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A Deep Learning Drug-Target Binding Affinity Prediction Based on Compound Microstructure and Its Application in COVID-19 Drug Screening
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作者 Yijie Guo Xiumin Shi Han Zhou 《Journal of Beijing Institute of Technology》 EI CAS 2023年第4期396-405,共10页
Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in v... Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery. 展开更多
关键词 compound microstructure drug-target interaction binding affinity deep learning COVID-19
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Stable titanium metal-organic framework with strong binding affinity for ethaneremoval
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作者 Puxu Liu Yong Wang +4 位作者 Yang Chen Xiaoqing Wang Jiangfeng Yang Libo Li Jinping Li 《Chinese Journal of Chemical Engineering》 SCIE EI CAS CSCD 2022年第2期35-41,共7页
Direct separation of high purity ethylene(C_(2)H_(4))from an ethane(C_(2)H_(6))/ethylene mixture is a critical and challenging task owing to the very similar molecular size and physical properties of the two component... Direct separation of high purity ethylene(C_(2)H_(4))from an ethane(C_(2)H_(6))/ethylene mixture is a critical and challenging task owing to the very similar molecular size and physical properties of the two components.While some studies have attempted this separation,there is a lack of excellent porous materials with strong binding affinity for C_(2)H_(6)-selective adsorption via an energy-efficient adsorptive separation process.Herein,we report a titanium metal-organic framework with strong binding affinity and excellent stability for the highly efficient removal of C_(2)H_(6) from C_(2)H_(6)/C_(2)H_(4) mixtures.Single component adsorption isotherms demonstrated a larger amount of adsorbed ethane(1.16 mmol·g^(-1) under 1 kPa)and high C_(2)H_(6)/C_(2)H_(4) selectivity(2.7)for equimolar C_(2)H_(6)/C_(2)H_(4) mixtures,especially in the low-pressure range,which is further confirmed by the results of grand canonical Monte Carlo simulations for C_(2)H_(6) adsorption in this framework.The experimental breakthrough curves showed that C_(2)H_(4) with a high purity was collected directly from both 1:9 and 1:15 C_(2)H_(6)/C_(2)H_(4)(volume ratio)mixtures at 298 K and 100 kPa.Moreover,the unchanged adsorption and separation performance after cycling experiments confirmed the promising applicability of this material in future. 展开更多
关键词 Titanium metal-organic framework ADSORPTION Separation Ethylene purification Strong binding affinity Molecular simulation
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Identification and characterization of GIP1,an Arabidopsis thaliana protein that enhances the DNA binding affinity and reduces the oligomeric state of G-box binding factors
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作者 Paul C.SEHNKE Beth J.LAUGHNER +2 位作者 Carla R.LYERLY LINEBARGER William B.GURLEY Robert J.FERL 《Cell Research》 SCIE CAS CSCD 2005年第8期567-575,共9页
Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding... Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors(GBFs).The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood.In an effort to identify potential GBF binding and control partners,maize GBF1 was used as bait in a yeast two-hybrid screen of an A.thaliana cDNA library.GBF Interacting Protein 1(GIP1)arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs.Northern analysis of A.thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript,predominantly in roots.Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus.In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A.thaliana GBF3 or maize GBF1,showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration,suggesting a transient association between GIP1 and GBF.Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP.These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar,and potentially regulates the multimeric state of GBFs,thereby contributing to bZIP-mediated gene regulation. 展开更多
关键词 G-box binding factor interacting protein nuclear chaperone DNA binding affinity.
