磷酸化调控蛋白质构象变化的理论研究
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摘要
蛋白质的磷酸化和去磷酸化过程是生物体内普遍存在的信息传导调节方式,几乎涉及所有的生理及病理过程,如糖代谢、细胞的生长发育、基因表达、神经递质的合成与释放,甚至癌变等,在信号传导过程中占有极其重要的地位。信号传导是维系外部刺激与细胞反应的桥梁。蛋白质在体内可逆的磷酸化和去磷酸化过程通过调节蛋白质构象的变化或蛋白之间相互作用,对生理过程起到类似“开关”的调节作用。
从20世纪90年代以来,随着计算机科学的发展,生物信息学得到了迅猛的发展,而蛋白质作为生物信息学研究的一个重要对象,有关蛋白质的理论模拟已经成为一个重要的研究领域。应用分子模拟的方法构建蛋白质三维模型,研究生物大分子的结构特点,分析蛋白质与底物相互作用,描述蛋白质的生化机理已经成为进行生物学和医学研究的一个主要手段。除了常规分子动力学模拟外,近年发展起来的拉伸分子动力学模拟通过引入外加力(势场)和减少蛋白质构象空间自由度等策略,使分子动力学应用范围更广。自由能计算方法为蛋白质构象变化提供定量的描述,对反应发生的路线和机理提供依据。
本论文选取两个磷酸化调控蛋白质构象变化和功能的体系作为研究对象,通过常规分子动力学模拟、拉伸分子动力学模拟和自由能计算三种方法相结合的手段,研究在蛋白质特定位点进行磷酸化以后,对蛋白质构象变化以及蛋白质之间结合情况带来的影响,及调控蛋白功能的分子机制。
1.Ser88位磷酸化调控LC8解离机理的理论研究
动力蛋白轻链是一类序列高度保守的蛋白质,在生理条件下以二聚体形式存在,参与一系列细胞内重要的生理过程。有实验证明,在细胞内动力蛋白轻链LC8的二聚体结构可以被蛋白激酶在Ser88位点磷酸化,导致二聚体解离,对哺乳细胞凋亡过程起到抑制作用。但从生化实验里面无法得到磷酸化的细节和对二聚体结构的影响,以及引起二聚体解离的机理。我们采用分子动力学模拟和自由能计算相结合的方法,为磷酸化导致LC8解离的机理提供了原子尺度的解释。
10 ns常规分子动力学模拟结果表明当在Ser88发生突变或磷酸化(S88E/pSer88)时,Ser88附近的残基和一些相互作用受到扰动。突变使原本紧密结合的Ser88和Ser88’由于同性负电荷的引入而互相排斥,原有的较为牢固的氢键作用被打破。同时,由于位于二聚体结合界面负电荷的引入,使蛋白局部极性增加,从而吸引周围溶剂中的水分子靠近表面,为水分子进入疏水结合界面打开了一个通道。从模拟的结果很清晰的看到,在突变体中水分子由C-端Glu88/pS88位置进入结合界面,通过与His55的侧链相互作用,干扰围绕His55周围的氢键网络。由于His55不再包埋在疏水界而内,而是更多的暴露在水环境中,从而导致其侧链pKa值增大,增加它的质子化几率。而以往的研究已经表明His55的质子化能够使二聚体结构失去稳定性。因此我们的研究表明,LC8在Ser88磷酸化导致二聚体结构解离的过程是通过间接调节His55的质子化状态来实现的。
自由能计算给出了由Ser88磷酸化引起二聚体结构稳定性下降的能量数据。S88E体系的⊿⊿GDisso是-6.6kcal/mol,与实验测得的结果(-8.1kcal/mol)符合的较好。我们的计算还给出了实验中难以检测到的pSer88体系的⊿⊿GDisso为-50.8kcal/mol。通过对自由能结果的进一步分析,发现自由能变化主要是由带负电的pSer88静电排斥作用引起,静电自由能变化项占主导作用,与实验结果吻合较好。以上结果都说明,对Ser88进行磷酸化确实会影响LC8二聚体的稳定性,使其更易发生解离。
2.磷酸化调控ZO-1 PDZ2与Cx43结合机理的研究
ZO-1 PDZ2结构域与连接蛋白(Connexin43, Cx43)的相互作用近年来广受关注,因为它们的相互作用在诸如心肌细胞、成纤维细胞和神经元细胞等诸多细胞中起到调节相邻细胞间隙联结(Gapjunction, GJ)的位置、移动和动念连接模式的作用。有研究发现在Cx43靠近C-端的S(-9)位被激酶磷酸化以后,Cx43与ZO-1PDZ2结构域的结合被打断,PDZ2组装Cx43形成六聚体GJ的功能消失,但是机理尚不明确。
我们采用分子动力学模拟的方法对ZO-1 PDZ2结合Cx43体系进行系统的研究,共研究了包括Free From(PDZ2未结合Cx43)、Short Form(PDZ2结合Cx43靠近C-端的9个残基的肽段体系)、Long Form(PDZ2结合Cx43靠近C-端的12个残基的肽段体系)、Long S(-9)(在Long Form基础上对S(-9)进行磷酸化的体系)和Long S(-9,-10)(在Long Form基础上同时对S(-9,-10)进行磷酸化的体系)。
