Solvent effect on the conformations of-bis(4-nitrophenoxy)-alkanes w th different chain Lengths(Nn)was studied by UV spectra.In poor solvents such as EG-H_2O and THF-H_2O,with the water content higher than 50%,the K-b...Solvent effect on the conformations of-bis(4-nitrophenoxy)-alkanes w th different chain Lengths(Nn)was studied by UV spectra.In poor solvents such as EG-H_2O and THF-H_2O,with the water content higher than 50%,the K-bands of N_4. N,N_6 and N_(10)in the UV absorption spectra shifted to longer wavelengths as compared wth 4-nitrophenoxyethane(N_0).It is suggested that in poor solvents the two aromatic gr(?)ps are close to each other in parallel,forming ground state complexes.The K- bead of N_4 showed a blue shift from that of N_0 when the water content was around 5%,probably attributable to a conformation with the nitro group of one benzene ring sit(?)ing on the plane of the other benzene ring.展开更多
Up to now,the DNA molecule adsorbed on a surface was believed to always preserve its native structure.This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although th...Up to now,the DNA molecule adsorbed on a surface was believed to always preserve its native structure.This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated.High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled.We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress(>30 pNnm)inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges.In addition,the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity.The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending.The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics.The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear.The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.展开更多
Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformat...Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformations.When the ratio of hydrophilic and hydrophobic segments is N_(g,g)∶N_(g,r)=3∶1,no core-shell structure is observed,and unsegregated chains or clusters are substituted.When N_(g,g)∶N_(g,r)=3∶2or 3∶3,the core-shell comb-like chains can be assembled into single micelles or structures where several small micelles are strung together by the backbone,which is similar to the pearl-necklace structure formed by the polyelectrolytes in poor solvent.With the increase of backbone length or grafting density,the probability of forming single micelles becomes lower,but the structures of two,three or more small micelles strung together are more observed.Our results indicate how to obtain the desired self-assembled structures of core-shell comb-like chains by regulating the architectural parameters,which could provide insights for the optimization of molecular design in various applications.展开更多
Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search ...Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti- cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.展开更多
An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential ener...An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface （PES） of OlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G＊, BHandHLYP/6-31G＊ and BHandHLYP/6-311＋＋G＊＊ in order to reliably find the low energy conformations. The eonformational energies were finally determined with the methods of BHandHLYP, cam- B3LYP, B97D, and MP2 using the basis set of 6-311＋＋G（3df,3pd）. The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.展开更多
Conformations and reaction energetics are important for understanding the interactions be- tween biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion aff...Conformations and reaction energetics are important for understanding the interactions be- tween biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion affinities of glutamine （Gln） binding with alkali and alkaline earth metal ions. An efficient and reliable method of searching low energy conformations of metalated Gln is proposed and applied to the complexes of Gln.Gln.M^＋/＋＋（M＋/＋＋=Li^＋、Na^＋、K^＋、Rb^＋、Cs^＋、Be^＋＋、Mg^＋＋、Ca^＋＋、Sr^＋＋ and Ba^＋＋）.. In addition to all conformers known in literatures, many new important conformations are located, demonstrating the power of the new method and the necessity of the conformational search performed here. The metal coordination modes, relative energies, dipole moments, and equilibrium distributions of all important conformations of Gln.M^＋/＋＋ are calculated by the methods of B3LYP, BHandHLYP, and MP2. IR spectra and metalation enthalpies and free energies are also presented and compared with the available experiments. The results form an extensive database for systematic examination of the metalation properties of Gln.展开更多
