Anti-parallel β-sheet crystallite as the main component of silk fibroin has attracted much attention due to its superior mechanical properties. In this study, we examine the processes of pulling a peptide chain from ...Anti-parallel β-sheet crystallite as the main component of silk fibroin has attracted much attention due to its superior mechanical properties. In this study, we examine the processes of pulling a peptide chain from β-sheet crystallite using steered molecular dynamics simulations to investigate the rupture behavior of the crystallite. We show that the failure of β-sheet crystallite was accompanied by a propagation of instability of hydrogen-bonds （H-bonds） in the crystallite. In addition, we find that there is an optimum size of the crystallite at which the H-bonds can work cooperatively to achieve the highest shear strength. In addition, we find that the stiffness of loading device and the loading rates have significant effects on the rupture behavior of β-sheet crystallite. The stiff loading device facilitates the rebinding of the Hbond network in the stick-slip motion between the chains, while the soft one suppresses it. Moreover, the rupture force of β-sheet crystallites decreases with loading rate. Particularly, when the loading rate decreases to a critical value, the rupture force of the β-sheet crystallite becomes independent of the loading rates. This study provides atomistic details of rupture behaviors of β-sheet crystallite, and, therefore, sheds valuable light on the underlying mechanism of the superior mechanical properties of silk fibroin.展开更多
Due to many remarkable physical and chemical properties, two-dimensional(2D) nanomaterials have become a hot spot in the field of condensed matter physics. In this paper, we have studied the structural, mechanical, an...Due to many remarkable physical and chemical properties, two-dimensional(2D) nanomaterials have become a hot spot in the field of condensed matter physics. In this paper, we have studied the structural, mechanical, and electronic properties of the 2D GaInO_3 system by first-principles method. We find that 2D Ga InO_3 can exist stably at ambient condition. Molecular dynamic simulations show that GaInO_3-sheet has excellent thermal stability and is stable up to1100 K. Electronic structural calculations show that GaInO_3-sheet has a band gap of 1.56 eV, which is close to the ideal band gap of solar cell materials, demonstrating great potential in future photovoltaic application. In addition, strain effect studies show that the GaInO_3-sheet structure always exhibits a direct band gap under biaxial compressive strain, and as the biaxial compressive strain increases, the band gap gradually decreases until it is converted into metal. While biaxial tensile strain can cause the 2D material to transform from a direct band gap semiconductor into an indirect band gap semiconductor,and even to metal. Our research expands the application of the Ga InO_3 system, which may have potential application value in electronic devices and solar energy.展开更多
The amino acid composition and the biased auto-correlation function are considered as features, BP neural network algorithm is used to synthesize these features. The prediction accuracy of this method is verified by u...The amino acid composition and the biased auto-correlation function are considered as features, BP neural network algorithm is used to synthesize these features. The prediction accuracy of this method is verified by using the independent non-homologous protein database. It is shown that the average absolute errors for resubstitution test are 0.070 and 0.068 with the standard deviations 0.049 and 0.047 for the prediction of the content of α-helix and β-sheet respectively. For cross-validation test, the average absolute errors are 0.075 and 0.070 with the standard deviations 0.050 and 0.049 for the prediction of the content of α-helix and β-sheet respectively. Compared with the other methods currently available, the BP neural network method combined with the amino acid composition and the biased auto-correlation function features can effectively improve the prediction accuracy.展开更多
The molecular conformations of four silk fibroin crystalline analogues [GAGAG-X] 16(G,Gly;A,Ala;X=Ala,Ser,Tyr or Val,designated eGA,eGS,eGY or eGV),carried out using molecular design and expressed by Escherichia coil(...The molecular conformations of four silk fibroin crystalline analogues [GAGAG-X] 16(G,Gly;A,Ala;X=Ala,Ser,Tyr or Val,designated eGA,eGS,eGY or eGV),carried out using molecular design and expressed by Escherichia coil(E.coli),were evaluated by Raman spectra analysis.The abilities of forming β-sheet structure were determined by thioflavin T(ThT) fluorescence spectra analysis.In terms of molecular conformation,except eGY that could not form significant typical molecular conformation,eGS and eGV were mainly composed of β-sheets while eGA tended to form β-turn.β-turn was also present in eGY and absent in eGS and eGV.In terms of β-sheet structure,eGS had the highest β-sheet content,followed by eGV,and eGA had the lowest content,furthermore,β-sheet structures were more stable in eGS and eGV than those in eGA and eGY.展开更多
