We used a combined quantum mechanics and molecular mechanics （QM/MM） method to investigate the solvent effects and potential of mean force of the CH3F＋CN- reaction in water. Comparing to gas phase, the water soluti...We used a combined quantum mechanics and molecular mechanics （QM/MM） method to investigate the solvent effects and potential of mean force of the CH3F＋CN- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects＇ contributions to the reaction： 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.展开更多
A statistical mechanics method is proposed for calculation of potential ofmean force (PMF). In the case of solvophobic or solvophilic macroparticles immersed in solvent bathof soft sphere or Lennard-Jones particles, p...A statistical mechanics method is proposed for calculation of potential ofmean force (PMF). In the case of solvophobic or solvophilic macroparticles immersed in solvent bathof soft sphere or Lennard-Jones particles, prediction accuracy for the PMF and MF from the simplestimplementation of the proposed method, where hypernetted chain approximation is adopted forcorrelation of the macroparticle-macroparticle at infinitely dilute limit, is comparable to that ofa recent more sophisticated approach based on mixture Ornstein—Zernike integral equation / bridgefunction from fundamental measure functional. Adaptation of the present method for general complexQuids is discussed, and method for improving the accuracy is suggested. Differences and relativemerits of the present recipe compared with that based on potential distribution theory is discussed.展开更多
Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins.Here we apply molecular dynamics(MD)simulation to the two-state protein GB1 and down-hill folding prot...Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins.Here we apply molecular dynamics(MD)simulation to the two-state protein GB1 and down-hill folding protein gpW to reveal the relationship of their free energy landscape and folding/unfolding dynamics.Results from the steered MD simulations show that gpW is much less mechanical resistant than GB1,and the unfolding process of gpW has more variability than that of GB1 according to their force-extension curves.The potential of mean force(PMF)of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference:PMF of GB1 along the coordinate of extension exhibits a kink transition point where the slope of PMF drops suddenly,while PMF of gpW increases with extension smoothly,which are consistent with two-state folding dynamics of GB1 and downhill folding dynamics of gpW,respectively.Our results provide insight to understand the fundamental mechanism of different folding dynamics of twostate proteins and downhill folding proteins.展开更多
A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles im...A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.展开更多
We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the the- oretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetic...We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the the- oretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equi- librium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications.展开更多
ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, unde...ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.展开更多
Mechanical force plays a critical role in the remodeling and degradation of cartilage tissues.The cartilage tissue generates,absorbs,and transmits mechanical force,enabling specific biological processes in our body.A ...Mechanical force plays a critical role in the remodeling and degradation of cartilage tissues.The cartilage tissue generates,absorbs,and transmits mechanical force,enabling specific biological processes in our body.A moderate intensity mechanical force is necessary for cartilage tissue remodeling and the adaptation of biomechanical properties,but a high intensity mechanical force can lead to pathological degradation of cartilage tissue.However,the molecular mechanism of cartilage degradation is still unclear.We use full atomistic simulations with SMD simulations to investigate whether the magnitude of mechanical force affects the unbinding pathway of the MMP8-Aggrecan_IGD complex.We find that when the pulling velocity is slow,the mechanical force required to unbind the Aggrecan_IGD from MMP8 is higher,and a three-step unbinding pathway is observed.On the other hand,when the pulling velocity is fast,the mechanical force required to unbind the Aggrecan_IGD from MMP8 is lower,and a two-step unbinding pathway is observed.Our results help us to understand how the magnitude of the mechanical force affects the unbinding pathway of the enzyme-ligand complex in cartilage tissue at the molecular level.展开更多
The molecular dynamics simulations are performed to show that in aque- ous environments, a short single-walled carbon nanotube （SWCNT） guided by a long SWCNT, either inside or outside the longer tube, is capable of ...The molecular dynamics simulations are performed to show that in aque- ous environments, a short single-walled carbon nanotube （SWCNT） guided by a long SWCNT, either inside or outside the longer tube, is capable of moving along the nanotube axis unidirectionally in an electric field perpendicular to the carbon nanotube （CNT） axis with the linear gradient. The design suggests a new way of molecule transportation or mass delivery. To reveal the mechanism behind this phenomenon, the free energy profiles of the system are calculated by the method of the potential of mean force （PMF）.展开更多
