The growth of single-wall carbon nanotube from graphite layers is studied by tight binding molecular dynamics simulation. Given temperature of 2500 K or 3500 K and an interval of 0.25 nm for the two layers of graphite...The growth of single-wall carbon nanotube from graphite layers is studied by tight binding molecular dynamics simulation. Given temperature of 2500 K or 3500 K and an interval of 0.25 nm for the two layers of graphite, a single-wall carbon nanotube with a zigzag shell will be produced. On the other conditions the carbon nanotube cannot grow or grows with too many defects. All carbon nanotube ends have pentagons which play an important role during the tube ends closing.展开更多
The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of...The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of 10~5 M^（-1） from fluorescence quenching studies.Negative ΔH°（-5.66 ＋ 0.14 kJ/mol） and positive（ΔS°）（＋ 79.96 ＋ 0.65J/mol K） indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°.The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate（SDS） due to probable hydrophobic association of baicalein with SDS,resulting in a negative ΔS°（-40.65 ＋ 0.87 J/mol K）.Matrix-assisted laser desorption ionization/time of flight（MALDI-TOF） experiments indicate a 1：1 complexation between baicalein and BSA.The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements.It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA.The presence of metal ions（Ag~＋,Mg^（2＋）,Ni^（2＋）,Mn^（2＋）,Co^（2＋） and Zn^（2＋）） increased the binding affinity of ligand towards BSA.The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism（CD） and Fourier transform infrared（FT-IR） spectroscopic techniques.Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1（subdomain MA） of BSA.展开更多
Tight binding molecular dynamicsand simulated annealingtechniquesareemployed tostudythestructuralpropertiesofsilicon clusterscontaining 2 14 atoms.Itisfoundthatour results for Si2 Si6 agree well with thoseobtained...Tight binding molecular dynamicsand simulated annealingtechniquesareemployed tostudythestructuralpropertiesofsilicon clusterscontaining 2 14 atoms.Itisfoundthatour results for Si2 Si6 agree well with thoseobtained using abinitiotechniques. Further Si cluster re search which givethesignificantprediction hasbeen made.展开更多
Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells.The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high ...Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells.The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high affinity adenosine triphosphate（ATP）binding site and analyzed absorption,distribution,metabolism,excretion and toxicity（ADME-toxicity）.The molecular docking analysis revealed that the flavanols showed competitive inhibition with ATP molecule at the active site and enhanced pharmacological parameters.展开更多
Soybean protein is of plant origin and is commonly appropriate for improving the processing characteristics of foods.This study aimed to explore a novel functional ingredient that contained soybean protein isolate(SPI...Soybean protein is of plant origin and is commonly appropriate for improving the processing characteristics of foods.This study aimed to explore a novel functional ingredient that contained soybean protein isolate(SPI)and blueberry anthocyanins(BANs).The spatial conformation and secondary structure of SPI-BANs complexes were analyzed using circular dichroism and fluorescence spectroscopy,the processing properties were investigated as well as the retention of antioxidant activity during thermal treatments.Results showed that the contents of free sulfhydryl and free amino groups in complexes increased to 3.50 and 1.19 folds than those of SPI,respectively,while the surface hydrophobicity decreased by 74.23%.Compared with SPI,the BANs-modified SPI had a smaller particle size of 29.12 nm and a lower zeta-potential of-8.73 mV and on the other hand,the complexes possessed higher solubility(83.08%)and foaming and emulsifying properties(115.08%and 54.03 m^(2)/g).After fortification with SPI-BANs,the baking loss rate and adhe-siveness of chiffon cake were reduced by 10.82%and improved to 0.24 N.mm,respectively.The high antioxidant activities of SPI-BANs under heat led to the cake’s bioactivities largely enhanced by 1.99~12.71 folds,being 345.19µg Trolox/g for the DPPH radical scavenging activity.This study developed the functional food ingredients as antioxidants and a substitute for animal-based proteins in bakery products,which was safe and sustainable by using the dietary components from plant resources.展开更多
Hand,foot,and mouth disease(HFMD),primarily instigated by Coxsackievirus A16(CVA16),poses a serious health concern,necessitating effective therapeutic interventions.The RNA-dependent RNA polymerase(RdRp)of CVA16 emerg...Hand,foot,and mouth disease(HFMD),primarily instigated by Coxsackievirus A16(CVA16),poses a serious health concern,necessitating effective therapeutic interventions.The RNA-dependent RNA polymerase(RdRp)of CVA16 emerges as a promising drug target for HFMD treatment.This study presents an in-silico pipeline for the identification of potential RdRp inhibitors against CVA16.A library of 91 natural compounds derived from Bacopa monnieri(brahmi)was virtually screened against the CVA16 RdRp.Here,Bacobitacin D emerged as a promising hit molecule,forming 8 hydrogen bonds including key catalytic site residues(Asp^(238)and Asp^(329))within the RdRp active site.Further,molecular dynamics(MD)simulations and MM/GBSA binding free energy calculations was applied on the top three hits that were selected based on exhaustive docking scores(≤-9.55 kcal/mol).Bacobitacin D exhibited sustainable stability,as evidenced by minimal deviation(RMSD=0.75±0.02 nm)during a 100 ns MD simulation.Importantly,Bacopaside IV exhibited the lowestΔGTOTAL binding free energy(-23.70 kcal/mol),while Bacobitacin D displayed a comparableΔGTOTAL of19.14 kcal/mol.Structural interpretation of the most populated cluster derived from MD simulations showed direct interactions of Bacobitacin D with pivotal catalytic residues,including Asp^(238)and Ser^(289).This comprehensive study confirmed Bacobitacin D as a potent inhibitor of CVA16 RdRp,offering a potential avenue for therapeutic intervention against HFMD.Experimental validation is required to confirm the inhibitory action of Bacobitacin D against HFMD.展开更多
文摘The growth of single-wall carbon nanotube from graphite layers is studied by tight binding molecular dynamics simulation. Given temperature of 2500 K or 3500 K and an interval of 0.25 nm for the two layers of graphite, a single-wall carbon nanotube with a zigzag shell will be produced. On the other conditions the carbon nanotube cannot grow or grows with too many defects. All carbon nanotube ends have pentagons which play an important role during the tube ends closing.