Beta amyloid (Aβ) aggregation has been characterized to be responsible for several amyloid diseases. Fourier transform infrared (FTIR) spectroscopy, fluorescence, and atomic force microscopy (AFM) are used to investi...Beta amyloid (Aβ) aggregation has been characterized to be responsible for several amyloid diseases. Fourier transform infrared (FTIR) spectroscopy, fluorescence, and atomic force microscopy (AFM) are used to investigate induced changes in the secondary structure of Aβ upon thermal denaturation and interaction with propofol and L-arginine. Spectral analysis has revealed an effective static quenching for the intrinsic fluorescence of Aβ by propofol and l-arginine with binding constants of 2.81 × 102 M-1 for Aβ-propofol and 0.37 × 102 M-1 for Aβ-L-arginine. Fourier self-deconvolution (FSD) technique has been used to evaluate the relative intensity changes in the spectra of the component bands in the amide I and amide II regions at different ligand’s concentration in the protein complex. The analysis showed a decrease in the intensities of the parallel beta bands of propofol and L-arginine interactions with Aβ, accompanied with an increase in the antiparallel bands for the Aβ-propofol interaction and a decrease for the Aβ-l-arginine interaction. The relative increase in peaks’ intensities at 1694 cm-1 and 1531 cm-1 for the propofol interaction is linked to the formation of oligomers in the protein.展开更多
基金supported by the National Science Foundation of China (Grants 11025208, 11372042, 11221202, and 11202026)the support from CSIRO-Intelligent Processing TCP+1 种基金CAFHS’ Capability Development FundCSIRO-Advanced Materials TCP
文摘Anti-parallel β-sheet crystallite as the main component of silk fibroin has attracted much attention due to its superior mechanical properties. In this study, we examine the processes of pulling a peptide chain from β-sheet crystallite using steered molecular dynamics simulations to investigate the rupture behavior of the crystallite. We show that the failure of β-sheet crystallite was accompanied by a propagation of instability of hydrogen-bonds （H-bonds） in the crystallite. In addition, we find that there is an optimum size of the crystallite at which the H-bonds can work cooperatively to achieve the highest shear strength. In addition, we find that the stiffness of loading device and the loading rates have significant effects on the rupture behavior of β-sheet crystallite. The stiff loading device facilitates the rebinding of the Hbond network in the stick-slip motion between the chains, while the soft one suppresses it. Moreover, the rupture force of β-sheet crystallites decreases with loading rate. Particularly, when the loading rate decreases to a critical value, the rupture force of the β-sheet crystallite becomes independent of the loading rates. This study provides atomistic details of rupture behaviors of β-sheet crystallite, and, therefore, sheds valuable light on the underlying mechanism of the superior mechanical properties of silk fibroin.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11847094,61764001,and U1404212)the Cheung Kong Scholars Programme of China+2 种基金the Program of Changjiang Scholars and Innovative Research Team in University,China(Grant No.IRT1132)Open Project of State Key Laboratory of Superhard Materials(Jilin University)China(Grant No.201703)
文摘Due to many remarkable physical and chemical properties, two-dimensional(2D) nanomaterials have become a hot spot in the field of condensed matter physics. In this paper, we have studied the structural, mechanical, and electronic properties of the 2D GaInO_3 system by first-principles method. We find that 2D Ga InO_3 can exist stably at ambient condition. Molecular dynamic simulations show that GaInO_3-sheet has excellent thermal stability and is stable up to1100 K. Electronic structural calculations show that GaInO_3-sheet has a band gap of 1.56 eV, which is close to the ideal band gap of solar cell materials, demonstrating great potential in future photovoltaic application. In addition, strain effect studies show that the GaInO_3-sheet structure always exhibits a direct band gap under biaxial compressive strain, and as the biaxial compressive strain increases, the band gap gradually decreases until it is converted into metal. While biaxial tensile strain can cause the 2D material to transform from a direct band gap semiconductor into an indirect band gap semiconductor,and even to metal. Our research expands the application of the Ga InO_3 system, which may have potential application value in electronic devices and solar energy.