The ground state hydrogen conformations and vibrational analysis of 3-deazauracil(3DAU)and 6-azauracil(6AU)tautomers(4-enol and 2,4-diol forms)have been calculated using ab initio Hartree-Fock(HF)and density functiona...The ground state hydrogen conformations and vibrational analysis of 3-deazauracil(3DAU)and 6-azauracil(6AU)tautomers(4-enol and 2,4-diol forms)have been calculated using ab initio Hartree-Fock(HF)and density functional theory(B3LYP)methods with 6-311++G(d,p)basis set level.The calculations have shown that the most probably preferential tautomer of 3DAU and 6AU are the 4-enol form,which gives best fit to the corresponding experimental data.The ground state conformer of the 2,4-diol form has two O—H bonds which are oriented externally and internally(to the N—H bond).The vibrational analyses of the ground state conformer of each tautomeric form of 3DAU and 6AU were done and their optimized geometry parameters(bond lengths and bond angles)were given.Furthermore,from the correlations values it was concluded that the B3LYP method is superior to the HF method for both the vibrational frequencies and the geometric parameters.展开更多
Conductances of different geometric conformations of boron ribbon devices are calculated by the ab initio method, The I-V characteristics of three devices are rather different due to the difference in structure. The c...Conductances of different geometric conformations of boron ribbon devices are calculated by the ab initio method, The I-V characteristics of three devices are rather different due to the difference in structure. The current of the hexagonal boron device is the largest and increases nonlinearly. The current of the hybrid hexagon-triangle boron device displays a large low-bias current and saturates at a value of about 5.2 uA, The current of the flat triangular boron flake exhibits a voltage gap at low bias and rises sharply with increasing voltage. The flat triangular boron device can be either conducting or insulating, depending on the field.展开更多
The melting and crystallization behavior have been investigated for an aromatic poly (azomethine ether)with non-linearly shaped molecular conformations. This polymer was found to undergo multiple melting processes and...The melting and crystallization behavior have been investigated for an aromatic poly (azomethine ether)with non-linearly shaped molecular conformations. This polymer was found to undergo multiple melting processes and its phase transition behavior was influenced sensitively by the thermal history of sample. A significant difference between the polymer chain aggregation abilities of samples cooled from the different states was observed. The possible molecular morphology and aggregation models for describing the structures of this polymer were proposed and discussed. The crystallization behavior of the samples cooled from the partially isotropic state and the influence of cooling rate on it have also been examined with DSC.展开更多
Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-acc...Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-accessible surface, and root-mean-square deviations are used to characterize the properties of VEF in aqueous solution. The VEF molecule is highly flexible in water and conformations can shift between the extended and folded states. The VEF molecule exists in extended state mostly in aqueous solution and the conformations bonded with ACE are also the extended ones. The findings indicate that MD simulations have a good agreement with the molecular docking analysis.展开更多
Conformational flexibility is essential to the stimuli-responsive property of organic materials,but achieving the reversible molecular transformation is still challenging in functional materials for the high energy ba...Conformational flexibility is essential to the stimuli-responsive property of organic materials,but achieving the reversible molecular transformation is still challenging in functional materials for the high energy barriers and restriction by intermolecular interactions.Herein,through the incorporation of various steric hindrances into phenothiazine derivatives with different positions and quantities to tune the molecular conformations by adjustable repulsive forces,the folded angles gradually changed from 180°to 90°in 17 compounds.When the angle located at 112°with moderated steric effect,dynamic and reversible transformation of conformations under mechanical force has been achieved for the low energy barriers and mutually regulated molecular motions,resulting in both selfrecoverable and stimuli-responsive phosphorescence properties for the first time.It opened up a new way to realize the self-recovery property of organic materials,which can facilitate the multi-functional property of smart materials with the opened avenue for other fields with inspiration.展开更多
