Nucleotide binding domain,leucine-rich repeat,and pyrin domain-containing 3(NLRP3)is an NLR-protein family member that can be activated by diverse exogenous and endogenous stimuli but without direct binding of any of ...Nucleotide binding domain,leucine-rich repeat,and pyrin domain-containing 3(NLRP3)is an NLR-protein family member that can be activated by diverse exogenous and endogenous stimuli but without direct binding of any of these pathogen ligands.Biological studies show that inactive NLRP3 is usually in an as-sembly state and its activation requires a kinase protein,NEK7.However,our re-cent computational studies as well as other biological investigations have demonstrated that NEK7 does not play a significant role in the activation of NLRP3 assembly and activation.In-stead,biological studies suggest that NEK7 is essential in the dissociation of inactive NLRP3 assemblies.Despite extensive research,the dissociation mechanism of the inactive NLRP3 as-sembly remains largely elusive.In this work,an improved MM-PBSA method is applied to the protein-protein binding free energies in the inactive NLRP3 decamer.Combined with the po-tential mean force(PMF)computation for the 0°→5°conformational change,the standard free-energy change,ΔG^(0)is calculated for NEK7-driven association of the inactive NLRP3 de-camer.Our calculations show that in the absence of NEK7,the dissociation of the inactive NLRP3 decamer is an energetically unfavorable process(ΔG^(0)=99.69 kcal/mol),whereas upon NEK7 binding,the overall standard free energy differenceΔG^(0)=-24.21 kcal/mol is obtained for the inactive NLRP3 decamer dissociation.The free-energy difference calcula-tions in this work also disclose an energetically optimized dissociation pathway,along which the inactive NLRP3 decamer is disunited by a one-by-one dissociation mechanism.展开更多
基金supported by Ministry of Science and Technology of China(2022YFA1303100)the National Natural Science Foundation of China(No.32090040)。
文摘Nucleotide binding domain,leucine-rich repeat,and pyrin domain-containing 3(NLRP3)is an NLR-protein family member that can be activated by diverse exogenous and endogenous stimuli but without direct binding of any of these pathogen ligands.Biological studies show that inactive NLRP3 is usually in an as-sembly state and its activation requires a kinase protein,NEK7.However,our re-cent computational studies as well as other biological investigations have demonstrated that NEK7 does not play a significant role in the activation of NLRP3 assembly and activation.In-stead,biological studies suggest that NEK7 is essential in the dissociation of inactive NLRP3 assemblies.Despite extensive research,the dissociation mechanism of the inactive NLRP3 as-sembly remains largely elusive.In this work,an improved MM-PBSA method is applied to the protein-protein binding free energies in the inactive NLRP3 decamer.Combined with the po-tential mean force(PMF)computation for the 0°→5°conformational change,the standard free-energy change,ΔG^(0)is calculated for NEK7-driven association of the inactive NLRP3 de-camer.Our calculations show that in the absence of NEK7,the dissociation of the inactive NLRP3 decamer is an energetically unfavorable process(ΔG^(0)=99.69 kcal/mol),whereas upon NEK7 binding,the overall standard free energy differenceΔG^(0)=-24.21 kcal/mol is obtained for the inactive NLRP3 decamer dissociation.The free-energy difference calcula-tions in this work also disclose an energetically optimized dissociation pathway,along which the inactive NLRP3 decamer is disunited by a one-by-one dissociation mechanism.
文摘细胞色素P450(以下简称CYP)与昆虫的抗药性密切相关。本研究运用Auto Dock分子对接技术和分子力学泊松-波尔兹曼表面积法(molecular mechanics Poisson-Boltzmann surface area,MM-PBSA)结合自由能计算方法,分析了甜菜夜蛾CYP9A11与3种杀虫剂结合的作用位点、作用力类型和大小。结果表明:CYP9A11与毒死蜱结合形成两个氢键,有8个氨基酸残基参与形成疏水作用力,二者结合自由能为–3 659.80 k J/mol;CYP9A11与灭多威结合形成5个氢键,有3个氨基酸残基形成疏水作用力,结合自由能为–470.92 k J/mol;CYP9A11中有7个氨基酸残基与氯氰菊酯结合形成疏水作用力,结合自由能为–473.44 k J/mol。范德华力是CYP9A11与毒死蜱结合的主要驱动力,极性溶剂化能是CYP9A11与氯氰菊酯和灭多威结合的主要驱动力,这些结果为阐明甜菜夜蛾CYP9A11与3种杀虫剂的结合机理提供了参考。
文摘运用分子动力学(molecular dynamics,MD)和MM-PBSA(molecular mechanics/Poisson Boltzmann surface area)相结合的方法预测了β-环糊精(cyclodextrin,CD)和甾类客体分子包结模式.通过重原子均方根偏差(root mean square deviation,RMSD)分析可得,两种包结模式下客体分子都可以和β-CD形成稳定的包结.在MD轨迹采样基础上,采用高效MM-PBSA方法计算了两种包结模式下的包结自由能.计算结果显示,β-CD和三个甾类客体分子包结的主要驱动力为范德华相互作用,而溶剂化能和熵变则不利于体系的包结.进一步分析平均构象和包结自由能发现,对于波尼松龙,D-up(D-ring up orientation)取向为优势包结模式;而乙炔雌二醇和雌三醇的优势包结模式均为A-up(A-ring up orientation)取向.通过比较β-CD和三个客体分子的理论包结自由能,预测包结稳定性的次序为乙炔雌二醇>雌三醇>波尼松龙,和实验结果相一致.
基金supported by grants from The National Natural Science Foundation of China(30670497)National Basic Research Program of China(2009CB930200)+1 种基金Beijing Natural Science Foundation(5072002,7082006)Research Fund for the Doctorate Program(X0015001200801)~~