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Residues important to the allosteric regulation on ligand binding affinity in β3 integrins
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作者 Jizhong Lou1,Wei Chen2,Mei-Yin Chou3,Cheng Zhu1,2,3,4(1Parker H.Petit Institute for Bioengineering and Bioscience,2Woodruff School of Mechanical Engineering,and 3School of Physics,4Coulter Department of Biomedical Engineering,,Georgia Institute of Technology,GA,USA) 《医用生物力学》 EI CAS CSCD 2009年第S1期20-20,共1页
Integrins are heterodimers that mediate cell adhesion and transduce signals bidirectionally across the cell membrane.Integrins often exist in low affinity(or inactive) states for
关键词 Residues important to the allosteric regulation on ligand binding affinity in
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Altered hACE2 binding affinity and S1/S2 cleavage efficiency of SARS-CoV-2 spike protein mutants affect viral cell entry 被引量:1
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作者 Ke Wang Yu Pan +5 位作者 Dianbing Wang Ye Yuan Min Li Yuanyuan Chen Lijun Bi Xian-En Zhang 《Virologica Sinica》 SCIE CAS CSCD 2023年第4期595-605,共11页
SARS-CoV-2 variants are constantly emerging,hampering public health measures in controlling the number of infections.While it is well established that mutations in spike proteins observed for the different variants di... SARS-CoV-2 variants are constantly emerging,hampering public health measures in controlling the number of infections.While it is well established that mutations in spike proteins observed for the different variants directly affect virus entry into host cells,there remains a need for further expansion of systematic and multifaceted comparisons.Here,we comprehensively studied the effect of spike protein mutations on spike expression and proteolytic activation,binding affinity,viral entry efficiency and host cell tropism of eight variants of concern(VOC)and variants of interest(VOI).We found that both the full-length spike and its receptor-binding domain(RBD)of Omicron bind to hACE2 with an affinity similar to that of the wild-type.In addition,Alpha,Beta,Delta and Lambda pseudoviruses gained significantly enhanced cell entry ability compared to the wild-type,while the Omicron pseudoviruses showed a slightly increased cell entry,suggesting the vastly increased rate of transmission observed for Omicron variant is not associated with its affinity to hACE2.We also found that the spikes of Omicron and Mu showed lower S1/S2 cleavage efficiency and inefficiently utilized TMPRSS2 to enter host cells than others,suggesting that they prefer the endocytosis pathway to enter host cells.Furthermore,all variants'pseudoviruses we tested gained the ability to enter the animal ACE2-expressing cells.Especially the infection potential of rats and mice showed significantly increased,strongly suggesting that rodents possibly become a reservoir for viral evolution.The insights gained from this study provide valuable guidance for a targeted approach to epidemic control,and contribute to a better understanding of SARS-CoV-2 evolution. 展开更多
关键词 SARS-CoV-2 Variants of Concern(VOC) Omicron binding affinity Viral entry Host-tropism
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FingerDTA:A Fingerprint-Embedding Framework for Drug-Target Binding Affinity Prediction
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作者 Xuekai Zhu Juan Liu +3 位作者 Jian Zhang Zhihui Yang Feng Yang Xiaolei Zhang 《Big Data Mining and Analytics》 EI CSCD 2023年第1期1-10,共10页
Many efforts have been exerted toward screening potential drugs for targets,and conducting wet experiments remains a laborious and time-consuming approach.Artificial intelligence methods,such as Convolutional Neural N... Many efforts have been exerted toward screening potential drugs for targets,and conducting wet experiments remains a laborious and time-consuming approach.Artificial intelligence methods,such as Convolutional Neural Network(CNN),are widely used to facilitate new drug discovery.Owing to the structural limitations of CNN,features extracted from this method are local patterns that lack global information.However,global information extracted from the whole sequence and local patterns extracted from the special domain can influence the drugtarget affinity.A fusion of global information and local patterns can construct neural network calculations closer to actual biological processes.This paper proposes a Fingerprint-embedding framework for Drug-Target binding Affinity prediction(FingerDTA),which uses CNN to extract local patterns and utilize fingerprints to characterize global information.These fingerprints are generated on the basis of the whole sequence of drugs or targets.Furthermore,FingerDTA achieves comparable performance on Davis and KIBA data sets.In the case study of screening potential drugs for the spike protein of the coronavirus disease 2019(COVID-19),7 of the top 10 drugs have been confirmed potential by literature.Ultimately,the docking experiment demonstrates that FingerDTA can find novel drug candidates for targets.All codes are available at http://lanproxy.biodwhu.cn:9099/mszjaas/FingerDTA.git. 展开更多
