Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been w...Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.展开更多
Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules qu...Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run(Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ?G_(i+j)^+, where two aggregates with sizes i and j associate to form the(i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i^+, which was obtained through MD calculations. The calculated ?G_(i+j)^+ was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy ∑_in_i( l,k)G_i^+ and the free energy of mixing ∑_in_i( l,k)k_BTln( n_i( l,k)/n( l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i aggregation path and k-th state, with n(l,k)= ∑_n_i( l,k). All the aggregation pathways were obtained from the initial i state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, t_(FPT). The calculated t_(FPT) was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.展开更多
Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In...Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.展开更多
The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa an...The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa and choosingappropriate reaction coordinae, a reasonable free energy dinram is constructed and thercorganhaion energy for the product state is calculated.展开更多
This paper studies the molecular rotational excitation and field-free spatial alignment in a nonresonant intense laser field numerically and analytically by using the time-dependent SchrSdinger equation. The broad rot...This paper studies the molecular rotational excitation and field-free spatial alignment in a nonresonant intense laser field numerically and analytically by using the time-dependent SchrSdinger equation. The broad rotational wave packets excited by the femtosecond pulse are defined in conjugate angle space, and their coefficients are obtained by solving a set of coupled linear equations. Both single molecule orientation angles and an ensemble of O2 and CO molecule angular distributions are calculated in detail. The numerical results show that, for single molecule highest occupied molecular orbital （HOMO） symmetry σ tends to have a molecular orientation along the laser polarization direction and the permanent dipole moment diminishes the mean of the orientation angles; for an ensemble of molecules, angular distributions provide more complex and additional information at times where there are no revivals in the single molecule plot. In particular, at the revival peak instant, with the increase of temperature of the molecular ensemble, the anisotropic angular distributions with respect to the laser polarization direction of the πg orbital gradually transform to the symmetrical distributions regarding the laser polarization vector and for two HOMO configurations angular distributions of all directions are confined within a smaller angle when the temperature of the molecular ensemble is higher.展开更多
基金supported by the National Science Foundation of China (10732050,10872115 and 11025208)Excellent Young Scholars Research Fund of Beijing Institute of Technology
文摘Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.
基金This work was supported by FLAGSHIP2020,MEXT within Priority Study 5(Development of New Fundamental Technologies for High-Efficiency Energy Creation,Conversion/Storage and Use)Using Computational Resources of the K Computer Provided by the RIKEN Advanced
文摘Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run(Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ?G_(i+j)^+, where two aggregates with sizes i and j associate to form the(i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i^+, which was obtained through MD calculations. The calculated ?G_(i+j)^+ was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy ∑_in_i( l,k)G_i^+ and the free energy of mixing ∑_in_i( l,k)k_BTln( n_i( l,k)/n( l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i aggregation path and k-th state, with n(l,k)= ∑_n_i( l,k). All the aggregation pathways were obtained from the initial i state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, t_(FPT). The calculated t_(FPT) was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.
基金supported by the National Natural Science Foundation of China(No.21973064)the Post-Doctor Research Project,West China Hospital,Sichuan University(No.2021HXBH017)。
文摘Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.
文摘The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa and choosingappropriate reaction coordinae, a reasonable free energy dinram is constructed and thercorganhaion energy for the product state is calculated.
基金supported by the Program of Excellent Team in Harbin Institute of Technologythe Program for New Century Excellent Talents in University (NCET)National Natural Science Foundation of China (Grant Nos 10774033,60878018 and 10674036)
文摘This paper studies the molecular rotational excitation and field-free spatial alignment in a nonresonant intense laser field numerically and analytically by using the time-dependent SchrSdinger equation. The broad rotational wave packets excited by the femtosecond pulse are defined in conjugate angle space, and their coefficients are obtained by solving a set of coupled linear equations. Both single molecule orientation angles and an ensemble of O2 and CO molecule angular distributions are calculated in detail. The numerical results show that, for single molecule highest occupied molecular orbital （HOMO） symmetry σ tends to have a molecular orientation along the laser polarization direction and the permanent dipole moment diminishes the mean of the orientation angles; for an ensemble of molecules, angular distributions provide more complex and additional information at times where there are no revivals in the single molecule plot. In particular, at the revival peak instant, with the increase of temperature of the molecular ensemble, the anisotropic angular distributions with respect to the laser polarization direction of the πg orbital gradually transform to the symmetrical distributions regarding the laser polarization vector and for two HOMO configurations angular distributions of all directions are confined within a smaller angle when the temperature of the molecular ensemble is higher.
