Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to d...Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to dynamically adjust their structures to accommodate functional needs.Mimicking this adaptability in synthetic systems is an ongoing challenge in supramolecular chemistry.展开更多
The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-d...The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-dicarboxylic acid(BCBDA))containing naphthalene rings on graphite surfaces have been investigated using scanning tunneling microscopy(STM).The transformation of nanostructures induced by the second components(EDA and PEBP-C4)have been also examined.Both CTTA and BCBDA molecules self-assemble at the 1-heptanoic acid(HA)/HOPG interface,forming porous network structures.The dimer represents the most elementary building unit due to the formation of double hydrogen bonds.Moreover,the flipping of naphthalene ring results in the isomerization of BCBDA molecule.The introduction of carboxylic acid derivative EDA disrupts the dimer,which subsequently undergoes a structural conformation to form a novel porous structure.Furthermore,upon the addition of pyridine derivative PEBP-C4,N–H⋯O hydrogen bonds are the dominant forces driving the three coassembled structures.We have also conducted density functional theory(DFT)calculations to determine the molecular conformation and analyze the mechanisms underlying the formation of nanostructures.展开更多
To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activi...To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activity of cathepsin B decreased with an increase in Na^(+)cation content and temperature.Additionally,decreasedα-helix content and increasedβ-sheet content were observed.The increase in sulfhydryl group content was attributed to the breaking of original disulfide bonds in the molecular structure or the release of embedded groups.Furthermore,the surface hydrophobicity gradually declined,which was consistent with the analysis of endogenous fluorescence spectroscopy.At the molecular level,the number of hydrogen bonds formed in NaCl-treated samples decreased,and the interactions between the hydrogen bonding were less powerful,which caused instability in the binding of the protein and substrate.The conformation of cathepsin B accurately characterized its activity,and the structural changes had a macroscopic effect on the decrease in protease activity.展开更多
Ovalbumin(OVA)is the major allergenic protein that can induce T helper 2(Th2)-allergic reactions,for which current treatment options are inadequate.In this study,we developed a polymerized hypoallergenic OVA product v...Ovalbumin(OVA)is the major allergenic protein that can induce T helper 2(Th2)-allergic reactions,for which current treatment options are inadequate.In this study,we developed a polymerized hypoallergenic OVA product via laccase/caffeic acid(Lac/CA)-catalyzed crosslinking in conjunction with galactomannan(Man).The formation of high molecular weight crosslinked polymers and the Ig G-binding were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE)and Western blotting.The study indicated that Lac/CA-catalyzed crosslinking plus Man conjugation substantially altered secondary and tertiary structures of OVA along with the variation in surface hydrophobicity.Gastrointestinal digestion stability assay indicated that crosslinked OVA exhibited less resistance in simulated gastric fluid(SGF)and simulated intestinal fluid(SIF).Mouse model study indicated that Lac-Man/OVA ameliorated eosinophilic airway inflammatory response and efficiently downregulated the expression of Th2-related cytokines(interleukin(IL)-4,IL-5,and IL-13),and upregulated IFN-γand IL-10 expression.Stimulation of bone marrow-derived dendritic cells with Lac-Man/OVA suppressed the expression of phenotypic maturation markers(CD80 and CD86)and MHC class II molecules,and suppressed the expression levels of proinflammatory cytokines.The knowledge obtained in the present study offers an effective way to acquire a hypoallergenic OVA product that can have a therapeutic effect in alleviating OVA-induced allergic asthma.展开更多
In a recent paper, solution-state ^(19)F NMR spectroscopy was used to probe the conformational dynamics of β-arrestin-1, an essential adaptor and signaling component of the G-protein couple receptor (GPCR) signaling ...In a recent paper, solution-state ^(19)F NMR spectroscopy was used to probe the conformational dynamics of β-arrestin-1, an essential adaptor and signaling component of the G-protein couple receptor (GPCR) signaling pathway. This work reveals a highly complex conformational energy landscape of β-arrestin-1, and illuminates the molecular mechanism of the membrane phosphoinositide PIP2-induced β-arrestin-1 activation at residue level.(https://doi.org/10.1038/s41467-023-43694-1).展开更多