In this work, the traditional method of potential of mean force (PMF) is improved for describing the protein-protein interactions. This method is developed at atomic level and is distance-dependent. Compared with the ...In this work, the traditional method of potential of mean force (PMF) is improved for describing the protein-protein interactions. This method is developed at atomic level and is distance-dependent. Compared with the traditional method, our model can reasonably consider the effects of the environ- mental factors. With this modification, we can obtain more reasonable and accurate pair potentials, which are the pre-requisite for precisely describing the protein-protein interactions and can help us to recognize the interaction rules of residues in protein systems. Our method can also be applied to other fields of protein science, e.g., protein fold recognition, structure prediction and prediction of thermo- stability.展开更多
钾离子通道作为细胞中阳离子浓度的调节器之一,在神经细胞动作电位去极化及复极化过程中起着重要作用.KcsA(K^(+)conduction and selectivity architecture)通道结构简单又具有钾离子通道的共性,常作为钾通道研究的模板.本文采用布朗动...钾离子通道作为细胞中阳离子浓度的调节器之一,在神经细胞动作电位去极化及复极化过程中起着重要作用.KcsA(K^(+)conduction and selectivity architecture)通道结构简单又具有钾离子通道的共性,常作为钾通道研究的模板.本文采用布朗动力学数值方法,系统地对KcsA钾通道的电学特性进行模拟.得到静电场作用下通道内离子的平均势能分布、均匀与非均匀溶液的电流-电压特性曲线、通道轴向的离子浓度分布曲线以及电导-浓度曲线.研究结果发现,KcsA钾离子通道选择性过滤区域几乎完全阻隔了Cl–通过,呈现倾向于K^(+)通过的特异选择特性;其电流-电压曲线基本呈线性分布,电导-浓度曲线呈现先增大后平缓的趋势,基本规律与实验现象一致.另外,还模拟分析了太赫兹场对通道K^(+)电流的影响,相比于仅施加同幅值静电场,选定的0.6 THz,1.2 THz,5 THz的太赫兹场可通过影响离子对之间的相互作用势能,降低通道平均力势,从而增大K^(+)电流.本文的研究不但加深了对于KcsA钾离子通道的规律性认识,还为其他类型离子通道以及太赫兹场对离子通道特性影响的研究提供了新思路.展开更多
三磷酸腺苷结合盒式(ATP-binding cassette,ABC)输出转运体是一类典型的蛋白质分子机器,这类分子机器通过门控运动进行“向外打开”(outward-facing,OF)和“向内打开”(inward-facing,IF)构象态之间转换,从而把底物转运输出生物膜外。...三磷酸腺苷结合盒式(ATP-binding cassette,ABC)输出转运体是一类典型的蛋白质分子机器,这类分子机器通过门控运动进行“向外打开”(outward-facing,OF)和“向内打开”(inward-facing,IF)构象态之间转换,从而把底物转运输出生物膜外。尽管结构和功能的研究已取得重大进展,但对ABC输出转运体构象门控的分子机制还没有完全理解。由于全原子分子动力学存在长时间尺度问题,因此对ABC蛋白质分子构象变化不能进行完全描述。本文应用粗粒化分子动力学(CG-MD)结合改善的抽样方法,对细菌ABC输出转运体MsbA进行计算模拟研究。本文计算得到的平均力势(potential of mean force,PMF)表明,从OF构象态到IF构象态之间的转变需要经过一个“阻塞态”(occluded state,OC),即MsbA的内门和外门都是关闭的状态。这种阻塞状态对ABC输出功能的方向单一性具有重要意义。我们的CG-MD计算模拟结果显示,随着MsbA的核苷酸结合域(nucleotide binding domain,NBD)的分离,外门的关闭和内门的打开是采用高度协作的方式。基于本文的计算模拟结果,我们提出了一个与目前文献中发表的有很大不同的机械力学模型,揭示了ABC输出转运体通过构象门控运动输运底物的分子机制。展开更多
Since solid-liquid interfacial nanobubbles(INBs)were first imaged,their long-term stability and large contact angle have been perplexing scientists.This study aimed to investigate the influence of internal gas density...Since solid-liquid interfacial nanobubbles(INBs)were first imaged,their long-term stability and large contact angle have been perplexing scientists.This study aimed to investigate the influence of internal gas density and external gas monolayers on the contact angle and stability of INB using molecular dynamics simulations.First,the contact angle of a water droplet was simulated at different nitrogen densities.The results showed that the contact angle increased sharply with an increase in nitrogen density,which was mainly caused by the decrease in solid-gas interfacial tension.However,when the nitrogen density reached 2.57 nm^(-3),an intervening gas monolayer(GML)was formed between the solid and water.After the formation of GML,the contact angle slightly increased with increasing gas density.The contact angle increased to 180°when the nitrogen density reached 11.38 nm^(-3),indicating that INBs transformed into a gas layer when they were too small.For substrates with different hydrophobicities,the contact angle after the formation of GML was always larger than 140°and it was weakly correlated with substrate hydrophobicity.The increase in contact angle with gas density represents the evolution of contact angle from macro-to nano-bubble,while the formation of GML may correspond to stable INBs.The potential of mean force curves demonstrated that the substrate with GML could attract gas molecules from a longer distance without the existence of a potential barrier compared with the bare substrate,indicating the potential of GML to act as a gas-collecting panel.Further research indicated that GML can function as a channel to transport gas molecules to INBs,which favors stability of INBs.This research may shed new light on the mechanisms underlying abnormal contact angle and long-term stability of INBs.展开更多
基金Project supported by the National Natural Science Foundation of China(Grant No.11774206)Taishan Scholarship Fund from Shandong Province,China
文摘We used a combined quantum mechanics and molecular mechanics （QM/MM） method to investigate the solvent effects and potential of mean force of the CH3F＋CN- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects＇ contributions to the reaction： 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.
