By using LKB2277 bioactivity monitor, we have studied the effect of Na 2SeO 3 on Bacillus subtilis Growth at two different media and found the antagonism of protein on its toxicity. Low concentration of Na 2SeO 3 ...By using LKB2277 bioactivity monitor, we have studied the effect of Na 2SeO 3 on Bacillus subtilis Growth at two different media and found the antagonism of protein on its toxicity. Low concentration of Na 2SeO 3 has promoting action, and high concentration of Na 2SeO 3 has inhibitory action. Half inhibitory concentration ( IC 50 ) of BPY medium is 4.2×10 -1 g / L, and IC 50 of PD medium is 2.2×10 -2 g / L.展开更多
The power-time curves of the germination of different rice and tree seeds have been studied by using a microcalorimeter set up by ourselves. Some characteristic values have been obtained from these curves in different...The power-time curves of the germination of different rice and tree seeds have been studied by using a microcalorimeter set up by ourselves. Some characteristic values have been obtained from these curves in different thermogenesising stages of the germination of rice and tree seeds. These parameters can be used in comparison of character and activity for different seeds,moreover the effects of different strain.germinating shape and temperature on the power-time curves of the germination of seeds have been discussed.展开更多
A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as...A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.展开更多
A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering...A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.展开更多
Ionic liquids have many unique properties as a new and remarkable class of environmental benign solvents,which promises widespread applications in industry and other areas. However,the ionic liq-uids with surface acti...Ionic liquids have many unique properties as a new and remarkable class of environmental benign solvents,which promises widespread applications in industry and other areas. However,the ionic liq-uids with surface activity are rarely reported. In this work,a series of novel ionic liquids was synthe-sized by using N-methyl-2-pyrrolidone and alkyl bromide. The physical properties of this family of ionic liquids have been characterized,which shows that these compounds have ionic liquids characteristics,surface activity and biocompatibility.展开更多
Integrase（IN） plays an essential role in the process of HIV-1 replication.IN inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular...Integrase（IN） plays an essential role in the process of HIV-1 replication.IN inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular Similarity Induces Analysis（CoMSIA） methods.A set of 42 compounds were randomly selected as the training set（35） and test set（7）.Firstly,a good pharmacophore（goodness of hit=0.787） was obtained and used to align ligands.Then,predictive models were constructed with the CoMFA and CoMSIA methods based on the pharmacophore alignment.As a result,the CoMS1A method yielded the best model with an r2 of 0.955 and a q2 of 0.665,which can predict the activities of the tested DKAs very well（r2=0.559）.Finally,DKAs were docked into IN,and the predicit modes were superimposed on the contour maps obtained from the best CoMSIA model.The superimposed maps gave a visualized and meaningful insight into the inhibitory behaviors,providing significantly useful information for the rational drug design of anti-IN agents.展开更多
A fast and effective model for predicting the salt and pH dependent properties of protein complexes is presented. It is based on the formal charge parameter sets of ionizable groups and applied in conjunction with the...A fast and effective model for predicting the salt and pH dependent properties of protein complexes is presented. It is based on the formal charge parameter sets of ionizable groups and applied in conjunction with the finite difference Poisson-Boltzmann (FDPB) method to calculate the electrostatic interactions. All simulations were performed on the native 2Zn insulin and its fast-acting mutants such as B9D (B9Ser→Asp), B9E (B9Aer→Glu), B9EB10D (B9Ser→ Glu, B10His→Asp), and B10D (B10His→Asp). The salt and pH dependent properties of these dimers were analyzed from the aspect of electrostatic interaction, and the theoretical basis of the fast-acting behavior of these mutants was explained. It is found that the results agree well with experimental observations.展开更多
The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble avera...The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.展开更多
The thermal behavior of dry solid ascorbic acid in nitrogen atmosphere in the temperature range of 25<sup>8</sup>00℃was investigated by TG-FTIR.During the thermal decomposition process,five evolved gaseou...The thermal behavior of dry solid ascorbic acid in nitrogen atmosphere in the temperature range of 25<sup>8</sup>00℃was investigated by TG-FTIR.During the thermal decomposition process,five evolved gaseous species,including H<sub>2</sub>O,CO<sub>2</sub>,CO,CH<sub>4</sub> and HCOOH,were identified and monitored,in which HCOOH was detected for the first time.The results indicated that ascorbic acid began to decompose at 191℃.Its decomposition process consisted of three stages,and dehydration and decarboxylation to form furfural were the possible principal mechanism.The kinetic analysis for the first decomposition stage was also carried out by the isoconversional method and the master plots method.The results indicated that this process can be described by the model of 1st order reaction.展开更多
文摘By using LKB2277 bioactivity monitor, we have studied the effect of Na 2SeO 3 on Bacillus subtilis Growth at two different media and found the antagonism of protein on its toxicity. Low concentration of Na 2SeO 3 has promoting action, and high concentration of Na 2SeO 3 has inhibitory action. Half inhibitory concentration ( IC 50 ) of BPY medium is 4.2×10 -1 g / L, and IC 50 of PD medium is 2.2×10 -2 g / L.