Achieving selectivity in cell penetrating peptide(CPP)design is crucial to mitigate systemic toxicity and enable precise targeting based on distinct cellular phenotypes.Herein,we designed an amphiphilic peptide,L17Yp,...Achieving selectivity in cell penetrating peptide(CPP)design is crucial to mitigate systemic toxicity and enable precise targeting based on distinct cellular phenotypes.Herein,we designed an amphiphilic peptide,L17Yp,by incorporating phosphorylated tyrosine into natural occurring M-lycotoxin peptide,known for its potent membrane-lytic activity.This strategic modification induced a conformational shift,as confirmed by circular dichroism spectroscopy,transitioning it from its bioactiveα-helix conformation to an inactive random coli configuration,effectively shielding its membrane-penetrating capacity.Upon exposure to alkaline phosphatase,L17Yp undergoes enzymatic dephosphorylation,prompting a conformational shift that restores its membrane-transduction capabilities.This unique property hold promises for selective drug delivery.This work introduces an enzymatic approach for targeted perturbation of the cell membrane,offering promising prospects for precise drug delivery applications.展开更多
The conformational entropy S and free energy F were calculated by exact enumeration of polysilane chain up to 23 segments with excluded volume (EV) and long-range van der Waals (VW) interaction. A nonlinear relation b...The conformational entropy S and free energy F were calculated by exact enumeration of polysilane chain up to 23 segments with excluded volume (EV) and long-range van der Waals (VW) interaction. A nonlinear relation between SEV+VW and chain length n was found though S-EV was found to vary linearly with n. We found that the second-order transition temperature of polysilane chain with VW interaction increases with the increase of chain length, while that of polysilane chain without VW interaction is chain length independent. Moreover, the free energies FEV+VW and F-EV are both linearly related with n, and FEV+VW < F-EV for all temperatures.展开更多
A two-dimensional generalized Langevin equation is proposed to describe the protein conformational change, compatible to the electron transfer process governed by atomic packing density model. We assume a fractional G...A two-dimensional generalized Langevin equation is proposed to describe the protein conformational change, compatible to the electron transfer process governed by atomic packing density model. We assume a fractional Gaussian noise and a white noise through bond and through space coordinates respectively, and introduce the coupling effect coming from both fluctuations and equilibrium variances. The general expressions for autocorrelation functions of distance fluctuation and fluorescence lifetime variation are derived, based on which the exact conformational change dynamics can be evaluated with the aid of numerical Laplace inversion technique. We explicitly elaborate the short time and long time approximations. The relationship between the two-diraensional description and the one-dimensional theory is also discussed.展开更多
Here, we report a convenient and efficient synthesis strategy for the total synthesis of cyclic peptide reniochalistatin E and its conformational isomers with 32% overall yield. We found the linear peptide precursor w...Here, we report a convenient and efficient synthesis strategy for the total synthesis of cyclic peptide reniochalistatin E and its conformational isomers with 32% overall yield. We found the linear peptide precursor without side chain gave better cyclization yield.展开更多
Herein,we designed and constructed two metallacycles,1 and 2,to illustrate the conformational effect of isomeric AIE fluoropho res on the platfo rm of supramolecular coordination complexe s(SCCs).Specifically,the dang...Herein,we designed and constructed two metallacycles,1 and 2,to illustrate the conformational effect of isomeric AIE fluoropho res on the platfo rm of supramolecular coordination complexe s(SCCs).Specifically,the dangling phenyl rings in TPE units of the metallacycle 1 align completely outside the main cyclic structure,while in the metallacycle 2,these phenyl rings align half inside and half outside.The experimental results showed that two metallacycles exhibited different behaviors in terms of AIE fluorescence and chemical sensing,which could be attributed to the subtle structural difference of the TPE units.This work repre sents the unification of topics such as self-assembly,AIE,and chemical sensing,and further promotes the understanding for the structure-property relationship of isomeric AIE fluorophores.展开更多