文摘A statistical mechanics method is proposed for calculation of potential ofmean force (PMF). In the case of solvophobic or solvophilic macroparticles immersed in solvent bathof soft sphere or Lennard-Jones particles, prediction accuracy for the PMF and MF from the simplestimplementation of the proposed method, where hypernetted chain approximation is adopted forcorrelation of the macroparticle-macroparticle at infinitely dilute limit, is comparable to that ofa recent more sophisticated approach based on mixture Ornstein—Zernike integral equation / bridgefunction from fundamental measure functional. Adaptation of the present method for general complexQuids is discussed, and method for improving the accuracy is suggested. Differences and relativemerits of the present recipe compared with that based on potential distribution theory is discussed.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11874309,11474237,and 11574310)the 111 Project,China(Grant No.B16029).
文摘Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins.Here we apply molecular dynamics(MD)simulation to the two-state protein GB1 and down-hill folding protein gpW to reveal the relationship of their free energy landscape and folding/unfolding dynamics.Results from the steered MD simulations show that gpW is much less mechanical resistant than GB1,and the unfolding process of gpW has more variability than that of GB1 according to their force-extension curves.The potential of mean force(PMF)of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference:PMF of GB1 along the coordinate of extension exhibits a kink transition point where the slope of PMF drops suddenly,while PMF of gpW increases with extension smoothly,which are consistent with two-state folding dynamics of GB1 and downhill folding dynamics of gpW,respectively.Our results provide insight to understand the fundamental mechanism of different folding dynamics of twostate proteins and downhill folding proteins.
文摘A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.
基金supported by the National Natural Science Foundation of China(Grant Nos.21274062,11474155,and 91027040)
文摘We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the the- oretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equi- librium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications.
基金supported by the National Natu-ral Science Foundation of China(No.21073170 and No.21273209).
文摘ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.
文摘Mechanical force plays a critical role in the remodeling and degradation of cartilage tissues.The cartilage tissue generates,absorbs,and transmits mechanical force,enabling specific biological processes in our body.A moderate intensity mechanical force is necessary for cartilage tissue remodeling and the adaptation of biomechanical properties,but a high intensity mechanical force can lead to pathological degradation of cartilage tissue.However,the molecular mechanism of cartilage degradation is still unclear.We use full atomistic simulations with SMD simulations to investigate whether the magnitude of mechanical force affects the unbinding pathway of the MMP8-Aggrecan_IGD complex.We find that when the pulling velocity is slow,the mechanical force required to unbind the Aggrecan_IGD from MMP8 is higher,and a three-step unbinding pathway is observed.On the other hand,when the pulling velocity is fast,the mechanical force required to unbind the Aggrecan_IGD from MMP8 is lower,and a two-step unbinding pathway is observed.Our results help us to understand how the magnitude of the mechanical force affects the unbinding pathway of the enzyme-ligand complex in cartilage tissue at the molecular level.