关键词 drug-target binding affinity FINGERPRINT new drug discovery
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Computational Assessment of Protein–protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes
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作者 Bo Wang Zhaoqian Su Yinghao Wu 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2021年第6期1012-1022,共11页
The cellular functions of proteins are maintained by forming diverse complexes.The stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can c... The cellular functions of proteins are maintained by forming diverse complexes.The stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can cause various diseases such as cancer and diabetes.As a result,accurate estimation of the binding stability and the effects of mutations on changes of binding affinity is a crucial step to understanding the biological functions of proteins and their dysfunctional consequences.It has been hypothesized that the stability of a protein complex is dependent not only on the residues at its binding interface by pairwise interactions but also on all other remaining residues that do not appear at the binding interface.Here,we computationally reconstruct the binding affinity by decomposing it into the contributions of interfacial residues and other non-interfacial residues in a protein complex.We further assume that the contributions of both interfacial and non-interfacial residues to the binding affinity depend on their local structural environments such as solvent-accessible surfaces and secondary structural types.The weights of all corresponding parameters are optimized by Monte-Carlo simulations.After cross-validation against a large-scale dataset,we show that the model not only shows a strong correlation between the absolute values of the experimental and calculated binding affinities,but can also be an effective approach to predict the relative changes of binding affinity from mutations.Moreover,we have found that the optimized weights of many parameters can capture the first-principle chemical and physical features of molecular recognition,therefore re-versely engineering the energetics of protein complexes.These results suggest that our method can serve as a useful addition to current computational approaches for predicting binding affinity and understanding the molecular mechanism of protein–protein interactions. 展开更多
关键词 Protein-protein interaction binding affinity Non-interfacial residue Knowledge-based potential Monte-Carlo simulation
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Accelerating Factor Xa inhibitor discovery with a de novo drug design pipeline
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作者 Yujing Zhao Qilei Liu +3 位作者 Jian Du Qingwei Meng Liang Sun Lei Zhang 《Chinese Journal of Chemical Engineering》 SCIE EI CAS CSCD 2024年第8期85-94,共10页
Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug ... Small-molecule drugs are essential for maintaining human health. The objective of this study is to identify a molecule that can inhibit the Factor Xa protein and be easily procured. An optimization-based de novo drug design framework, Drug CAMD, that integrates a deep learning model with a mixed-integer nonlinear programming model is used for designing drug candidates. Within this framework, a virtual chemical library is specifically tailored to inhibit Factor Xa. To further filter and narrow down the lead compounds from the designed compounds, comprehensive approaches involving molecular docking,binding pose metadynamics(BPMD), binding free energy calculations, and enzyme activity inhibition analysis are utilized. To maximize efficiency in terms of time and resources, molecules for in vitro activity testing are initially selected from commercially available portions of customized virtual chemical libraries. In vitro studies assessing inhibitor activities have confirmed that the compound EN300-331859shows potential Factor Xa inhibition, with an IC_(50)value of 34.57 μmol·L^(-1). Through in silico molecular docking and BPMD, the most plausible binding pose for the EN300-331859-Factor Xa complex are identified. The estimated binding free energy values correlate well with the results obtained from biological assays. Consequently, EN300-331859 is identified as a novel and effective sub-micromolar inhibitor of Factor Xa. 展开更多
关键词 Chemical product design Mathematical programming method Deep learning binding affinity Factor Xa inhibitor
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Toxicity and binding analyses of Bacillus thuringiensis toxin Vip3A in Cry1Ac-resistant and-susceptible strains of Helicoverpa armigera(Hübner)