A full-relaxation optimization of molecule and the Dreiding force field are employed to obtain the geometry parameters and the conformational energy surfaces of meso or racemic dyad of poly(acrylic acid) (PAA) and pol...A full-relaxation optimization of molecule and the Dreiding force field are employed to obtain the geometry parameters and the conformational energy surfaces of meso or racemic dyad of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). Three different carbonyl-bond orientations of side-groups resulted in the differences in depth of potential wells in their energetic contours for a meso or a racemic dyad. These discrepancies are interpreted as a result of various fine structures corresponding to grid search conformations as well as thereby different interactions. The analysis on the most stable conformations of PMAA confirmed that the ester groups are nearly perpendicular to the plane defined by the two adjacent skeletal bonds but may possibly change their relative orientations to meet the requirement of lower energy during the conformational state transition. For each polymer, two global energy maps of a meso and a racemic dyad were finally constructed from the superposition of energy data for the three kinds of side-group orientations by the Boltzmann factors. From an ensemble average, the proposed scheme with three rotational isomeric states (RIS) allowed us to access the experimentally unperturbed dimensions of PAA chain via the configurational statistical mechanics. Although the calculation was based on the short-range, local interactions, it was interested to note that the experimental characteristic ratios just fell within the range calculated for atactic chains.展开更多
The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution. This paper uses the AMBER8 package to investigate the electrolyte concentrati...The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution. This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d（CGCGAATTCGCG）2. The results from the restrained molecular dynamics （MD） simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA, and that the A→B conformational transition in aqueous NaCl solution is a downhill process. The results from the unrestrained MD simulations, as judged by the average distance between the C5＇ atoms （average helical rise per ten base pair）, show that the concentrated NaC1 solution slows down the A→B conformational transition. This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.展开更多
ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, unde...ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.展开更多
The title complex is widely used as an efficient key component of Ziegler-Natta catalyst for stereospecific polymerization of dienes to produce synthetic rubbers. However, the quantitative structure-activity relations...The title complex is widely used as an efficient key component of Ziegler-Natta catalyst for stereospecific polymerization of dienes to produce synthetic rubbers. However, the quantitative structure-activity relationship（QSAR） of this kind of complexes is still not clear mainly due to the difficulties to obtain their geometric molecular structures through laboratory experiments. An alternative solution is the quantum chemistry calculation in which the comformational population shall be determined. In this study, ten conformers of the title complex were obtained with the function of molecular dynamics conformational search in Gabedit 2.4.8, and their geometry optimization and thermodynamics calculation were made with a Sparkle/PM7 approach in MOPAC 2012. Their Gibbs free energies at 1 atm. and 298.15 K were calculated. Population of the conformers was further calculated out according to the theory of Boltzmann distribution, indicating that one of the ten conformers has a dominant population of 77.13%.展开更多
Structure-based virtual screening（molecular docking）is now one of the most pragmatic techniques to leverage target structure for ligand discovery.Accurate binding pose prediction is critical to molecular docking.Her...Structure-based virtual screening（molecular docking）is now one of the most pragmatic techniques to leverage target structure for ligand discovery.Accurate binding pose prediction is critical to molecular docking.Here,we describe a general strategy to improve the accuracy of docking pose prediction by implementing the structural descriptor-based fltering and KGS-penalty function-based conformational clustering in an unbiased manner.We assessed our method against 150 high-quality protein–ligand complex structures.Surprisingly,such simple components are suffcient to improve the accuracy of docking pose prediction.The success rate of predicting near-native docking pose increased from 53%of the targets to 78%.We expect that our strategy may have general usage in improving currently available molecular docking programs.展开更多
Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability dis...Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization,from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.展开更多
Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional materials.Although NTE behaviors have been found in kinds of compounds,it remains challeng...Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional materials.Although NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE property.In this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related polymers.In order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB conformation.This rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.展开更多
Theoretical results of normal coordinate analysis of polybenzamide performed with two conformational isomerized models, the cis trans and the all-trans conformation, have been adopted to examine a number of infrared s...Theoretical results of normal coordinate analysis of polybenzamide performed with two conformational isomerized models, the cis trans and the all-trans conformation, have been adopted to examine a number of infrared spectra of films of the polymer treated in a subsequent annealing process and a cooling process. It shows, in this investigation, that two sets of infrared spectral profiles around 1400 cm^(-1) and 900 cm^(-1) behave quite attractively. Their spectral behaviours have been correlated to the conformational defect variation in samples, and reasonably predicted by the normal coordinate calculation.展开更多
Objective:To do mapping and modeling of conformational B cell epitope regions of highly conserved and protective regions of three merozoitecandidate vaccine proteins of Plasmodium vivax(P.vivax),ie.merozoite purface p...Objective:To do mapping and modeling of conformational B cell epitope regions of highly conserved and protective regions of three merozoitecandidate vaccine proteins of Plasmodium vivax(P.vivax),ie.merozoite purface protein-1(PvMSP-1),apical membrane antigen-1 domainⅡ(PvAMA1-DⅡ)and regionⅡof the Duffy binding protein(PvDBPⅡ).and to analyze the immunogenie properties of these predicted epitopes.Methods:3-D structures of amino acid haplotypes from Sri Lanka(available in GeneBank)of PvMSP-1_(19)(n=27),PvAMA1-DⅡ(n=21)and PvDBPⅡ(n=33)were modeled.SEPPA,selected as the best online server was used for conformational epitope predictions,while prediction and moodeling of protein structuve and properties related to immunogenicity was carried out with Geno3D server.SCRATCH Protein Server,NetSurfP Server and standaloneroftware,Genious 5.4.4.Results:SEPPA revealed that regions of predicted conformational epitopes formed 4 clusters in PvMSP-I_(19),and 3 clusters each in PvAMA1-DⅡand PvDBPⅡ,all of which displayed a high degree of hydrophilicity,contained solveut exposed residues,displayed high probability of antigenicity and showed positive antigenic propensity values,that indicated high degree of immunogenicity.Conclusions:Findings of this study revealed and confirmed that different parts of the sequences of each of the conserved regions of the three selected potential vaccine candidate antigens of P.vivax are important with regard to conformational epitope prediction that warrants further laboratory experimental invertigations in in vivo animal models.展开更多
Proteins are crucial to most biological processes, such as enzymes, and in various catalytic processes a dynamic motion is required. The dynamics of protein are embodied as a conformational change, which is closely re...Proteins are crucial to most biological processes, such as enzymes, and in various catalytic processes a dynamic motion is required. The dynamics of protein are embodied as a conformational change, which is closely related to the flexibility of protein. Recently, nanopore sensors have become accepted as a low cost and high throughput method to study the features of proteins. In this article, we used a SiN nanopore device to study the flexibility of T7 RNA polymerase（RNAP） and its complex with DNA promoter. By calculating full-width at half-maximum（FWHM） of Gaussian fits to the blockade histograms, we found that T7 RNAP becomes more flexible after binding DNA promoter. Moreover, the distribution of fractional current blockade suggests that flexibility alters due to a breath-like change of the volume.展开更多
基金the Natural Science Foundation of China(No.22301131)the Natural Science Foundation of Jiangsu Province(Nos.BK20220781,BK20240679)the National Key Research and Development Program of China(No.2024YFB3815700)are greatly acknowledged.
文摘Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to dynamically adjust their structures to accommodate functional needs.Mimicking this adaptability in synthetic systems is an ongoing challenge in supramolecular chemistry.