Background:Phosphorylated signal transducer and activator of transcription 3(p-STAT3)has emerged as a critical modulator of hepatocellular carcinoma(HCC)progression.However,its role in three-dimensional(3D)chromatin c...Background:Phosphorylated signal transducer and activator of transcription 3(p-STAT3)has emerged as a critical modulator of hepatocellular carcinoma(HCC)progression.However,its role in three-dimensional(3D)chromatin conformation and the expression of genes linked to HCC aggressiveness remains largely unexplored.This study aimed to identify HCC 3D chromatin conformations that are regulated by sustained STAT3 activation and validate the molecular mechanisms underlying the aggressiveness of HCC.Methods:Comparative analyses were performed using HCC cell lines with varying levels of STAT3 activation.Chromatin immunoprecipitation-sequencing(ChIP-seq)for p-STAT3 and H3K27ac was conducted to map p-STAT3-associated genomic regions and assess its influence on chromatin states.Chromatin conformation sequencings(high-throughput chromosome conformation capture and high-throughput chromosome conformation capture followed by immunoprecipitation)were employed to investigate the 3D genome landscape and identify conformational changes linked to sustained p-STAT3 activation.RNAsequencing was performed to assess transcriptional changes in response to these chromatin rearrangements.Functional assays,including invasion and tube formation assays,were carried out to validate the phenotypic impact of p-STAT3 activation on HCC progressiveness.Pharmacological inhibition of STAT3 was tested to explore potential therapeutic avenues and resistance mechanisms.Results:We found that sustained activation of p-STAT3 was significantly associated with poor prognostic outcomes in HCC patients.ChIP-seq demonstrated that p-STAT3 regulated chromatin interactions,leading to the formation of frequently interacting regions(FIREs),stable structural units within the 3D genome.Genes within these p-STAT3-associated FIREs exhibited coordinated expression,with many involved in aggressiveness HCC phenotypes like invasion and tube formation.Chromatin conformation data indicated that these FIREs altered topologically associating domains(TADs),potentially influencing broader chromatin organization.Despite STAT3 inhibition,p-STAT3-associated chromatin conformations remained intact,maintaining the expression of genes within FIREs and contributing to drug resistance.Conclusions:Sustained p-STAT3 activation significantly alters the 3D chromatin conformation inHCC,particularly through the formation of FIREs.These p-STAT3-associated FIREs drive the expression of genes involved inHCC aggressiveness and remain active despite STAT3-targeted treatments,suggesting a mechanism of drug resistance.These findings highlight the potential of targeting 3D chromatin dynamics as a therapeutic strategy in HCC,especially in cases of STAT3 inhibitor resistance.展开更多
Based on the perfect rotational isomeric state model of isotactic polypropylene, the separation distances between an initial left helix stem and its re-entry stems have been investigated. The intervals are defined by ...Based on the perfect rotational isomeric state model of isotactic polypropylene, the separation distances between an initial left helix stem and its re-entry stems have been investigated. The intervals are defined by the formulae $$D_1 = \frac{{1.54}}{3}\sqrt {8(k_1^2 + k_2^2 + k_1 k_2 )/3} ( \times 10^{ - 1} nm)$$ for the left helix re-entry stem and $$D_2 = \frac{{1.54}}{3}\sqrt {8[k_1^2 + k_2^2 + (k_1 - 1)k_2 + 1/3]/3} ( \times 10^{ - 1} nm)$$ for the right helix re-entry stem, wherek 1 andk 2 are integers. The right helix one is less existing because of possessing high energy. The most plausible fold conformation is tg? tg? tg+ g+ g? for the most adjacent (010) fold. The next minimum energy fold segments are tg? g? tg+ tg+ tg?, g+g? tg?tg+g+ t and g+g?g?tg+ tg+ t.展开更多
Dear Editor, Potassium channels are integral membrane proteins that selectively con duct K^+ ions across cell membra ne (Hille, 2001). They play essential roles in maintaining cellular ionic homoeostasis and generatin...Dear Editor, Potassium channels are integral membrane proteins that selectively con duct K^+ ions across cell membra ne (Hille, 2001). They play essential roles in maintaining cellular ionic homoeostasis and generating action membrane potentials in excitable cells. The mechanism of K^+ selectivity has been evaluated in many biophysical and physiological studies (Zhou et al., 2001;Liu et al., 2015;Schewe et al., 2016). A highly con served signature seque nee, TVGYG, in the selectivity filter of potassium channels (e.g., KcsA) is known to coordinate K^+ ions (Zhou et al., 2001). Carbonyls of these residues point toward the pore, forming four continuous ion binding sites (S1-S4) and resulting in higher selectivity for K^+ over Na^+(Zhou et al., 2001). The NaK channel from Bacillus cereus is a norvselective cation channel that shares high structural homology with KcsA (Shi et al., 2006). Owing to a distinctive primary sequenee of 63TVGDG67, the selectivity filter of NaK preserves only two ion binding sites, allocated similarly as S3 and S4 in KcsA (Alam and Jiang, 2009a, b). Remarkably, the D66Y and N68D double mutations of NaK channel (Fig. S1) transform it into a K^+ selective channel (termed as NaK2K)(Sauer et al., 2013). Crystal structure of NaK and NaK2K have revealed distinet binding coordination of Na^+ and K^+ ions in their selectivity filter (Figs. S2 and S3)(Alam and Jiang, 2009a, b;Sauer et al., 2013). However, dynamics of the NaK and NaK2K selectivity filter with the bind泊g of Na+ or K^+ are still elusive. Especially, it has been known that the membrane environment is highly diverse from deterge nt micelles, which was con sidered to in flue nee the structure and functi on of membrane protei ns dramatically (Cross et al., 2011). Thus, it is necessary to study the cation and binding properties of NaK NaK2K channels in lipid bilayers.展开更多
