collectively,these results revealed that 13n represents a promising tubulin polymerization inhibitor that deserves further investigation for its efficacy in treating gastric cancers.展开更多
文摘Molecular recognition of bioreceptors and enzymes relies on orthogonal interactions with small molecules within their cavity. To date, Chinese scientists have developed three types of strategies for introducing active sites inside the cavity of macrocyclic arenes to better mimic molecular recognition of bioreceptors and enzymes.The editorial aims to enlighten scientists in this field when they develop novel macrocycles for molecular recognition, supramolecular assembly, and applications.
基金supported by the National Natural Science Foundation of China(Grant No.12204118)the Guizhou University Talent Fund(Grant No.[2022]30).
文摘Accurate identification of RNA-ligand binding sites is essential for elucidating RNA function and advancing structurebased drug discovery.Here,we present RLsite,a novel deep learning framework that integrates energy-,structure-and sequence-based features to predict nucleotide-level binding sites with high accuracy.RLsite leverages energy-based threedimensional representations,obtained from atomic probe interactions using a pre-trained ITScore-NL potential,and models their contextual features through a 3D convolutional neural network(3D-CNN)augmented with self-attention.In parallel,structure-based features,including network properties,Laplacian norm,and solvent-accessible surface area,together with sequence-based evolutionary constraint scores,are mapped along the RNA sequence and used as sequential descriptors.These descriptors are modeled using a bidirectional long short-term memory(BiLSTM)network enhanced with multihead self-attention.By effectively fusing these complementary modalities,RLsite achieves robust and precise binding site prediction.Extensive evaluations across four diverse RNA-ligand benchmark datasets demonstrate that RLsite consistently outperforms state-of-the-art methods in terms of precision,recall,Matthews correlation coefficient(MCC),area under the curve(AUC),and overall robustness.Notably,on a particularly challenging test set composed of RNA structures containing junctions,RLsite surpasses the second-best method by 7.3%in precision,3.4%in recall,7.5%in MCC,and 10.8%in AUC,highlighting its potential as a powerful tool for RNA-targeted molecular design.
基金supported by funds from the National Key R&D Program of China (2016YFC0901603)the China 863 Program (2015AA020108)+1 种基金the State Key Laboratory of Protein and Plant Gene Researchsupported in part by the National Program for Support of Top-notch Young Professionals
文摘Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 10674172 and 10874229)
文摘In this paper a new continuous variable called core-ratio is defined to describe the probability for a residue to be in a binding site, thereby replacing the previous binary description of the interface residue using 0 and 1. So we can use the support vector machine regression method to fit the core-ratio value and predict the protein binding sites. We also design a new group of physical and chemical descriptors to characterize the binding sites. The new descriptors are more effective, with an averaging procedure used. Our test shows that much better prediction results can be obtained by the support vector regression （SVR） method than by the support vector classification method.
文摘Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein-protein interactions occur on comparatively fiat regions whereas protein-ligand bindings involve crevices. In the search for such sites various approaches have been designed and developed each of which is algorithmically unique. The use of grid units or voxels has been demonstrated in early studies with relatively good results obtained. We present here an approximated approach comprising of the use of voxels and computer vision methods in the search for ligand-binding areas. Each test protein is modelled and analysed in 2D with all corresponding residues graphically presented for successfully identified sites. The study was carried out on 2 sets of proteins： FK506-bound proteins and heme-bound proteins with promising results obtained for all test cases.
基金Supported by Recurrent Grants from Institut National de la Santéet de la Recherche Médicale to the INSERM U1048.
文摘BACKGROUND Despite overt insulin resistance,adipocytes of genetically obese Zucker rats accumulate the excess of calorie intake in the form of lipids.AIM To investigate whether factors can replace or reinforce insulin lipogenic action by exploring glucose uptake activation by hydrogen peroxide,since it is produced by monoamine oxidase(MAO)and semicarbazide-sensitive amine oxidase(SSAO)in adipocytes.METHODS 3H-2-deoxyglucose uptake(2-DG)was determined in adipocytes from obese and lean rats in response to insulin or MAO and SSAO substrates such as tyramine and benzylamine.14C-tyramine oxidation and binding of imidazolinic radioligands[3H-Idazoxan,3H-(2-benzofuranyl)-2-imidazoline]were studied in adipocytes,the liver,and muscle.The influence of in vivo administration of tyramine+vanadium on glucose handling was assessed in lean and obese rats.RESULTS 2-DG uptake and lipogenesis stimulation by insulin were dampened in adipocytes from obese rats,when compared to their lean littermates.Tyramine and benzylamine activation of hexose uptake was vanadate-dependent and was also limited,while MAO was increased and SSAO decreased.These changes were adipocyte-specific and accompanied by a greater number of imidazoline I2 binding sites in the obese rat,when compared to the lean.In vitro,tyramine precluded the binding to I2 sites,while in vivo,its administration together with vanadium lowered fasting plasma levels of glucose and triacylglycerols in obese CONCLUSION The adipocytes from obese Zucker rats exhibit increased MAO activity and imidazoline binding site number.However,probably as a consequence of SSAO down-regulation,the glucose transport stimulation by tyramine is decreased as much as that of insulin in these insulin-resistant adipocytes.The adipocyte amine oxidases deserve more studies with respect to their putative contribution to the management of glucose and lipid handling.