基金financially supported by the National Natural Science Foundation of China(No.22272039)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB36000000)+1 种基金the Youth Program of the Liaoning Education Department(No.LJKQZ20222280)the Jilin Chinese Academy of Sciences-Yanshen Technology Co.,Ltd.
文摘The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-dicarboxylic acid(BCBDA))containing naphthalene rings on graphite surfaces have been investigated using scanning tunneling microscopy(STM).The transformation of nanostructures induced by the second components(EDA and PEBP-C4)have been also examined.Both CTTA and BCBDA molecules self-assemble at the 1-heptanoic acid(HA)/HOPG interface,forming porous network structures.The dimer represents the most elementary building unit due to the formation of double hydrogen bonds.Moreover,the flipping of naphthalene ring results in the isomerization of BCBDA molecule.The introduction of carboxylic acid derivative EDA disrupts the dimer,which subsequently undergoes a structural conformation to form a novel porous structure.Furthermore,upon the addition of pyridine derivative PEBP-C4,N–H⋯O hydrogen bonds are the dominant forces driving the three coassembled structures.We have also conducted density functional theory(DFT)calculations to determine the molecular conformation and analyze the mechanisms underlying the formation of nanostructures.
基金supported by the National Natural Science Foundation of China(31972097)Jiangsu Key Research and Development Plan(Modern Agriculture)(BE2020302)+1 种基金the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(24KJB550003)2024 Huaiyin Institute of Technology Talent Recruitment Research Startup Fund Project(Z301B24521)。
文摘To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activity of cathepsin B decreased with an increase in Na^(+)cation content and temperature.Additionally,decreasedα-helix content and increasedβ-sheet content were observed.The increase in sulfhydryl group content was attributed to the breaking of original disulfide bonds in the molecular structure or the release of embedded groups.Furthermore,the surface hydrophobicity gradually declined,which was consistent with the analysis of endogenous fluorescence spectroscopy.At the molecular level,the number of hydrogen bonds formed in NaCl-treated samples decreased,and the interactions between the hydrogen bonding were less powerful,which caused instability in the binding of the protein and substrate.The conformation of cathepsin B accurately characterized its activity,and the structural changes had a macroscopic effect on the decrease in protease activity.
基金supported by the Guangdong Basic and Applied Basic Research Foundation(2021B15151300042021B1515140021)+2 种基金the Scientific Research Start-up Funding of Guangdong Medical University(1026/4SG21229G)China Postdoctoral Science Foundation(2021M702781)Guangdong Medical University Post-doctoral Research Funding(2BH19006P)。
文摘Ovalbumin(OVA)is the major allergenic protein that can induce T helper 2(Th2)-allergic reactions,for which current treatment options are inadequate.In this study,we developed a polymerized hypoallergenic OVA product via laccase/caffeic acid(Lac/CA)-catalyzed crosslinking in conjunction with galactomannan(Man).The formation of high molecular weight crosslinked polymers and the Ig G-binding were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE)and Western blotting.The study indicated that Lac/CA-catalyzed crosslinking plus Man conjugation substantially altered secondary and tertiary structures of OVA along with the variation in surface hydrophobicity.Gastrointestinal digestion stability assay indicated that crosslinked OVA exhibited less resistance in simulated gastric fluid(SGF)and simulated intestinal fluid(SIF).Mouse model study indicated that Lac-Man/OVA ameliorated eosinophilic airway inflammatory response and efficiently downregulated the expression of Th2-related cytokines(interleukin(IL)-4,IL-5,and IL-13),and upregulated IFN-γand IL-10 expression.Stimulation of bone marrow-derived dendritic cells with Lac-Man/OVA suppressed the expression of phenotypic maturation markers(CD80 and CD86)and MHC class II molecules,and suppressed the expression levels of proinflammatory cytokines.The knowledge obtained in the present study offers an effective way to acquire a hypoallergenic OVA product that can have a therapeutic effect in alleviating OVA-induced allergic asthma.
