Mycobacterium tuberculosis(Mtb)is responsible for the spread of tuberculosis(TB).The current study employed virtual screening of 2569 natural compounds against the DNA-directed RNA polymerase(RNAP)of Mtb to identify t...Mycobacterium tuberculosis(Mtb)is responsible for the spread of tuberculosis(TB).The current study employed virtual screening of 2569 natural compounds against the DNA-directed RNA polymerase(RNAP)of Mtb to identify the possible binders that can inhibit its function.The in-silico methodology included molecular docking to the compounds,further,the stability and flexibility of the best complexes were studied using molecular dynamics simulation,the MM/GBSA binding free energy technique with energy decomposition,PCA,FEL,steered MD simulation,and umbrella sampling.Individual virtual screenings were conducted for the five RNAP subunits(chains A,B,C,D,and E)to identify a compound capable of inhibiting RNAP oligomerization.A promising compound,isoestradiol 3-benzoate,exhibited a low binding score(−7.28kcal/mol to−8.21kcal/mol)and showed binding ability with all subunits of the protein.Thus,the five complexes with isoestradiol 3-benzoate were selected for molecular dynamics simulation analysis.Furthermore,RMSD showed that isoestradiol 3-benzoate bound with chain E showed the lowest RMSD of 0.49nm,while with chains A and B it had the most stable and consistent conformations with RMSD of 1.75nm and 1.2nm,respectively.The H-bond between isoestradiol 3-benzoate and chains C and E showed the highest occupancy(58.27%,45.33%,and 50.80%,42.25%,11.75%).Moreover,the MMPBSA technique showed that isoestradiol 3-benzoate had a strong association with chains B and C(ΔGbind=−126.25±2.03 and−129.27±2.25).Additionally,free energy decomposition,PCA,FEL-steered MD simulation,and umbrella sampling were also performed to validate the association of the ligand with the protein.Isoestradiol 3-benzoate binds strongly to chains B and E;therefore,it should be considered as viable candidate for inhibiting the formation of RNAP protein complex,concluded in this study.展开更多
为了研究温度变化对生物膜跨膜传输能力的影响,本文以钾离子跨膜通道蛋白为研究对象,利用Gromacs分子生物学模拟软件包和Gromos96(53a6)分子力场,通过分子动力模拟技术和伞状采样方法详细研究了300K和275K两个温度条件下钾离子跨膜通道...为了研究温度变化对生物膜跨膜传输能力的影响,本文以钾离子跨膜通道蛋白为研究对象,利用Gromacs分子生物学模拟软件包和Gromos96(53a6)分子力场,通过分子动力模拟技术和伞状采样方法详细研究了300K和275K两个温度条件下钾离子跨膜通道蛋白对单个钾离子的传输机理和Potentials of Means Force自由能在整个传输过程中的变化曲线。分析伞状采样的计算结果表明,温度的下降对钾离子跨膜通道蛋白的传输能力具有较大影响,300K时,钾离子在跨膜通道蛋白中的传输过程是热力学自发过程;然而,当温度下降到275K后,跨膜通道蛋白前沿空腔对钾离子的捕捉能力明显下降,选择性位点的能垒和传输通道的自由能普遍上升,导致跨膜通道蛋白出口的自由能高于其入口的自由能,最终使钾离子跨膜通道蛋白对钾离子传输方向发生逆转。同时该结果还可以对冷害发生的机理和防治给予重要的启示:说明温度下降后,果蔬体内物质传输能力的下降和停滞是造成冷害发生的一个主要原因。展开更多
The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The inte...The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs.展开更多
Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions.However,when ...Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions.However,when applied to complex biological macromolecules,the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes,leading to inherent timescale gaps between molecular dynamics simulations and real biological processes.To address this issue,several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics.In this review,the theoretical basis,practical applications,and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized.Furthermore,the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.展开更多
In studies of ion channel systems,due to the huge computational cost of polarizable force elds,classical force elds remain the most widely used for a long time.In this work,we used the AMOEBA polarizable atomic multip...In studies of ion channel systems,due to the huge computational cost of polarizable force elds,classical force elds remain the most widely used for a long time.In this work,we used the AMOEBA polarizable atomic multipole force eld in enhanced sampling simula-tions of single-channel gramicidin A(gA)and double-channel gA systems and investigated its reliability in characterizing ion-transport properties of the gA ion channel under dimer-ization.The inuence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance,di usion coeffcient,and free energy pro le.Results from the polarizable force eld simulations show that the conductance of potassium and sodium ions passing through the single-and double-channel agrees well with experimental values.Further data analysis reveals that the molecular mechanism of protein dimerization a ects the ion-transport properties of gA channels,i.e.,protein dimer-ization accelerates the permeation of potassium and sodium ions passing through the double-channel by adjusting the environment around gA protein(the distribution of phospholipid head groups,ions outside the channel,and bulk water),rather than directly adjusting the conformation of gA protein.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
基金We appreciate Prince Sattam bin Abdulaziz University for funding this project(PSAU/2023/R/1444).