Peptide-modified delivery systems are enabling the improvement of the targeting specificity,biocompatibility,stability,etc.However,the precise design of a peptide-decorated surface for a designated function has remain...Peptide-modified delivery systems are enabling the improvement of the targeting specificity,biocompatibility,stability,etc.However,the precise design of a peptide-decorated surface for a designated function has remained to be challenging due to a lack of mechanistic understanding of the interactions between surface-bound peptide ligands and their receptors.Enlightened by the recent report on pairwise interactions between peptides in the solution state and surface-immobilized state,we used computational simulations to explore the contributing mechanisms underlining the observed binding affinity characteristics.Molecular dynamics simulations were performed to sample and compare conformations of homo-octapeptides free in solution(mobile peptides)and bound to the surface(N-terminal fixed peptides).We found that peptides converged to more extended and rigid conformations when immobilized to the surface and confirmed that the extended structures could increase the space available to counter-interacting peptides during the peptide–peptide interactions.In addition,studies on interactions between stationary and mobile peptides revealed that main-chain/side-chain and side-chain/side-chain hydrogen bonds play an important role.The presented efforts in this work may provide supportive references for peptide design and modification on the nanoparticle surface as well as guidance for analyzing peptide–receptor interactions through an emphasis on hydrogen bonds during peptide design and an understanding of the influence on the binding affinity by the sequence-dependant conformational changes after peptide immobilization.展开更多
Audio-visual speech recognition(AVSR),which integrates audio and visual modalities to improve recognition performance and robustness in noisy or adverse acoustic conditions,has attracted significant research interest....Audio-visual speech recognition(AVSR),which integrates audio and visual modalities to improve recognition performance and robustness in noisy or adverse acoustic conditions,has attracted significant research interest.However,Conformer-based architectures remain computational expensive due to the quadratic increase in the spatial and temporal complexity of their softmax-based attention mechanisms with sequence length.In addition,Conformerbased architectures may not provide sufficient flexibility for modeling local dependencies at different granularities.To mitigate these limitations,this study introduces a novel AVSR framework based on a ReLU-based Sparse and Grouped Conformer(RSG-Conformer)architecture.Specifically,we propose a Global-enhanced Sparse Attention(GSA)module incorporating an efficient context restoration block to recover lost contextual cues.Concurrently,a Grouped-scale Convolution(GSC)module replaces the standard Conformer convolution module,providing adaptive local modeling across varying temporal resolutions.Furthermore,we integrate a Refined Intermediate Contextual CTC(RIC-CTC)supervision strategy.This approach applies progressively increasing loss weights combined with convolution-based context aggregation,thereby further relaxing the constraint of conditional independence inherent in standard CTC frameworks.Evaluations on the LRS2 and LRS3 benchmark validate the efficacy of our approach,with word error rates(WERs)reduced to 1.8%and 1.5%,respectively.These results further demonstrate and validate its state-of-the-art performance in AVSR tasks.展开更多
文摘Solvent effect on the conformations of-bis(4-nitrophenoxy)-alkanes w th different chain Lengths(Nn)was studied by UV spectra.In poor solvents such as EG-H_2O and THF-H_2O,with the water content higher than 50%,the K-bands of N_4. N,N_6 and N_(10)in the UV absorption spectra shifted to longer wavelengths as compared wth 4-nitrophenoxyethane(N_0).It is suggested that in poor solvents the two aromatic gr(?)ps are close to each other in parallel,forming ground state complexes.The K- bead of N_4 showed a blue shift from that of N_0 when the water content was around 5%,probably attributable to a conformation with the nitro group of one benzene ring sit(?)ing on the plane of the other benzene ring.