文摘The power-time curves of the germination of different rice and tree seeds have been studied by using a microcalorimeter set up by ourselves. Some characteristic values have been obtained from these curves in different thermogenesising stages of the germination of rice and tree seeds. These parameters can be used in comparison of character and activity for different seeds,moreover the effects of different strain.germinating shape and temperature on the power-time curves of the germination of seeds have been discussed.
文摘A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.
基金supported by grants from the National Natural Science Foundation of China (Grant Nos. 10974008 and 20773006)the Specialized Research Fund for the Doctoral Program of Higher Education (Grant No. 200800050003)+1 种基金the National Basic Research Program of China (Grant No. 2009CB930200)the Beijing Natural Science Foundation (Grant No. 4102006)
文摘A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.
基金Supported by the National Natural Science Foundation of China (Grant Nos. 20233010 and 20573079)
文摘Ionic liquids have many unique properties as a new and remarkable class of environmental benign solvents,which promises widespread applications in industry and other areas. However,the ionic liq-uids with surface activity are rarely reported. In this work,a series of novel ionic liquids was synthe-sized by using N-methyl-2-pyrrolidone and alkyl bromide. The physical properties of this family of ionic liquids have been characterized,which shows that these compounds have ionic liquids characteristics,surface activity and biocompatibility.
基金Supported by the National Natural Science Foundation of China（Nos.31100523,31171267,21173014） and the Beijing Outstanding Personnel Training Foundation,China（No.2012D005015000006）.
文摘Integrase（IN） plays an essential role in the process of HIV-1 replication.IN inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular Similarity Induces Analysis（CoMSIA） methods.A set of 42 compounds were randomly selected as the training set（35） and test set（7）.Firstly,a good pharmacophore（goodness of hit=0.787） was obtained and used to align ligands.Then,predictive models were constructed with the CoMFA and CoMSIA methods based on the pharmacophore alignment.As a result,the CoMS1A method yielded the best model with an r2 of 0.955 and a q2 of 0.665,which can predict the activities of the tested DKAs very well（r2=0.559）.Finally,DKAs were docked into IN,and the predicit modes were superimposed on the contour maps obtained from the best CoMSIA model.The superimposed maps gave a visualized and meaningful insight into the inhibitory behaviors,providing significantly useful information for the rational drug design of anti-IN agents.
基金This work was supported in part by the National Natural Science Foundation of China (Grant No. 29992590-2)the Beijing Natural Science Foundation (Grant No. 5992002)the Development Project of Scientific Technology of the Education Commission of Beiji
文摘A fast and effective model for predicting the salt and pH dependent properties of protein complexes is presented. It is based on the formal charge parameter sets of ionizable groups and applied in conjunction with the finite difference Poisson-Boltzmann (FDPB) method to calculate the electrostatic interactions. All simulations were performed on the native 2Zn insulin and its fast-acting mutants such as B9D (B9Ser→Asp), B9E (B9Aer→Glu), B9EB10D (B9Ser→ Glu, B10His→Asp), and B10D (B10His→Asp). The salt and pH dependent properties of these dimers were analyzed from the aspect of electrostatic interaction, and the theoretical basis of the fast-acting behavior of these mutants was explained. It is found that the results agree well with experimental observations.
基金Supported by the National Natural Science Foundation of China (Grant No.30670497)the Beijing Natural Science Foundation (Grant No.5072002)the Specialized Research Foundation for the Doctoral Program of Higher Education (Grant No.200800050003)
文摘The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.
文摘The thermal behavior of dry solid ascorbic acid in nitrogen atmosphere in the temperature range of 25<sup>8</sup>00℃was investigated by TG-FTIR.During the thermal decomposition process,five evolved gaseous species,including H<sub>2</sub>O,CO<sub>2</sub>,CO,CH<sub>4</sub> and HCOOH,were identified and monitored,in which HCOOH was detected for the first time.The results indicated that ascorbic acid began to decompose at 191℃.Its decomposition process consisted of three stages,and dehydration and decarboxylation to form furfural were the possible principal mechanism.The kinetic analysis for the first decomposition stage was also carried out by the isoconversional method and the master plots method.The results indicated that this process can be described by the model of 1st order reaction.