基金supported by grants from the Key Research and Development Project of Shandong Province (the Agricultural Variety Improvement Project,2023LZGC002)the National Key R&D Program of China (2023YFF1001600)+1 种基金the National Natural Science Foundation of China (32388201)the Ministry of Agriculture and Rural Affairs of China and the New Cornerstone Science Foundation。
文摘Dear Editor,Bread wheat(Triticum aestivum L.,2n=42,AABBDD),one of the three major food crops,is crucial for global food security and human sustenance.Significant efforts have been made in breeding programs to modify yield-related traits to enhance wheat productivity,with grain size being one of the critical targets for achieving this objective.
基金This work was supported by the National Natural Science Foundation of China(Grant No.30371689)the Nat ional“973”Fundamental Research Projects of China(Grants No.G1998051104).
文摘The studies of novel inhibitors of DNA topoisomerase I(Topo I)have already be-come very promising in cancer chemotherapy.Identifying the new drug-binding residues is playing an important role in the design and optimization of Topo I inhibitors.The designed com-pounds may have novel scaffolds,thus will be helpful to overcome the toxicities of current camptothecin(CPT)drugs and may provide a solution to cross resistance with these drugs.Mul-tiple sequence alignments were performed on eukaryotic DNA topoisomerase I superfamily and thus the evolutionary tree was constructed.The Evolutionary Trace method was applied to iden-tify functionally important residues of human Topo I.It has been demonstrated that class-specific hydrophobic residues Ala351,Met428,Pro431 are located around the 7,9-position of CPT,indi-cating suitable substitution of hydrophobic group on CPT will increase antitumor activity.The conservative residue Lys436 in the superfamily is of particular interest and new CPT derivatives designed based on this residue may greatly increase water solubility of such drugs.It has also been demonstrated that the residues Asn352 and Arg364 were conservative in the superfamily,whose mutation will render CPT resistance.As our molecular docking studies demonstrated they did not make any direct interaction with CPT,they are important drug-binding site residues for future design of novel non-camptothecin lead compounds.This work provided a strong basis for the design and synthesis of novel highly potent CPT derivatives and virtual screening for novel lead compounds.
基金supported by the Shandong Taishan Scholar programthe Shandong Natural Science Foundation(ZR2012CM022, ZRB019E7)the Laboratory of Biotechnology of Qingdao Agricultural University
文摘The plant actin depolymerizing factor （ADF） binds to both monomeric and filamentous actin, and is directly involved in the depolymerization of actin filaments. To better understand the actin binding sites of the Arabidopsis thaliana L. AtADF1, we generated mutants of AtADF1 and investigated their functions in vitro and in vivo. Analysis of mutants harboring amino acid substitutions revealed that charged residues （Arg98 and Lys100） located at the α-helix 3 and forming an actin binding site together with the N-terminus are essential for both G- and F-actin binding. The basic residues on the β-strand 5 （K82/A） and the α-helix 4 （R135/A, R137/A） form another actin binding site that is important for F-actin binding. Using transient expression of CFP-tagged AtADF1 mutant proteins in onion （Allium cepa） peel epidermal cells and transgenic Arabidopsis thaliana L. plants overexpressing these mutants, we analyzed how these mutant proteins regulate actin organization and affect seedling growth. Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional, unless the affinity for actin monomers is also affected. The G-actin binding activity of the ADF plays an essential role in actin binding, depolymerization of actin polymers, and therefore in the control of actin organization.
基金supported by the Central Publicinterest Scientific Institution Basic Research Found(S2022ZD02)the Excellent Young Scientists Fund(Overseas)of National Natural Science Foundation of China+2 种基金the Fundamental Research Funds from the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences(S2020YC07,S2021YC03)the Major Basic Research Program of Shandong Natural Science Foundation(ZR2019ZD15)the Top Talents Program“One Case One Discussion(Yishiyiyi)”of Shandong Province,China。
文摘Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat(Triticum aestivum.L.,BBAADD)is hypothesized to increase its adaptability and/or plasticity.However,the molecular basis of expression divergence remains unclear.Squamosa promoter-binding protein-like(SPL)transcription factors are critical for a wide array of biological processes.In this study,we constructed expression regulatory networks by combining DAP-seq for 40 SPLs,ATACseq,and RNA-seq.Our findings indicate that a group of low-affinity SPL binding regions(SBRs)were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif.The SBRs including the low-affinity ones are evolutionarily conserved,enriched GWAS signals related to important agricultural traits.However,those SBRs are highly diversified among the cis-regulatory regions(CREs)of syntenic genes,with less than 8%SBRs coexisting in triad genes,suggesting that CRE variations are critical for subgenome differentiations.Knocking out of Ta SPL7A/B/D and Ta SPL15A/B/D subfamily further proved that both high-and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes.Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.