基金This work was supported in part by a grant from Russian Scientific Foundation(Project No.17-75-30064).
文摘Up to now,the DNA molecule adsorbed on a surface was believed to always preserve its native structure.This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated.High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled.We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress(>30 pNnm)inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges.In addition,the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity.The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending.The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics.The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear.The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.
基金financially supported by the Scientific Research Project of Yili Normal University(No.2022YSYB009)the National Natural Science Foundation of China(No.2019M651340)。
文摘Combining Brownian dynamics simulations and self-consistent field theory,we demonstrate that the architectural parameters of coreshell comb-like chains have a decisive influence on their final self-assembled conformations.When the ratio of hydrophilic and hydrophobic segments is N_(g,g)∶N_(g,r)=3∶1,no core-shell structure is observed,and unsegregated chains or clusters are substituted.When N_(g,g)∶N_(g,r)=3∶2or 3∶3,the core-shell comb-like chains can be assembled into single micelles or structures where several small micelles are strung together by the backbone,which is similar to the pearl-necklace structure formed by the polyelectrolytes in poor solvent.With the increase of backbone length or grafting density,the probability of forming single micelles becomes lower,but the structures of two,three or more small micelles strung together are more observed.Our results indicate how to obtain the desired self-assembled structures of core-shell comb-like chains by regulating the architectural parameters,which could provide insights for the optimization of molecular design in various applications.
文摘Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti- cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.
基金This work was supported by the National Natu- ral Science Foundation of China （No.11374272） and the Specialized Research Fund for the Doctoral Pro- gram of Higher Education （No.20113402110038 and No.20123402110064）.
文摘An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface （PES） of OlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G＊, BHandHLYP/6-31G＊ and BHandHLYP/6-311＋＋G＊＊ in order to reliably find the low energy conformations. The eonformational energies were finally determined with the methods of BHandHLYP, cam- B3LYP, B97D, and MP2 using the basis set of 6-311＋＋G（3df,3pd）. The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.
基金ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China （No.11074233 and No.11374272） and the Specialized Research Fund for the Doctoral Program of Higher Education （No.20113402110038 and No.20123402110064）
文摘Conformations and reaction energetics are important for understanding the interactions be- tween biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion affinities of glutamine （Gln） binding with alkali and alkaline earth metal ions. An efficient and reliable method of searching low energy conformations of metalated Gln is proposed and applied to the complexes of Gln.Gln.M^＋/＋＋（M＋/＋＋=Li^＋、Na^＋、K^＋、Rb^＋、Cs^＋、Be^＋＋、Mg^＋＋、Ca^＋＋、Sr^＋＋ and Ba^＋＋）.. In addition to all conformers known in literatures, many new important conformations are located, demonstrating the power of the new method and the necessity of the conformational search performed here. The metal coordination modes, relative energies, dipole moments, and equilibrium distributions of all important conformations of Gln.M^＋/＋＋ are calculated by the methods of B3LYP, BHandHLYP, and MP2. IR spectra and metalation enthalpies and free energies are also presented and compared with the available experiments. The results form an extensive database for systematic examination of the metalation properties of Gln.