基金Project supported by the National Natural Science Foundation of China(Nos.11372175 and 11272197)the Research Fund for the Doctoral Program of Higher Education of China(No.20103108110004)the Innovation Program of Shanghai Municipality Education Commission(No.14ZZ095)
文摘The molecular dynamics simulations are performed to show that in aque- ous environments, a short single-walled carbon nanotube （SWCNT） guided by a long SWCNT, either inside or outside the longer tube, is capable of moving along the nanotube axis unidirectionally in an electric field perpendicular to the carbon nanotube （CNT） axis with the linear gradient. The design suggests a new way of molecule transportation or mass delivery. To reveal the mechanism behind this phenomenon, the free energy profiles of the system are calculated by the method of the potential of mean force （PMF）.
基金the National Natural Science Foundation of China (Grant Nos. 90403120, 10474041 and 10504012)
文摘In this work, the traditional method of potential of mean force (PMF) is improved for describing the protein-protein interactions. This method is developed at atomic level and is distance-dependent. Compared with the traditional method, our model can reasonably consider the effects of the environ- mental factors. With this modification, we can obtain more reasonable and accurate pair potentials, which are the pre-requisite for precisely describing the protein-protein interactions and can help us to recognize the interaction rules of residues in protein systems. Our method can also be applied to other fields of protein science, e.g., protein fold recognition, structure prediction and prediction of thermo- stability.
基金supported by the National Natural Science Foundation of China(21073170,21273209).
文摘三磷酸腺苷结合盒式(ATP-binding cassette,ABC)输出转运体是一类典型的蛋白质分子机器,这类分子机器通过门控运动进行“向外打开”(outward-facing,OF)和“向内打开”(inward-facing,IF)构象态之间转换,从而把底物转运输出生物膜外。尽管结构和功能的研究已取得重大进展,但对ABC输出转运体构象门控的分子机制还没有完全理解。由于全原子分子动力学存在长时间尺度问题,因此对ABC蛋白质分子构象变化不能进行完全描述。本文应用粗粒化分子动力学(CG-MD)结合改善的抽样方法,对细菌ABC输出转运体MsbA进行计算模拟研究。本文计算得到的平均力势(potential of mean force,PMF)表明,从OF构象态到IF构象态之间的转变需要经过一个“阻塞态”(occluded state,OC),即MsbA的内门和外门都是关闭的状态。这种阻塞状态对ABC输出功能的方向单一性具有重要意义。我们的CG-MD计算模拟结果显示,随着MsbA的核苷酸结合域(nucleotide binding domain,NBD)的分离,外门的关闭和内门的打开是采用高度协作的方式。基于本文的计算模拟结果,我们提出了一个与目前文献中发表的有很大不同的机械力学模型,揭示了ABC输出转运体通过构象门控运动输运底物的分子机制。
基金This work was supported by the National Natural Science Foundation of China(51920105007,51904300 and 52104277)the Jiangsu Natural Science Fund-Youth Fund(BK20210500).
文摘Since solid-liquid interfacial nanobubbles(INBs)were first imaged,their long-term stability and large contact angle have been perplexing scientists.This study aimed to investigate the influence of internal gas density and external gas monolayers on the contact angle and stability of INB using molecular dynamics simulations.First,the contact angle of a water droplet was simulated at different nitrogen densities.The results showed that the contact angle increased sharply with an increase in nitrogen density,which was mainly caused by the decrease in solid-gas interfacial tension.However,when the nitrogen density reached 2.57 nm^(-3),an intervening gas monolayer(GML)was formed between the solid and water.After the formation of GML,the contact angle slightly increased with increasing gas density.The contact angle increased to 180°when the nitrogen density reached 11.38 nm^(-3),indicating that INBs transformed into a gas layer when they were too small.For substrates with different hydrophobicities,the contact angle after the formation of GML was always larger than 140°and it was weakly correlated with substrate hydrophobicity.The increase in contact angle with gas density represents the evolution of contact angle from macro-to nano-bubble,while the formation of GML may correspond to stable INBs.The potential of mean force curves demonstrated that the substrate with GML could attract gas molecules from a longer distance without the existence of a potential barrier compared with the bare substrate,indicating the potential of GML to act as a gas-collecting panel.Further research indicated that GML can function as a channel to transport gas molecules to INBs,which favors stability of INBs.This research may shed new light on the mechanisms underlying abnormal contact angle and long-term stability of INBs.
基金supported by the National Natural Science Foundation of China(11405113)Science and Technology Plan of Sichuan Province+2 种基金China(2010JY0122)Science Research Fund of Sichuan Normal UniversityChina(10MSL02)