文摘Mycobacterium tuberculosis(Mtb)is responsible for the spread of tuberculosis(TB).The current study employed virtual screening of 2569 natural compounds against the DNA-directed RNA polymerase(RNAP)of Mtb to identify the possible binders that can inhibit its function.The in-silico methodology included molecular docking to the compounds,further,the stability and flexibility of the best complexes were studied using molecular dynamics simulation,the MM/GBSA binding free energy technique with energy decomposition,PCA,FEL,steered MD simulation,and umbrella sampling.Individual virtual screenings were conducted for the five RNAP subunits(chains A,B,C,D,and E)to identify a compound capable of inhibiting RNAP oligomerization.A promising compound,isoestradiol 3-benzoate,exhibited a low binding score(−7.28kcal/mol to−8.21kcal/mol)and showed binding ability with all subunits of the protein.Thus,the five complexes with isoestradiol 3-benzoate were selected for molecular dynamics simulation analysis.Furthermore,RMSD showed that isoestradiol 3-benzoate bound with chain E showed the lowest RMSD of 0.49nm,while with chains A and B it had the most stable and consistent conformations with RMSD of 1.75nm and 1.2nm,respectively.The H-bond between isoestradiol 3-benzoate and chains C and E showed the highest occupancy(58.27%,45.33%,and 50.80%,42.25%,11.75%).Moreover,the MMPBSA technique showed that isoestradiol 3-benzoate had a strong association with chains B and C(ΔGbind=−126.25±2.03 and−129.27±2.25).Additionally,free energy decomposition,PCA,FEL-steered MD simulation,and umbrella sampling were also performed to validate the association of the ligand with the protein.Isoestradiol 3-benzoate binds strongly to chains B and E;therefore,it should be considered as viable candidate for inhibiting the formation of RNAP protein complex,concluded in this study.
基金This work was supported by the National Natural Science Foundation of China(No.22173032 and No.21933010).We also acknowledge the support of NYU Shanghai and ECNU Multifunctional Platform for Innovation(No.001).
文摘为了研究温度变化对生物膜跨膜传输能力的影响,本文以钾离子跨膜通道蛋白为研究对象,利用Gromacs分子生物学模拟软件包和Gromos96(53a6)分子力场,通过分子动力模拟技术和伞状采样方法详细研究了300K和275K两个温度条件下钾离子跨膜通道蛋白对单个钾离子的传输机理和Potentials of Means Force自由能在整个传输过程中的变化曲线。分析伞状采样的计算结果表明,温度的下降对钾离子跨膜通道蛋白的传输能力具有较大影响,300K时,钾离子在跨膜通道蛋白中的传输过程是热力学自发过程;然而,当温度下降到275K后,跨膜通道蛋白前沿空腔对钾离子的捕捉能力明显下降,选择性位点的能垒和传输通道的自由能普遍上升,导致跨膜通道蛋白出口的自由能高于其入口的自由能,最终使钾离子跨膜通道蛋白对钾离子传输方向发生逆转。同时该结果还可以对冷害发生的机理和防治给予重要的启示:说明温度下降后,果蔬体内物质传输能力的下降和停滞是造成冷害发生的一个主要原因。
文摘The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs.
基金supported by the National Natural Science Foundation of China(No.31700647,No.21625302,and No.21573217)
文摘Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions.However,when applied to complex biological macromolecules,the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes,leading to inherent timescale gaps between molecular dynamics simulations and real biological processes.To address this issue,several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics.In this review,the theoretical basis,practical applications,and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized.Furthermore,the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.
基金This work is supported by the National Natural Sci-ence Foundation of China(No.21933010).
文摘In studies of ion channel systems,due to the huge computational cost of polarizable force elds,classical force elds remain the most widely used for a long time.In this work,we used the AMOEBA polarizable atomic multipole force eld in enhanced sampling simula-tions of single-channel gramicidin A(gA)and double-channel gA systems and investigated its reliability in characterizing ion-transport properties of the gA ion channel under dimer-ization.The inuence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance,di usion coeffcient,and free energy pro le.Results from the polarizable force eld simulations show that the conductance of potassium and sodium ions passing through the single-and double-channel agrees well with experimental values.Further data analysis reveals that the molecular mechanism of protein dimerization a ects the ion-transport properties of gA channels,i.e.,protein dimer-ization accelerates the permeation of potassium and sodium ions passing through the double-channel by adjusting the environment around gA protein(the distribution of phospholipid head groups,ions outside the channel,and bulk water),rather than directly adjusting the conformation of gA protein.
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)
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.