基金supported by Research Fund of the Erzincan University(Project no:FEN-A-150615-0149)
文摘The ground state hydrogen conformations and vibrational analysis of 3-deazauracil(3DAU)and 6-azauracil(6AU)tautomers(4-enol and 2,4-diol forms)have been calculated using ab initio Hartree-Fock(HF)and density functional theory(B3LYP)methods with 6-311++G(d,p)basis set level.The calculations have shown that the most probably preferential tautomer of 3DAU and 6AU are the 4-enol form,which gives best fit to the corresponding experimental data.The ground state conformer of the 2,4-diol form has two O—H bonds which are oriented externally and internally(to the N—H bond).The vibrational analyses of the ground state conformer of each tautomeric form of 3DAU and 6AU were done and their optimized geometry parameters(bond lengths and bond angles)were given.Furthermore,from the correlations values it was concluded that the B3LYP method is superior to the HF method for both the vibrational frequencies and the geometric parameters.
文摘Conductances of different geometric conformations of boron ribbon devices are calculated by the ab initio method, The I-V characteristics of three devices are rather different due to the difference in structure. The current of the hexagonal boron device is the largest and increases nonlinearly. The current of the hybrid hexagon-triangle boron device displays a large low-bias current and saturates at a value of about 5.2 uA, The current of the flat triangular boron flake exhibits a voltage gap at low bias and rises sharply with increasing voltage. The flat triangular boron device can be either conducting or insulating, depending on the field.
基金Project supported by the Youth Science Foundation of Academia Sinica and the National Natural Science Foundation of China.
文摘The melting and crystallization behavior have been investigated for an aromatic poly (azomethine ether)with non-linearly shaped molecular conformations. This polymer was found to undergo multiple melting processes and its phase transition behavior was influenced sensitively by the thermal history of sample. A significant difference between the polymer chain aggregation abilities of samples cooled from the different states was observed. The possible molecular morphology and aggregation models for describing the structures of this polymer were proposed and discussed. The crystallization behavior of the samples cooled from the partially isotropic state and the influence of cooling rate on it have also been examined with DSC.
基金Supported by the National Natural Science Foundation of China(No.20903026)the Talents Introduction Foundation for Universities of Guangdong Province(2011)Scientific Research Foundation of the Natural Science Foundation of Guangdong Province(No.S2011010002483)
文摘Molecular dynamic simulations and molecular docking are performed to study the conformations and hydrogen bonding interactions of ACE inhibitory tripeptide VEF. Intramolecular distance, radius of gyration, solvent-accessible surface, and root-mean-square deviations are used to characterize the properties of VEF in aqueous solution. The VEF molecule is highly flexible in water and conformations can shift between the extended and folded states. The VEF molecule exists in extended state mostly in aqueous solution and the conformations bonded with ACE are also the extended ones. The findings indicate that MD simulations have a good agreement with the molecular docking analysis.
基金supported by the National Natural Science Foundation of China(22122504,22235006)Foundation of Hubei Scientific Committee(2022BAA015 and 2022EHB010).
文摘Conformational flexibility is essential to the stimuli-responsive property of organic materials,but achieving the reversible molecular transformation is still challenging in functional materials for the high energy barriers and restriction by intermolecular interactions.Herein,through the incorporation of various steric hindrances into phenothiazine derivatives with different positions and quantities to tune the molecular conformations by adjustable repulsive forces,the folded angles gradually changed from 180°to 90°in 17 compounds.When the angle located at 112°with moderated steric effect,dynamic and reversible transformation of conformations under mechanical force has been achieved for the low energy barriers and mutually regulated molecular motions,resulting in both selfrecoverable and stimuli-responsive phosphorescence properties for the first time.It opened up a new way to realize the self-recovery property of organic materials,which can facilitate the multi-functional property of smart materials with the opened avenue for other fields with inspiration.