文摘In a recent paper, solution-state ^(19)F NMR spectroscopy was used to probe the conformational dynamics of β-arrestin-1, an essential adaptor and signaling component of the G-protein couple receptor (GPCR) signaling pathway. This work reveals a highly complex conformational energy landscape of β-arrestin-1, and illuminates the molecular mechanism of the membrane phosphoinositide PIP2-induced β-arrestin-1 activation at residue level.(https://doi.org/10.1038/s41467-023-43694-1).
基金supported by the National Natural Science Foundation of China(No.21975068)Natural Science Foundation of Hunan(No.2022JJ10008)+1 种基金Science and Technology and Development Foundation of Shenzhen(No.JCYJ20210324122403010)Natural Science Foundation of Changsha(No.kq2202152)。
文摘Achieving selectivity in cell penetrating peptide(CPP)design is crucial to mitigate systemic toxicity and enable precise targeting based on distinct cellular phenotypes.Herein,we designed an amphiphilic peptide,L17Yp,by incorporating phosphorylated tyrosine into natural occurring M-lycotoxin peptide,known for its potent membrane-lytic activity.This strategic modification induced a conformational shift,as confirmed by circular dichroism spectroscopy,transitioning it from its bioactiveα-helix conformation to an inactive random coli configuration,effectively shielding its membrane-penetrating capacity.Upon exposure to alkaline phosphatase,L17Yp undergoes enzymatic dephosphorylation,prompting a conformational shift that restores its membrane-transduction capabilities.This unique property hold promises for selective drug delivery.This work introduces an enzymatic approach for targeted perturbation of the cell membrane,offering promising prospects for precise drug delivery applications.
文摘The conformational entropy S and free energy F were calculated by exact enumeration of polysilane chain up to 23 segments with excluded volume (EV) and long-range van der Waals (VW) interaction. A nonlinear relation between SEV+VW and chain length n was found though S-EV was found to vary linearly with n. We found that the second-order transition temperature of polysilane chain with VW interaction increases with the increase of chain length, while that of polysilane chain without VW interaction is chain length independent. Moreover, the free energies FEV+VW and F-EV are both linearly related with n, and FEV+VW < F-EV for all temperatures.
基金This work was supported by the National Natural Science Foundation of China （No.20973119 and No.21033008）.
文摘A two-dimensional generalized Langevin equation is proposed to describe the protein conformational change, compatible to the electron transfer process governed by atomic packing density model. We assume a fractional Gaussian noise and a white noise through bond and through space coordinates respectively, and introduce the coupling effect coming from both fluctuations and equilibrium variances. The general expressions for autocorrelation functions of distance fluctuation and fluorescence lifetime variation are derived, based on which the exact conformational change dynamics can be evaluated with the aid of numerical Laplace inversion technique. We explicitly elaborate the short time and long time approximations. The relationship between the two-diraensional description and the one-dimensional theory is also discussed.
基金supported by the National Natural Science Foundation of China(No. 21372183)Program for Innovative Teams of Outstanding Young and Middle-aged Researchers in the Higher Education Institutions of Hubei Province(No. T201702)
文摘Here, we report a convenient and efficient synthesis strategy for the total synthesis of cyclic peptide reniochalistatin E and its conformational isomers with 32% overall yield. We found the linear peptide precursor without side chain gave better cyclization yield.
基金This work was financially supported by the National Natrual Science Foundation of China(Nos.21901161 and 22071152)Natural Science Foundation of Shanghai(No.20ZR1429200)+1 种基金the China Postdoctoral Science Foundation(No.2020M671094)Basic Research Program of Xi'an Jiaotong University(No.XZY022020018).