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作者 ZHANG Qian CHEN Li-zhen +2 位作者 LU Qiong ZHANG Yan LIANG Ge-mei 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2015年第2期347-354,共8页
The Bacillus thuringiensis vegetative insecticidal protein, Vip3 A, represents a new family of Bt toxin and is currently applied to commercial transgenic cotton. To determine whether the Cry1Ac-resistant Helicoverpa a... The Bacillus thuringiensis vegetative insecticidal protein, Vip3 A, represents a new family of Bt toxin and is currently applied to commercial transgenic cotton. To determine whether the Cry1Ac-resistant Helicoverpa armigera is cross-resistant to Vip3 Aa protein, insecticidal activities, proteolytic activations and binding properties of Vip3 Aa toxin were investigated using Cry1Ac-susceptible(96S) and Cry1Ac-resistant H. armigera strain(Cry1Ac-R). The toxicity of Vip3 Aa in Cry1Ac-R slightly reduced compared with 96 S, the resistance ratio was only 1.7-fold. The digestion rate of full-length Vip3 Aa by gut juice extracts from 96 S was little faster than that from Cry1Ac-R. Surface plasmon resonance(SPR) showed there was no significant difference between the binding affinity of Vip3 Aa and BBMVs between 96 S and Cry1Ac-R strains, and there was no significant competitive binding between Vip3 Aa and Cry1 Ac in susceptible or resistant strains. So there had little cross-resistance between Vip3 Aa and Cry1 Ac,Vip3A+Cry proteins maybe the suitable pyramid strategy to control H. armigera in China in the future. 展开更多
关键词 vegetative insecticidal proteins(Vip3Aa) Bacillus thuringiensis Helicoverpa armigera CROSS-RESISTANCE binding affinity
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Effective anti-inflammatory phenolic compounds from dandelion:identification and mechanistic insights using UHPLC-ESI-MS/MS,fluorescence quenching and anisotropy,molecular docking and dynamics simulation 被引量:1
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作者 Hui Zou Tingting Ben +2 位作者 Ping Wu Geoffrey I.N.Waterhouse Yilun Chen 《Food Science and Human Wellness》 SCIE CSCD 2023年第6期2184-2194,共11页
This novel study identifi es the effective anti-inflammatory phenolic compounds in dandelion and provides mechanistic insights into their interactions with receptor proteins(toll-like receptor 4,TLR4;co-receptor myelo... This novel study identifi es the effective anti-inflammatory phenolic compounds in dandelion and provides mechanistic insights into their interactions with receptor proteins(toll-like receptor 4,TLR4;co-receptor myeloid differentiation protein-2,MD-2)using UHPLC-ESI-MS/MS,lipopolysaccharide(LPS)-stimulated THP-1 cell line,fluorescence quenching and anisotropy,molecular docking(single ligand and multi-ligand docking)and molecular dynamics simulation.A 50%aqueous methanol extract had a greater anti-inflammatory effect and higher chicoric acid content,compared with the 100%water and 100%methanol extracts.Chicoric acid,chlorogenic acid,methylophiopogonone A,caffeic acid,gallic acid monohydrate and 4’-O-demethylbroussonin A had relatively high binding energies and contents in all extracts.Chicoric acid competed with chlorogenic acid,4’-O-demethylbroussonin A and quercetin for MD-2.Among dandelion’s phenolics,chicoric acid most effectively hindered TLR4-MD-2 complex formation,with a quenching constant of 0.62×10^(6) L/mol for MD-2 or TLR4 at 320 K,and binding energies of-6.87 and-5.97 kcal/mol,respectively,for MD-2 and TLR4. 展开更多
关键词 Dandelion extracts Phenolic compounds binding affinity TLR4-MD-2 antagonist Anti-inflammatory agent
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Early-life exposure to per-and polyfluoroalkyl substances:Analysis of levels,health risk and binding abilities to transport proteins 被引量:1
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作者 Yaqi Xu Xinyao Sui +5 位作者 Jinhong Li Liyi Zhang Pengpeng Wang Yang Liu Huijing Shi Yunhui Zhang 《Eco-Environment & Health》 2024年第3期308-316,共9页
Per-and polyfluoroalkyl substances(PFAS)can pass through the placenta and adversely affect fetal development.However,there is a lack of comparison of legacy and emerging PFAS levels among different biosamples in pregn... Per-and polyfluoroalkyl substances(PFAS)can pass through the placenta and adversely affect fetal development.However,there is a lack of comparison of legacy and emerging PFAS levels among different biosamples in pregnant women and their offspring.This study,based on the Shanghai Maternal–Child Pairs Cohort,analyzed the concentrations of 16 PFAS in the maternal serum,cord serum,and breast milk samples from 1,076 motherchild pairs.The placental and breastfeeding transfer efficiencies of PFAS were determined in maternal-cord and maternal-milk pairs,respectively.The binding affinities of PFAS to five transporters were