基金National Research Foundation of KoreaMinistry of Science and ICT,Korea,Grant/Award Numbers:2022M3A9B6017424,NRF-2021R1A6A1A03038890,2023R1A2C1005868,2022M3A9B6017654+2 种基金Korea Basic Science InstituteNational Research Facilities and Equipment CenterMinistry of Education of Korea,Grant/Award Number:RS-2024-00436674。
文摘Background:Phosphorylated signal transducer and activator of transcription 3(p-STAT3)has emerged as a critical modulator of hepatocellular carcinoma(HCC)progression.However,its role in three-dimensional(3D)chromatin conformation and the expression of genes linked to HCC aggressiveness remains largely unexplored.This study aimed to identify HCC 3D chromatin conformations that are regulated by sustained STAT3 activation and validate the molecular mechanisms underlying the aggressiveness of HCC.Methods:Comparative analyses were performed using HCC cell lines with varying levels of STAT3 activation.Chromatin immunoprecipitation-sequencing(ChIP-seq)for p-STAT3 and H3K27ac was conducted to map p-STAT3-associated genomic regions and assess its influence on chromatin states.Chromatin conformation sequencings(high-throughput chromosome conformation capture and high-throughput chromosome conformation capture followed by immunoprecipitation)were employed to investigate the 3D genome landscape and identify conformational changes linked to sustained p-STAT3 activation.RNAsequencing was performed to assess transcriptional changes in response to these chromatin rearrangements.Functional assays,including invasion and tube formation assays,were carried out to validate the phenotypic impact of p-STAT3 activation on HCC progressiveness.Pharmacological inhibition of STAT3 was tested to explore potential therapeutic avenues and resistance mechanisms.Results:We found that sustained activation of p-STAT3 was significantly associated with poor prognostic outcomes in HCC patients.ChIP-seq demonstrated that p-STAT3 regulated chromatin interactions,leading to the formation of frequently interacting regions(FIREs),stable structural units within the 3D genome.Genes within these p-STAT3-associated FIREs exhibited coordinated expression,with many involved in aggressiveness HCC phenotypes like invasion and tube formation.Chromatin conformation data indicated that these FIREs altered topologically associating domains(TADs),potentially influencing broader chromatin organization.Despite STAT3 inhibition,p-STAT3-associated chromatin conformations remained intact,maintaining the expression of genes within FIREs and contributing to drug resistance.Conclusions:Sustained p-STAT3 activation significantly alters the 3D chromatin conformation inHCC,particularly through the formation of FIREs.These p-STAT3-associated FIREs drive the expression of genes involved inHCC aggressiveness and remain active despite STAT3-targeted treatments,suggesting a mechanism of drug resistance.These findings highlight the potential of targeting 3D chromatin dynamics as a therapeutic strategy in HCC,especially in cases of STAT3 inhibitor resistance.
文摘Based on the perfect rotational isomeric state model of isotactic polypropylene, the separation distances between an initial left helix stem and its re-entry stems have been investigated. The intervals are defined by the formulae $$D_1 = \frac{{1.54}}{3}\sqrt {8(k_1^2 + k_2^2 + k_1 k_2 )/3} ( \times 10^{ - 1} nm)$$ for the left helix re-entry stem and $$D_2 = \frac{{1.54}}{3}\sqrt {8[k_1^2 + k_2^2 + (k_1 - 1)k_2 + 1/3]/3} ( \times 10^{ - 1} nm)$$ for the right helix re-entry stem, wherek 1 andk 2 are integers. The right helix one is less existing because of possessing high energy. The most plausible fold conformation is tg? tg? tg+ g+ g? for the most adjacent (010) fold. The next minimum energy fold segments are tg? g? tg+ tg+ tg?, g+g? tg?tg+g+ t and g+g?g?tg+ tg+ t.
基金Chinese Key Research Plan- Protein Science (2015CB910100 and 2016YFA0400900)the Chinese Natural Science Foundation (U1332138 and U1432136)the CAS-Hefei Science Center grant (2015HSC-SRG051).