基金Department of Science and Technology(DST,Project no.SR/SO/BB-54/2007),Government of India for financial support
文摘The interaction of baicalein with bovine serum albumin（BSA） was investigated with the help of spectroscopic and molecular docking studies.The binding affinity of baicalein towards BSA was estimated to be in order of 10~5 M^（-1） from fluorescence quenching studies.Negative ΔH°（-5.66 ＋ 0.14 kJ/mol） and positive（ΔS°）（＋ 79.96 ＋ 0.65J/mol K） indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°.The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate（SDS） due to probable hydrophobic association of baicalein with SDS,resulting in a negative ΔS°（-40.65 ＋ 0.87 J/mol K）.Matrix-assisted laser desorption ionization/time of flight（MALDI-TOF） experiments indicate a 1：1 complexation between baicalein and BSA.The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements.It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA.The presence of metal ions（Ag~＋,Mg^（2＋）,Ni^（2＋）,Mn^（2＋）,Co^（2＋） and Zn^（2＋）） increased the binding affinity of ligand towards BSA.The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism（CD） and Fourier transform infrared（FT-IR） spectroscopic techniques.Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1（subdomain MA） of BSA.
文摘Tight binding molecular dynamicsand simulated annealingtechniquesareemployed tostudythestructuralpropertiesofsilicon clusterscontaining 2 14 atoms.Itisfoundthatour results for Si2 Si6 agree well with thoseobtained using abinitiotechniques. Further Si cluster re search which givethesignificantprediction hasbeen made.
文摘Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells.The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high affinity adenosine triphosphate（ATP）binding site and analyzed absorption,distribution,metabolism,excretion and toxicity（ADME-toxicity）.The molecular docking analysis revealed that the flavanols showed competitive inhibition with ATP molecule at the active site and enhanced pharmacological parameters.
基金supported by the Jiangsu Agricultural Science and Technology Innovation Fund[Grant No.CX(22)2026],Chinathe Scholarship Program of China Scholarship Council[Grant No.202108320143],Chinathe Science and Technology Program of Changshu City[Grant No.CN202208],China.
文摘Soybean protein is of plant origin and is commonly appropriate for improving the processing characteristics of foods.This study aimed to explore a novel functional ingredient that contained soybean protein isolate(SPI)and blueberry anthocyanins(BANs).The spatial conformation and secondary structure of SPI-BANs complexes were analyzed using circular dichroism and fluorescence spectroscopy,the processing properties were investigated as well as the retention of antioxidant activity during thermal treatments.Results showed that the contents of free sulfhydryl and free amino groups in complexes increased to 3.50 and 1.19 folds than those of SPI,respectively,while the surface hydrophobicity decreased by 74.23%.Compared with SPI,the BANs-modified SPI had a smaller particle size of 29.12 nm and a lower zeta-potential of-8.73 mV and on the other hand,the complexes possessed higher solubility(83.08%)and foaming and emulsifying properties(115.08%and 54.03 m^(2)/g).After fortification with SPI-BANs,the baking loss rate and adhe-siveness of chiffon cake were reduced by 10.82%and improved to 0.24 N.mm,respectively.The high antioxidant activities of SPI-BANs under heat led to the cake’s bioactivities largely enhanced by 1.99~12.71 folds,being 345.19µg Trolox/g for the DPPH radical scavenging activity.This study developed the functional food ingredients as antioxidants and a substitute for animal-based proteins in bakery products,which was safe and sustainable by using the dietary components from plant resources.
文摘Hand,foot,and mouth disease(HFMD),primarily instigated by Coxsackievirus A16(CVA16),poses a serious health concern,necessitating effective therapeutic interventions.The RNA-dependent RNA polymerase(RdRp)of CVA16 emerges as a promising drug target for HFMD treatment.This study presents an in-silico pipeline for the identification of potential RdRp inhibitors against CVA16.A library of 91 natural compounds derived from Bacopa monnieri(brahmi)was virtually screened against the CVA16 RdRp.Here,Bacobitacin D emerged as a promising hit molecule,forming 8 hydrogen bonds including key catalytic site residues(Asp^(238)and Asp^(329))within the RdRp active site.Further,molecular dynamics(MD)simulations and MM/GBSA binding free energy calculations was applied on the top three hits that were selected based on exhaustive docking scores(≤-9.55 kcal/mol).Bacobitacin D exhibited sustainable stability,as evidenced by minimal deviation(RMSD=0.75±0.02 nm)during a 100 ns MD simulation.Importantly,Bacopaside IV exhibited the lowestΔGTOTAL binding free energy(-23.70 kcal/mol),while Bacobitacin D displayed a comparableΔGTOTAL of19.14 kcal/mol.Structural interpretation of the most populated cluster derived from MD simulations showed direct interactions of Bacobitacin D with pivotal catalytic residues,including Asp^(238)and Ser^(289).This comprehensive study confirmed Bacobitacin D as a potent inhibitor of CVA16 RdRp,offering a potential avenue for therapeutic intervention against HFMD.Experimental validation is required to confirm the inhibitory action of Bacobitacin D against HFMD.