基金supported by grants from the Natural Science Foundation of Guangdong Province(No.06025159)the Natural Science Foundation from Department of Education of Guangdong Province(No.126(2005)).
文摘Nucleotide-binding and oligomerization domain 2(NOD2),a member of the NOD protein family,plays an important role in innate immunity.In response to pathogen attack,NOD2 stimulates cytokine and defensin production by activating nuclear factor(NF)-kB,a key transcription factor responsible for mediating downstream reactions.However,the mechanism linking NOD2 regulation and NF-kB activation is poorly understood.Using bioinformatics,we found a completely preserved canonical NF-kB binding site in the NOD2 core promoter(216 to 225 bp)in both humans and chimpanzees.The functional role of this NF-kB binding site was investigated using the enhanced green fluorescent protein(EGFP)reporter system,site-directed mutagenesis,the NF-kB activation inhibitor(JSH-23)and the chromatin immunoprecipitation(ChIP)assay.The results show that the NF-kB binding site is critical for regulation of the NOD2 gene.Either deletion of the NF-kB binding elements within the NOD2 promoter or treatment with an NF-kB activation inhibitor could lead to a significant loss of NOD2 promoter activity as detected by reporter gene assay.The canonical NF-kB binding site was bound by NF-kB as determined by the ChIP method.Based on these results,we suggest a positive feedback regulation between NF-kB and NOD2,which may represent an efficient mechanism in response to pathogen invasion.
文摘Bone Morphogenetic proteins(BMPs)like BMP2 and BMP7 have shown great potential in the treatment of severe bone defects.In recent in vitro studies,BMP9 revealed the highest osteogenic potential compared to other BMPs,possibly due to its unique signaling pathways that differs from other osteogenic BMPs.However,in vivo the bone forming capacity of BMP9-adsorbed scaffolds is not superior to BMP2 or BMP7.In silico analysis of the BMP9 protein sequence revealed that BMP9,in contrast to other osteogenic BMPs such as BMP2,completely lacks so-called heparin binding motifs that enable extracellular matrix(ECM)interactions which in general might be essential for the BMPs’osteogenic function.Therefore,we genetically engineered a new BMP9 variant by adding BMP2-derived heparin binding motifs to the N-terminal segment of BMP9′s mature part.The resulting protein(BMP9 HB)showed higher heparin binding affinity than BMP2,similar osteogenic activity in vitro and comparable binding affinities to BMPR-II and ALK1 compared to BMP9.However,remarkable differences were observed when BMP9 HB was adsorbed to collagen scaffolds and implanted subcutaneously in the dorsum of rats,showing a consistent and significant increase in bone volume and density compared to BMP2 and BMP9.Even at 10-fold lower BMP9 HB doses bone tissue formation was observed.This innovative approach of significantly enhancing the osteogenic properties of BMP9 simply by addition of ECM binding motifs,could constitute a valuable replacement to the commonly used BMPs.The possibility to use lower protein doses demonstrates BMP9 HB’s high translational potential.
基金supported by the National Science Foundation #DBI-0844749 and #DBI-1356459 to JTG
文摘Transcription Factors（TFs） are a very diverse family of DNA-binding proteins that play essential roles in the regulation of gene expression through binding to specific DNA sequences. They are considered as one of the prime drug targets since mutations and aberrant TF-DNA interactions are implicated in many diseases.Identification of TF-binding sites on a genomic scale represents a critical step in delineating transcription regulatory networks and remains a major goal in genomic annotations. Recent development of experimental high-throughput technologies has provided valuable information about TF-binding sites at genome scale under various physiological and developmental conditions. Computational approaches can provide a cost-effective alternative and complement the experimental methods by using the vast quantities of available sequence or structural information. In this review we focus on structure-based prediction of transcription factor binding sites. In addition to its potential in genomescale predictions, structure-based approaches can help us better understand the TF-DNA interaction mechanisms and the evolution of transcription factors and their target binding sites. The success of structure-based methods also bears a translational impact on targeted drug design in medicine and biotechnology.