文摘Dear Editor, Potassium channels are integral membrane proteins that selectively con duct K^+ ions across cell membra ne (Hille, 2001). They play essential roles in maintaining cellular ionic homoeostasis and generating action membrane potentials in excitable cells. The mechanism of K^+ selectivity has been evaluated in many biophysical and physiological studies (Zhou et al., 2001;Liu et al., 2015;Schewe et al., 2016). A highly con served signature seque nee, TVGYG, in the selectivity filter of potassium channels (e.g., KcsA) is known to coordinate K^+ ions (Zhou et al., 2001). Carbonyls of these residues point toward the pore, forming four continuous ion binding sites (S1-S4) and resulting in higher selectivity for K^+ over Na^+(Zhou et al., 2001). The NaK channel from Bacillus cereus is a norvselective cation channel that shares high structural homology with KcsA (Shi et al., 2006). Owing to a distinctive primary sequenee of 63TVGDG67, the selectivity filter of NaK preserves only two ion binding sites, allocated similarly as S3 and S4 in KcsA (Alam and Jiang, 2009a, b). Remarkably, the D66Y and N68D double mutations of NaK channel (Fig. S1) transform it into a K^+ selective channel (termed as NaK2K)(Sauer et al., 2013). Crystal structure of NaK and NaK2K have revealed distinet binding coordination of Na^+ and K^+ ions in their selectivity filter (Figs. S2 and S3)(Alam and Jiang, 2009a, b;Sauer et al., 2013). However, dynamics of the NaK and NaK2K selectivity filter with the bind泊g of Na+ or K^+ are still elusive. Especially, it has been known that the membrane environment is highly diverse from deterge nt micelles, which was con sidered to in flue nee the structure and functi on of membrane protei ns dramatically (Cross et al., 2011). Thus, it is necessary to study the cation and binding properties of NaK NaK2K channels in lipid bilayers.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB36000000)the National Key R&D Program of China(No.2022YFA1203200)the National Natural Science Foundation of China(No.32027801).
文摘Peptide-modified delivery systems are enabling the improvement of the targeting specificity,biocompatibility,stability,etc.However,the precise design of a peptide-decorated surface for a designated function has remained to be challenging due to a lack of mechanistic understanding of the interactions between surface-bound peptide ligands and their receptors.Enlightened by the recent report on pairwise interactions between peptides in the solution state and surface-immobilized state,we used computational simulations to explore the contributing mechanisms underlining the observed binding affinity characteristics.Molecular dynamics simulations were performed to sample and compare conformations of homo-octapeptides free in solution(mobile peptides)and bound to the surface(N-terminal fixed peptides).We found that peptides converged to more extended and rigid conformations when immobilized to the surface and confirmed that the extended structures could increase the space available to counter-interacting peptides during the peptide–peptide interactions.In addition,studies on interactions between stationary and mobile peptides revealed that main-chain/side-chain and side-chain/side-chain hydrogen bonds play an important role.The presented efforts in this work may provide supportive references for peptide design and modification on the nanoparticle surface as well as guidance for analyzing peptide–receptor interactions through an emphasis on hydrogen bonds during peptide design and an understanding of the influence on the binding affinity by the sequence-dependant conformational changes after peptide immobilization.
基金supported in part by the National Natural Science Foundation of China:61773330.
文摘Audio-visual speech recognition(AVSR),which integrates audio and visual modalities to improve recognition performance and robustness in noisy or adverse acoustic conditions,has attracted significant research interest.However,Conformer-based architectures remain computational expensive due to the quadratic increase in the spatial and temporal complexity of their softmax-based attention mechanisms with sequence length.In addition,Conformerbased architectures may not provide sufficient flexibility for modeling local dependencies at different granularities.To mitigate these limitations,this study introduces a novel AVSR framework based on a ReLU-based Sparse and Grouped Conformer(RSG-Conformer)architecture.Specifically,we propose a Global-enhanced Sparse Attention(GSA)module incorporating an efficient context restoration block to recover lost contextual cues.Concurrently,a Grouped-scale Convolution(GSC)module replaces the standard Conformer convolution module,providing adaptive local modeling across varying temporal resolutions.Furthermore,we integrate a Refined Intermediate Contextual CTC(RIC-CTC)supervision strategy.This approach applies progressively increasing loss weights combined with convolution-based context aggregation,thereby further relaxing the constraint of conditional independence inherent in standard CTC frameworks.Evaluations on the LRS2 and LRS3 benchmark validate the efficacy of our approach,with word error rates(WERs)reduced to 1.8%and 1.5%,respectively.These results further demonstrate and validate its state-of-the-art performance in AVSR tasks.