文摘Herein,we designed and constructed two metallacycles,1 and 2,to illustrate the conformational effect of isomeric AIE fluoropho res on the platfo rm of supramolecular coordination complexe s(SCCs).Specifically,the dangling phenyl rings in TPE units of the metallacycle 1 align completely outside the main cyclic structure,while in the metallacycle 2,these phenyl rings align half inside and half outside.The experimental results showed that two metallacycles exhibited different behaviors in terms of AIE fluorescence and chemical sensing,which could be attributed to the subtle structural difference of the TPE units.This work repre sents the unification of topics such as self-assembly,AIE,and chemical sensing,and further promotes the understanding for the structure-property relationship of isomeric AIE fluorophores.
基金This work was supported by the Youth Science Foundation of Acedemia Sinica the China Postdoctoral Science Foundation, the National Natural Science Foundation of China, and Polymer Physics Laboratory,Academia Sinica
文摘A full-relaxation optimization of molecule and the Dreiding force field are employed to obtain the geometry parameters and the conformational energy surfaces of meso or racemic dyad of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). Three different carbonyl-bond orientations of side-groups resulted in the differences in depth of potential wells in their energetic contours for a meso or a racemic dyad. These discrepancies are interpreted as a result of various fine structures corresponding to grid search conformations as well as thereby different interactions. The analysis on the most stable conformations of PMAA confirmed that the ester groups are nearly perpendicular to the plane defined by the two adjacent skeletal bonds but may possibly change their relative orientations to meet the requirement of lower energy during the conformational state transition. For each polymer, two global energy maps of a meso and a racemic dyad were finally constructed from the superposition of energy data for the three kinds of side-group orientations by the Boltzmann factors. From an ensemble average, the proposed scheme with three rotational isomeric states (RIS) allowed us to access the experimentally unperturbed dimensions of PAA chain via the configurational statistical mechanics. Although the calculation was based on the short-range, local interactions, it was interested to note that the experimental characteristic ratios just fell within the range calculated for atactic chains.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.20876083 and 20736003)Specialized Research Fund for the Doctorial Program of Higher Education of China(Grant No.2007003009)
文摘The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution. This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A→B conformational transition of DNA duplex d（CGCGAATTCGCG）2. The results from the restrained molecular dynamics （MD） simulations indicate that the total energies of the systems for A-DNA are always higher than those for B-DNA, and that the A→B conformational transition in aqueous NaCl solution is a downhill process. The results from the unrestrained MD simulations, as judged by the average distance between the C5＇ atoms （average helical rise per ten base pair）, show that the concentrated NaC1 solution slows down the A→B conformational transition. This observation can be well understood by analyses of the difference between the counterion distributions around A-DNA and B-DNA.
基金supported by the National Natu-ral Science Foundation of China(No.21073170 and No.21273209).
文摘ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.
基金supported by the National Natural Science Foundation of China(No.21476119)
文摘The title complex is widely used as an efficient key component of Ziegler-Natta catalyst for stereospecific polymerization of dienes to produce synthetic rubbers. However, the quantitative structure-activity relationship（QSAR） of this kind of complexes is still not clear mainly due to the difficulties to obtain their geometric molecular structures through laboratory experiments. An alternative solution is the quantum chemistry calculation in which the comformational population shall be determined. In this study, ten conformers of the title complex were obtained with the function of molecular dynamics conformational search in Gabedit 2.4.8, and their geometry optimization and thermodynamics calculation were made with a Sparkle/PM7 approach in MOPAC 2012. Their Gibbs free energies at 1 atm. and 298.15 K were calculated. Population of the conformers was further calculated out according to the theory of Boltzmann distribution, indicating that one of the ten conformers has a dominant population of 77.13%.
文摘Structure-based virtual screening（molecular docking）is now one of the most pragmatic techniques to leverage target structure for ligand discovery.Accurate binding pose prediction is critical to molecular docking.Here,we describe a general strategy to improve the accuracy of docking pose prediction by implementing the structural descriptor-based fltering and KGS-penalty function-based conformational clustering in an unbiased manner.We assessed our method against 150 high-quality protein–ligand complex structures.Surprisingly,such simple components are suffcient to improve the accuracy of docking pose prediction.The success rate of predicting near-native docking pose increased from 53%of the targets to 78%.We expect that our strategy may have general usage in improving currently available molecular docking programs.