基金Supported by Microsystem and Terahertz Research Center,Institute of Electronic Engineering,China Academy of Engineering Physics(CAEP-IEE)National Key Basic Research Program of China(973 Program)(2015CB755406)Defense Industrial Technology Development Program with(JCKY2016212C045,JCKY2017212C002)
文摘The amino acid composition and the biased auto-correlation function are considered as features, BP neural network algorithm is used to synthesize these features. The prediction accuracy of this method is verified by using the independent non-homologous protein database. It is shown that the average absolute errors for resubstitution test are 0.070 and 0.068 with the standard deviations 0.049 and 0.047 for the prediction of the content of α-helix and β-sheet respectively. For cross-validation test, the average absolute errors are 0.075 and 0.070 with the standard deviations 0.050 and 0.049 for the prediction of the content of α-helix and β-sheet respectively. Compared with the other methods currently available, the BP neural network method combined with the amino acid composition and the biased auto-correlation function features can effectively improve the prediction accuracy.
基金National Natural Science Foundation of China (No. 51075422)Natural Science Foundation of Jiangsu Province,China(No. BK2009147,No. BK2010253)+1 种基金Society Development Foundation of Suzhou City,China (No. SYG201001)the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)
文摘The molecular conformations of four silk fibroin crystalline analogues [GAGAG-X] 16(G,Gly;A,Ala;X=Ala,Ser,Tyr or Val,designated eGA,eGS,eGY or eGV),carried out using molecular design and expressed by Escherichia coil(E.coli),were evaluated by Raman spectra analysis.The abilities of forming β-sheet structure were determined by thioflavin T(ThT) fluorescence spectra analysis.In terms of molecular conformation,except eGY that could not form significant typical molecular conformation,eGS and eGV were mainly composed of β-sheets while eGA tended to form β-turn.β-turn was also present in eGY and absent in eGS and eGV.In terms of β-sheet structure,eGS had the highest β-sheet content,followed by eGV,and eGA had the lowest content,furthermore,β-sheet structures were more stable in eGS and eGV than those in eGA and eGY.
文摘Beta amyloid (Aβ) aggregation has been characterized to be responsible for several amyloid diseases. Fourier transform infrared (FTIR) spectroscopy, fluorescence, and atomic force microscopy (AFM) are used to investigate induced changes in the secondary structure of Aβ upon thermal denaturation and interaction with propofol and L-arginine. Spectral analysis has revealed an effective static quenching for the intrinsic fluorescence of Aβ by propofol and l-arginine with binding constants of 2.81 × 102 M-1 for Aβ-propofol and 0.37 × 102 M-1 for Aβ-L-arginine. Fourier self-deconvolution (FSD) technique has been used to evaluate the relative intensity changes in the spectra of the component bands in the amide I and amide II regions at different ligand’s concentration in the protein complex. The analysis showed a decrease in the intensities of the parallel beta bands of propofol and L-arginine interactions with Aβ, accompanied with an increase in the antiparallel bands for the Aβ-propofol interaction and a decrease for the Aβ-l-arginine interaction. The relative increase in peaks’ intensities at 1694 cm-1 and 1531 cm-1 for the propofol interaction is linked to the formation of oligomers in the protein.