simulated using molecular docking.The results suggested that PFAS were frequently detected in different biosamples.The median concentration of perfluorooctane sulfonate(PFOS)was the highest at 8.85 ng/mL,followed by perfluorooctanoic acid(PFOA)at 7.13 ng/mL and 6:2 chlorinated polyfluorinated ether sulfonate at 5.59 ng/mL in maternal serum.The median concentrations of PFOA were highest in cord serum(4.23 ng/mL)and breast milk(1.08 ng/mL).PFAS demonstrated higher placental than breastfeeding transfer efficiencies.The transfer efficiencies and the binding affinities of most PFAS to proteins exhibited alkyl chain length-dependent patterns.Furthermore,we comprehensively assessed the estimated daily intakes(EDIs)of PFAS in breastfeeding infants of different age groups and used the hazard quotient(HQ)to characterize the potential health risk.EDIs decreased with infant age,and PFOS had higher HQs than PFOA.These findings highlight the significance of considering PFAS exposure,transfer mechanism,and health risks resulting from breast milk intake in early life. 展开更多
关键词 Emerging PFAS Placental transfer Breast milk Health risk binding affinity
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A larval specific OBP able to bind the major female sex pheromone component in Spodoptera exigua(Hübner) 被引量:6
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作者 JIN Rong LIU Nai-yong +1 位作者 LIU Yan DONG Shuang-lin 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2015年第7期1356-1366,共11页
Odorant binding proteins (OBPs) in insects are postulated to solubilize and transport the hydrophobic odorants across the hydrophilic antennal lymph to the olfactory receptors (ORs) located on the dendrite membran... Odorant binding proteins (OBPs) in insects are postulated to solubilize and transport the hydrophobic odorants across the hydrophilic antennal lymph to the olfactory receptors (ORs) located on the dendrite membrane of the sensory neurons. OBPs in adult insects have been intensively reported, but those in larvae are rarely addressed. In our study, a full-length OBP cDNA, namely SexiOBP13, was cloned by RT-PCR and RACE strategy from the heads of Spodoptera exigua larvae. The quantitative real-time PCR (qPCR) measurement indicated that SexiOBP13 was highly expressed in larval head, but very low in other parts of larva and was not detected in any tissues of adult. The binding affinities of SexiOBP13 to plant volatiles and female sex pheromone components were measured by competitive binding assays. Interestingly, SexiOBP13 displayed a high binding affinity (Ki=3.82 IJmol L-1) to Z9,E12-14:Ac, the major sex pheromone component of S. exigua, while low affinities to the tested host plant volatiles (Ki〉27 μmol L-l). The behavioral tests further confirmed that Z9,E12-14:Ac was indeed active to elicit the behavioral activity of the third instar larvae of S. exigua. Taken together, our results suggest that SexiOBP13 may play a role in reception of female sex pheromone in S. exigua larvae. The ecological significance of the larvae preference to the adult female sex pheromone was discussed. 展开更多
关键词 odorant binding protein female sex pheromone larval specificity binding affinity behavioral response
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CHEMICAL DERIVATION OF HUMAN INSULIN SUPERAGONISM
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作者 MA Baoquan KANG Wei YAN Junkai 《Chinese Journal of Reactive Polymers》 2007年第1期90-95,共6页
The role of three highly conserved insulin residues Tyr^B26 was studied to better understand the relationship between insulin and receptor from rat adipose tissue plasma membranes, lnsulin analogues with a single amin... The role of three highly conserved insulin residues Tyr^B26 was studied to better understand the relationship between insulin and receptor from rat adipose tissue plasma membranes, lnsulin analogues with a single amino acid substitution or single N-methylation of the peptide bond in the position B26 were all shortened in the C-terminus of the B-chain by four amino acids. The effect of modifications was followed by the binding to the insulin receptor. From our results, we can deduce several conclusions: (1) the replacement of tyrosine in the position B26 by histidine, [N-MeHis^B26]-des-tetrapeptide-(B27-B30)-insulin-B26-amide and [N-MeGlu^B26]-des-tetrapeptide- (B2-B30)-insulin-B26-amide, have no significant effect on the binding affinity and they show binding affinity 105%, 190% and 208%, respectively, of that of human insulin; (2) [Aad^B26] -des-tetrapeptide-(B27-B30)-insulin-B26-amide and [Phe(4-carboxy^B26)]-des-tetrapeptide- (B27~B30)-insulin-B26-amide affect the potency highly positively in vitro studies; they show binding affinity 529 and 289 %, respectively, of that of human insulin. 展开更多
关键词 lnsulin binding affinity [N-MeHis^B26]-des-tetrapeptide-(B27-B30)-insulin-B26-amide.