基金the program "Small Systems Nonequilibrium Fluctuations,Dynamics and Stochastics,and Anomalous Behavior" of the Kavli Institute for Theoretical Physics China at the Chinese Academy of Sciences(KITPC),held in Bejing in July 2013funded by the French Institut de la Recherche M'edicale,under Grant MICROMEGAS PC201104+1 种基金the French Institut National du Cancer,under Grant INCa-5960the French Agence Nationale de la Recherche under Grant No.ANR-13-BSV5-0010-03.UPMC belongs to Sorbonne Universit'es
文摘Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization,from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.
基金supported by the National Natural Science Foundation of China (Nos.51633001,51721002 and 51873040)National Key R&D Program of China (No.2016YFC1100300)。
文摘Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional materials.Although NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE property.In this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related polymers.In order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB conformation.This rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.
文摘Theoretical results of normal coordinate analysis of polybenzamide performed with two conformational isomerized models, the cis trans and the all-trans conformation, have been adopted to examine a number of infrared spectra of films of the polymer treated in a subsequent annealing process and a cooling process. It shows, in this investigation, that two sets of infrared spectral profiles around 1400 cm^(-1) and 900 cm^(-1) behave quite attractively. Their spectral behaviours have been correlated to the conformational defect variation in samples, and reasonably predicted by the normal coordinate calculation.
文摘Objective:To do mapping and modeling of conformational B cell epitope regions of highly conserved and protective regions of three merozoitecandidate vaccine proteins of Plasmodium vivax(P.vivax),ie.merozoite purface protein-1(PvMSP-1),apical membrane antigen-1 domainⅡ(PvAMA1-DⅡ)and regionⅡof the Duffy binding protein(PvDBPⅡ).and to analyze the immunogenie properties of these predicted epitopes.Methods:3-D structures of amino acid haplotypes from Sri Lanka(available in GeneBank)of PvMSP-1_(19)(n=27),PvAMA1-DⅡ(n=21)and PvDBPⅡ(n=33)were modeled.SEPPA,selected as the best online server was used for conformational epitope predictions,while prediction and moodeling of protein structuve and properties related to immunogenicity was carried out with Geno3D server.SCRATCH Protein Server,NetSurfP Server and standaloneroftware,Genious 5.4.4.Results:SEPPA revealed that regions of predicted conformational epitopes formed 4 clusters in PvMSP-I_(19),and 3 clusters each in PvAMA1-DⅡand PvDBPⅡ,all of which displayed a high degree of hydrophilicity,contained solveut exposed residues,displayed high probability of antigenicity and showed positive antigenic propensity values,that indicated high degree of immunogenicity.Conclusions:Findings of this study revealed and confirmed that different parts of the sequences of each of the conserved regions of the three selected potential vaccine candidate antigens of P.vivax are important with regard to conformational epitope prediction that warrants further laboratory experimental invertigations in in vivo animal models.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.51622201,91733301,and 61571015)
文摘Proteins are crucial to most biological processes, such as enzymes, and in various catalytic processes a dynamic motion is required. The dynamics of protein are embodied as a conformational change, which is closely related to the flexibility of protein. Recently, nanopore sensors have become accepted as a low cost and high throughput method to study the features of proteins. In this article, we used a SiN nanopore device to study the flexibility of T7 RNA polymerase（RNAP） and its complex with DNA promoter. By calculating full-width at half-maximum（FWHM） of Gaussian fits to the blockade histograms, we found that T7 RNAP becomes more flexible after binding DNA promoter. Moreover, the distribution of fractional current blockade suggests that flexibility alters due to a breath-like change of the volume.