文摘With a view to finding out precisely how small peptides recognize a particular binding site of DNA, we have accomplished DNA binding studies of two peptides, H-Tyr-Arg-OH (YR) and H-Gly-Gly-His-OH (GGH) by using measurements in comparison with the binding between DNA and Hoechst 33258. The inhibition mode by YR and GGH to DNA binding of Hoechst 33258 was analyzed by Lineweaver-Burk plot which shows the plot of typical competitive inhibition at concentration of Hoechst 33258 from 3.66 ( 10-9 mol / L to 1.09 ( 10-8 mol / L. And it is concluded that YR binds to DNA in its minor groove (AT rich regions) with a binding constant K = 1.02 ( 108 (mol / L)-1. The GGH(s specificity is reduced at high concentration because it can also bind GC base pair.
基金supported by Higher Education Commission, Pakistan(Grant No.20-1493/R&D/09)
文摘Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//www.fi-pk.com/trfast.html.
基金supported by the Yat-Sen Innovative Talents Cultivation Program for Excellent Tutors
文摘Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.
基金This work was supported by the National Institutes of Health Grant No.7R01GM118467-05the National Natural Science Foundation of China(31720103901).
文摘Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear.Ethambutol(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance problems.Genomic studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB resistance.EmbR-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B proteins.However,the EmbR binding site on PknH was unknown.We conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding site.Hydrogen bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA domain.Also,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation status.The discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding affinity.This approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.
基金Work supported by the National Natural Science Foundation of China
文摘Upon addition of Tb^(3+) to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb^(3+), but with much different intensity, upon excitation in the aromatic region of bases. The result suggested that nucleotides with at least one carbonyl group in nucleotide bases are better enhancers to the fluorescence of Tb3+. The complexes of ATP, GDP and GTP with T5^(3+) are synthesized as two types of models. Guanine tpye nucleotides with one carbonyl group in the bases are the best enhancers, while adenine type nucleotides with no carbonyl group in the bases are poorest enhancers to the fluorescence of Tb^(3+). Comparing the IR spectra of ATP, GTP, GDP and their Tb^(3+) complexes suggested that C-6 carbonyl group in GTP and GDP may be involved in complex formation, which may be responsible for the effective energy transfer. This is further supported by comparing the UV spectra of ATP, Poly(A), GTP, and Poly(G) with their Tb^(3+) complexes in water solution.
文摘Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensable tool in the design and discovery of novel drugs by facilitating the analysis of biological datasets and aiding in the identification of potential therapeutic targets.With the rise of antibiotic resistance among bacterial species,the demand for new drug development has intensified.However,the process of drug discovery remains labor-intensive,costly,and time-consuming.The identification of new drugs involves multiple critical stages,including target identification,structural analysis of the target protein,selection of potential drug candidates,safety and efficacy assessments,drug optimization,and ultimately,validation.Bioinformatics contributes significantly to each of these phases.For instance,through the analysis of protein sequences and genetic data,researchers can pinpoint potential drug targets.Once a target protein is identified,bioinformatics tools enable detailed structural analysis of the protein.Upon locating the potential ligand-binding site,large compound databases can be screened to discover viable drug candidates.Simulations further aid in examining the interaction between the target protein and biomolecules,providing valuable insights into the drug’s safety and efficacy.Moreover,bioinformatics-driven drug optimization helps improve both safety and effectiveness.Recent advances,such as pharmacophore modeling and molecular docking techniques,have accelerated the screening process,narrowing thousands of candidate molecules down to a select few with promising therapeutic potential.In this study,bioinformatics was leveraged within the framework of network pharmacology to design and discover new drugs.
基金supported by the National Natural Science Foundation of China(Nos.82273782 and U2004123)Training Program for Young Key Teachers of Colleges and Universities in Henan Province(No.2023GGJS008)。
文摘In this work,we employed a ring-opening strategy to develop a series of novel N-benzyl arylamide derivatives as tubulin polymerization inhibitors.Notably,13n(MY-1388)exhibited remarkable antiproliferative potency on fifteen human cancer cell lines,with half maximal inhibitory concentration(IC_(50))values ranging from 8 nmol/L to 48 nmol/L.Furthermore,13n effectively suppressed tubulin polymerization by targeting the colchicine-binding site(IC_(50)=0.62μmol/L).13n also exhibited significant inhibition of cell colony formation,as well as displayed potent effects on inducing G2/M phase cell cycle arrest and promoting apoptosis.Importantly,13n exhibited enhanced and adequate liver microsomal stability in human and rat liver microsomes,and also exhibited a moderate half-life(T_(1/2)=0.938 h)in vivo.Meanwhile,13n demonstrated effective antitumor effects in vivo in suppressing tumor growth in the MGC-803xenograft model(tumor growth inhibition(TGI)value was 76.4%at the dosage of 30 mg kg^(-1)day^(-1))with a good safety profile.Collectively,these results revealed that 13n represents a promising tubulin polymerization inhibitor that deserves further investigation for its efficacy in treating gastric cancers.