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Expression and functional characterization of odorant-binding protein 2 in the predatory mite Neoseiulus barkeri
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作者 Yixia Wu Yaying Li +4 位作者 Wenqiang Chu Tiandi Niu Xiaotian Feng Rongjiang Ma Huai Liu 《Insect Science》 SCIE CAS CSCD 2023年第5期1493-1506,共14页
Olfaction plays a crucial role for arthropods in foraging,mating,and oviposition.The odorant-binding protein(OBP)gene is considered one of the most important olfactory genes.However,little is known about its functions... Olfaction plays a crucial role for arthropods in foraging,mating,and oviposition.The odorant-binding protein(OBP)gene is considered one of the most important olfactory genes.However,little is known about its functions in predatory mites.Here,we used Neoseiulus barkeri,an important commercialized natural pest control,to explore the chemosensory characteristics of OBP.In this study,N.barkeri was attracted by methyl salicylate(MeSA)and showed higher crawling speeds under MeSA treatment.Then,we identified and cloned an OBP gene named Nbarobp2 and analyzed its expression profiles in the predatory mite.Nbarobp2 was 663 bp,was highly expressed in larval and nymphal stages,and was significantly upregulated in N.barkeri under MeSA treatment.Nbarobp2 encoded 202 amino acid residues with a molecular weight of 23 kDa(after removing the signal peptide).Sequence comparisons revealed that the OBPs in Arachnida shared 6 conserved cysteine sites,but were distinguishable from the OBPs of Insecta on the phylogenetic tree.RNA interference,Western blotting,and binding affinity assays further proved that Nbarobp2 was involved in volatile perception in predatory mites.This study shed light on the functional characteristics of OBPs in predatory mites,providing a new insight for better biological control. 展开更多
关键词 binding affinity crawling speed heterologous expression methyl salicylate olfactory behavior RNA interference
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Molecular Modelling of the Therapeutic agents for COVID-19 Treatment
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作者 Akram Ranjbar Ranjbar Sara Torabi Torabi +2 位作者 Davood Nematollahi Nematollahi Mahdi Jamshidi Jamshidi Hadi Ghasemi Ghasemi 《Infectious Diseases Research》 2021年第1期1-9,共9页
Objective:We aimed to develop a bioinformatics approach for drug discovery variety of effective drugs for Coronavirus disease treatment(COVID-19).Methods:First,the structure of relevant drugs have been optimized and p... Objective:We aimed to develop a bioinformatics approach for drug discovery variety of effective drugs for Coronavirus disease treatment(COVID-19).Methods:First,the structure of relevant drugs have been optimized and prepared as input data for docking software.Then,The X-ray structure of SARS CoV-2(PDB ID:6VWW)and 2019-nCoV(PDB ID:6M0J)receptors is prepared by eliminating water molecules and unique ligands.Finally,significant interactions have been reported with Discovery Studio 4.5 Client software.Results:The MolDock Score value indicated the positive effect of drugs on the inactivation of COVID-19.Cobicistat and Ritonavir drugs have the most inhibitory effect(MolDock Scores:-160.49 and-205.91 kj/mol),and a wide spectrum of interactions such as Van der Waals,conventional hydrogen bond,carbon-hydrogen bond,Pi-doner hydrogen bond,Pi-Pi stacked,Pi Pi T-shaped,Alkyl,and Pi Alkyl is contributed in final binding affinity. 展开更多
关键词 Novel coronavirus COVID-19 Virtualscreening Molecular docking MolergroVirtualDocker MolDock Score binding affinity
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Principles of amino-acid–ribonucleotide interaction revealed by binding affinities between homogeneous oligopeptides and singlestranded RNA molecules
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作者 Pengyu Wang Xiaocui Fang +3 位作者 Ping Li Minxian Li Yanlian Yang Chen Wang 《Nano Research》 SCIE EI CSCD 2023年第12期13294-13300,共7页
