The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding ene...The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.展开更多
By making use of the fluorescence quenching properties of safranine T(ST) in its long range assembly on the molecular surfaces of nucleic acids, the assembly number and constant of ST with calf thymus DNA, fish sperm ...By making use of the fluorescence quenching properties of safranine T(ST) in its long range assembly on the molecular surfaces of nucleic acids, the assembly number and constant of ST with calf thymus DNA, fish sperm DNA and yeast RNA were determined at 12℃. The corresponding free energy change, enthalpy change and entropy change of the long range assembly were calculated at the same temperature. It was found the assembly complexes are very stable and the assembly is a spontaneous process characterized an entropy increase.展开更多
The interactions of phenothiazine such as chlorpromazine hydrochloride(CPZ·HCl)and promethazine hydrochloride(PZ·HCl),with nucleic acids(NA)have been investigated.The CPZ-NA system can produce very intense r...The interactions of phenothiazine such as chlorpromazine hydrochloride(CPZ·HCl)and promethazine hydrochloride(PZ·HCl),with nucleic acids(NA)have been investigated.The CPZ-NA system can produce very intense resonance Rayleigh scattering(RRS),but the RRS intensity of the PZ-NA system is very weak.The energy relationship of the two reaction systems has been calculated by the AM1 and B3LYP of density functional methods for quantum chemistry,the binding site and interacting model of CPZ-NA and PZ-NA are studied.The results show that CPZ has strong binding ability with nucleic acids,but PZ hardly react with nucleic acids.It can be expected that RRS method may be a useful means for molecular recognition of nucleic acids and the molecular design of gene medicine in the future.Moreover,the method is used for the quan-titative determination of nucleic acids by employing chlorpromazine hydrochloride as reagent,which has very high sensitivity and good selectivity.Therefore,a sensitive,simple and rapid new method has been developed for the determination of nucleic acids.展开更多
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11874045 and 11774147)。
文摘The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.
文摘By making use of the fluorescence quenching properties of safranine T(ST) in its long range assembly on the molecular surfaces of nucleic acids, the assembly number and constant of ST with calf thymus DNA, fish sperm DNA and yeast RNA were determined at 12℃. The corresponding free energy change, enthalpy change and entropy change of the long range assembly were calculated at the same temperature. It was found the assembly complexes are very stable and the assembly is a spontaneous process characterized an entropy increase.
基金supported by the National Natural Science Foundation of China(Grant No.20475045)the Municipal Science Foundation of Chongqing City.
文摘The interactions of phenothiazine such as chlorpromazine hydrochloride(CPZ·HCl)and promethazine hydrochloride(PZ·HCl),with nucleic acids(NA)have been investigated.The CPZ-NA system can produce very intense resonance Rayleigh scattering(RRS),but the RRS intensity of the PZ-NA system is very weak.The energy relationship of the two reaction systems has been calculated by the AM1 and B3LYP of density functional methods for quantum chemistry,the binding site and interacting model of CPZ-NA and PZ-NA are studied.The results show that CPZ has strong binding ability with nucleic acids,but PZ hardly react with nucleic acids.It can be expected that RRS method may be a useful means for molecular recognition of nucleic acids and the molecular design of gene medicine in the future.Moreover,the method is used for the quan-titative determination of nucleic acids by employing chlorpromazine hydrochloride as reagent,which has very high sensitivity and good selectivity.Therefore,a sensitive,simple and rapid new method has been developed for the determination of nucleic acids.