We have determined the binding strengths between ribonucleotides of adenine(A),guanine(G),uracil(U),and cytosine(C)in homogeneous single-stranded ribonucleic acids(ssRNAs)and homo-decapeptides consisting of 20 common ... We have determined the binding strengths between ribonucleotides of adenine(A),guanine(G),uracil(U),and cytosine(C)in homogeneous single-stranded ribonucleic acids(ssRNAs)and homo-decapeptides consisting of 20 common amino acids.We use a bead-based fluorescence assay for these measurements in which decapeptides are immobilized on the bead surface and ssRNAs are in solutions.The results provide a molecular basis for analyzing selectivity,specificity,and polymorphisms of amino-acid–ribonucleotide interactions.Comparative analyses of the distribution of the binding energies reveal unique binding strength patterns assignable to each pair of amino acid and ribonucleotide originating from the chemical structures.Pronounced favorable(such as Arg–G)and unfavorable(such as Met–U)binding interactions can be identified in selected groups of amino acid and ribonucleotide pairs that could provide basis to elucidate energetics of amino-acid–ribonucleotide interactions.Such interaction selectivity,specificity,and polymorphism manifest the contributions from RNA backbone,RNA bases,as well as main chain and side chain of the amino acids.Such characteristics in peptide–RNA interactions might be helpful for understanding the mechanism of protein–RNA specific recognition and the design of RNA nano-delivery systems based on peptides and their derivatives. 展开更多
关键词 PEPTIDES single-stranded ribonucleic acid(ssRNA) binding affinity flow cytometry
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Q-BioLiP:A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions
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作者 Hong Wei Wenkai Wang +1 位作者 Zhenling Peng Jianyi Yang 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2024年第1期151-159,共9页
Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand... Since its establishment in 2013,BioLiP has become one of the widely used resources for protein-ligand interactions.Nevertheless,several known issues occurred with it over the past decade.For example,the protein-ligand interactions are represented in the form of single chain-based tertiary structures,which may be inappropriate as many interactions involve multiple protein chains(known as quaternary structures).We sought to address these issues,resulting in Q-BioLiP,a comprehensive resource for quaternary structure-based protein-ligand interactions.The major features of Q-BioLiP include:(1)representing protein structures in the form of quaternary structures rather than single chain-based tertiary structures;(2)pairing DNA/RNA chains properly rather than separation;(3)providing both experimental and predicted binding affinities;(4)retaining both biologically relevant and irrelevant interactions to alleviate the wrong justification of ligands’biological relevance;and(5)developing a new quaternary structure-based algorithm for the modelling of protein-ligand complex structure.With these new features,Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions,including protein-small molecule interaction,protein-metal ion interaction,protein-peptide interaction,protein-protein interaction,protein-DNA/RNA interaction,and RNA-small molecule interaction.Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/. 展开更多
关键词 Protein-ligand interaction Quaternary structure Protein-ligand binding site Protein-protein interaction binding affinity
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Covalent Organic Framework with Predesigned Single-Ion Traps for Highly Efficient Palladium Recovery from Wastes
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作者 Yinghui Xie Qiuyu Rong +7 位作者 Caimei Wen Xiaolu Liu Mengjie Hao Zhongshan Chen Hui Yang Geoffrey I.N.Waterhouse Shengqian Ma Xiangke Wang 《CCS Chemistry》 CSCD 2024年第8期1908-1919,共12页
The recovery of palladium from waste streams is of importance for metal recycling and environmental remediation.Herein,we present a“single-ion trap”strategy for efficiently recovering Pd(II)from superacidic solution... The recovery of palladium from waste streams is of importance for metal recycling and environmental remediation.Herein,we present a“single-ion trap”strategy for efficiently recovering Pd(II)from superacidic solutions and laboratory wastes.This was realized by rational design and synthesis of an antiparallel stacked covalent organic framework(ACOF)with hydrazine-carbonyl sites and pyridine sites for cooperative Pd(II)capture.The single-ion traps provided Lewis base sites with a high Pd(II)binding affinity,enabling the trapping of Pd(II)ions under a wide range of conditions.The developed ACOF-1 adsorbent demonstrated fast kinetics,excellent selectivity,and a high adsorption capacity of 412.9±14.2 mg/g for Pd(II)in a 3M HNO_(3) solution.When applied in a packed column,ACOF-1 dynamically captured Pd(II)from3M HNO_(3) solutions or laboratorywastes containing trace amounts of palladium and many other metals,realizing extraction efficiencies of 232.9 and 320.9 mg/g,respectively.Detailed experimental and theoretical studies revealed that the single-ion traps offered exceptionally strong binding of Pd(II)under both acidic and high ionic strength conditions,enabling selective adsorptive behavior not accessible using traditional adsorbents.Importantly,the general design strategy reported here could be used to create porous adsorbents for the capture of other precious metals. 展开更多
关键词 antiparallel stacking covalent organic frameworks binding affinity selective adsorption Pd(II)recovery
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Target binding and residence:a new determinant of DNA double-strand break repair pathway choice in CRISPR/Cas9 genome editing 被引量:2
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作者 Yili FENG Sicheng LIU +1 位作者 Ruodan CHEN Anyong XIE 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2021年第1期73-86,共14页
The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms,and holds trem... The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)is widely used for targeted genomic and epigenomic modifications and imaging in cells and organisms,and holds tremendous promise in clinical applications.The efficiency and accuracy of the technology are partly determined by the target binding affinity and residence time of Cas9-single-guide RNA(sgRNA)at a given site.However,little attention has been paid to the effect of target binding affinity and residence duration on the repair of Cas9-induced DNA double-strand breaks(DSBs).We propose that the choice of DSB repair pathway may be altered by variation in the binding affinity and residence duration of Cas9-sgRNA at the cleaved target,contributing to significantly heterogeneous mutations in CRISPR/Cas9 genome editing.Here,we discuss the effect of Cas9-sgRNA target binding and residence on the choice of DSB repair pathway in CRISPR/Cas9 genome editing,and the opportunity this presents to optimize Cas9-based technology. 展开更多
关键词 CRISPR/Cas9 genome editing Double-strand break(DSB)repair pathway choice Target binding affinity Target residence
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High affinity soluble ILT2 receptor:a potent inhibitor of CD8^(+)T cell activation 被引量:1
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作者 Ruth K.Moysey Yi Li +17 位作者 Samantha J.Paston Emma E.Baston Malkit S.Sami Brian J.Cameron Jessie Gavarret Penio Todorov Annelise Vuidepot Steven M.Dunn Nicholas J.Pumphrey Katherine J.Adams Fang Yuan Rebecca E.Dennis Deborah H.Sutton Andy D.Johnson Joanna E.Brewer Rebecca Ashfield Nikolai M.Lissin Bent K.Jakobsen 《Protein & Cell》 SCIE CSCD 2010年第12期1118-1127,共10页
Using directed mutagenesis and phage display on a soluble fragment of the human immunoglobulin superfamily receptor ILT2(synonyms:LIR1,MIR7,CD85j),we have selected a range of mutants with binding affinities enhanced b... Using directed mutagenesis and phage display on a soluble fragment of the human immunoglobulin superfamily receptor ILT2(synonyms:LIR1,MIR7,CD85j),we have selected a range of mutants with binding affinities enhanced by up to 168,000-fold towards the conserved region of major histocompatibility complex(MHC)class I molecules.Produced in a dimeric form,either by chemical cross-linking with bivalent polyethylene glycol(PEG)derivatives or as a genetic fusion with human IgG Fc-fragment,the mutants exhibited a further increase in ligand-binding strength due to the avidity effect,with resident half-times(t1/2)on the surface of MHC I-positive cells of many hours.The novel compounds antagonized the interaction of CD8 co-receptor with MHC I in vitro without affecting the peptide-specific binding of T-cell receptors(TCRs).In both cytokine-release assays and cell-killing experiments the engineered receptors inhibited the activation of CD8^(+)cytotoxic T lymphocytes(CTLs)in the presence of their target cells,with subnanomolar potency and in a dose-dependent manner.As a selective inhibitor of CD8^(+)CTL responses,the engineered high affinity ILT2 receptor presents a new tool for studying the activation mechanism of different subsets of CTLs and could have potential for the development of novel autoimmunity therapies. 展开更多
关键词 CD8^(+)T cells cellular activation AUTOIMMUNITY cell surface molecules binding affinity phage display
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