研究结果表明,无论是否结合Cx43肽段以及肽段长短、是否被磷酸化,ZO-1PDZ2二聚体结构都具有较大的柔性,两个单体以两条反平行的β-链相互作用的结合中心为中点,两个单体的相对位置在模拟过程中在一定幅度内振动,单体本身不发生大的构象变化。四个结合肽段体系中,Cx43肽段与PDZ2二聚体有不同的结合强度和结合模式。通过比较X-ray晶体结构(ZO-1 PDZ2结合9个氨基酸Cx43肽段体系,Short Form)和ZO-1 PDZ2结合12个氨基酸Cx43肽段(Long Form)结合情况发现,Short Form体系中,Cx43肽段N-端脱离于PDZ2表面的结合,向自身C-端折叠形成发卡状构象,而Long Form体系中肽段则与PDZ2形成稳定的结合,说明在Short Form中Cx43的N-端增加的三个氨基酸ASS对于稳定Cx43在PDZ2上的结合有不可忽略的重要性。对Long Form体系的S(-9)做磷酸化突变,或者同时磷酸化S(-9)和S(-10)以后,磷酸根的引入使Cx43与PDZ2的结合作用被削弱,在20 ns动力学模拟过程中,肽段与PDZ2没有在固定的结合位点形成稳定的结合作用。我们的模拟结果证明磷酸化确实对Cx43与ZO-1 PDZ2的相互作用起到调节作用,且调节机制主要是缘于磷酸根基团负电荷的引入带来的静电扰动,破坏了Cx43与PDZ2之间原有的氢键和盐桥相互作用导致的。
The reversible phosphorylation of proteins regulates almost all aspects of cell life, and provides a fast and efficient way to regulate protein functions, and it is used to control all basic cellular processes, including metabolism, signaling, motility, growth, proliferation, differentiation, organelle trafficking and membrane transport. Abnormal phosphorylation is a cause or consequence of many diseases. In many cases, phosphorylation regulates conformation changes of proteins and results in switch-like changes in protein function.
From the nineties of the 20th century, with the development of computer science as well as the human genome project implementation, bioinformatics has been developed rapidly. Protein is an indispensable research object in bioinformatics, therefore, computer simulation of proteins has become a well-established and important research area. Via molecular modeling can build the three-dimensional model of proteins, to research the structure characteristics of the macromolecules, analyze the interaction between the protein and substrate, and describe protein biochemistry functions, thus molecular simulation has already become a powerful tool for biology experiments and drug design. Besides the conventional molecular dynamics simulation, the steered molecular dynamics simulation method became a good complement to it through modifying the energy function to effectively reduce the height of barriers separating low-energy states. In this thesis, we have carried out molecular simulation technology combined with steered molecular dynamics simulation and free energy calculations to study protein conformation changes and protein-inhibitor interactions induced by phosphorylation. The computer simulations of the protein and substrate interactions may understand some problems that can not been solved in the experiment. The simulation results can support the further studies on them and direct the design of new inhibitors and drugs. The main results are summarized as follows:
1. Mechanism of Ser88 phosphorylation induced dimer dissociation in dynein light chain LC8.
Dynein light chain LC8 is a highly conserved, dimeric protein involving in a variety of essential cellular events. Phosphorylation at Ser88 was found to promote mammalian cell survival and regulate the dimer to monomer transition at physiological pH condition. Combining molecular dynamics (MD) simulation and free energy calculation methods, we explored the atomistic mechanism of the phosphorylation induced dimer dissociation. The MD simulation revealed that phosphorylation/phosphomimetic mutation at Ser88 opens an entrance into the dimer interface for water molecules, which disturbs the hydrogen bond network around His55 and is expected to raise the pKa value and protonation ratio of His55 as well. The free energy calculations showed that S88E mutation destabilized the dimer by 6.6 kcal/mol, in good agreement with the experimental value of 8.1 kcal/mol. The calculated destabilization upon phosphorylation is 50.8 kcal/mol, showing that phosphorylation definitely prevents dimer formation at physiological condition. Further analysis of the calculated free energy changes demonstrated that the electrostatic contribution dominates the impact of phosphorylation on dimer dissociation.
2. Mechanism of phosphorylation regulated interaction between ZO-1 PDZ2 and Cx43.
The interactions of connexins (especially connexin43, Cx43), the most abundant connexin in mammals) with the second PDZ domain of ZO-1 received particular attention in recent years in the context of GJ formation and regulation. Accumulating evidence indicates that ZO-1 actively participates in the dynamic remodeling of GJs in a number of cellular systems, including cardiomyocytes, fibroblasts and neurons. There are evidences that the phosphorylation of connexin on the carboxyl terminal domain may regulate, or are correlated, with gap junction turnover, but the regulating mechanism is not clear yet. With molecular dynamics simulation, we explore the atomics mechanism of S(-9)/S(-10) phosphorylation regulated Cx43 binding with ZO-1 PDZ2 domain. The MD simulation shows that two monomers of PDZ2 domain have good flexibility and fluctuates toward each other during simulation whether binding with Cx43 or not. Cx43 with 12 residues shows better binding affinity than 9 residues peptide with PDZ2, while the latter forms 'hair-pin' during simulations. While S(-9) or S(-9,-10) was phosphorylated, the interaction between Cx43 peptide and PDZ2 was interrupted or weakened. Because the phosphate carries a -2 charge and the resulting large electrostatic perturbation modulates the energy landscapes governing protein-protein interaction. Hydrogen bonds formed by S(-9), S(-10) from Cx43 and E210, E238 from PDZ2 were disrupted because of phosphorylation. Long-Form Cx43 (with 12 residues) has the best binding affinity with PDZ2, in good agreement with experiment data.
从20世纪90年代以来,随着计算机科学的发展,生物信息学得到了迅猛的发展,而蛋白质作为生物信息学研究的一个重要对象,有关蛋白质的理论模拟已经成为一个重要的研究领域。应用分子模拟的方法构建蛋白质三维模型,研究生物大分子的结构特点,分析蛋白质与底物相互作用,描述蛋白质的生化机理已经成为进行生物学和医学研究的一个主要手段。除了常规分子动力学模拟外,近年发展起来的拉伸分子动力学模拟通过引入外加力(势场)和减少蛋白质构象空间自由度等策略,使分子动力学应用范围更广。自由能计算方法为蛋白质构象变化提供定量的描述,对反应发生的路线和机理提供依据。
本论文选取两个磷酸化调控蛋白质构象变化和功能的体系作为研究对象,通过常规分子动力学模拟、拉伸分子动力学模拟和自由能计算三种方法相结合的手段,研究在蛋白质特定位点进行磷酸化以后,对蛋白质构象变化以及蛋白质之间结合情况带来的影响,及调控蛋白功能的分子机制。
1.Ser88位磷酸化调控LC8解离机理的理论研究
动力蛋白轻链是一类序列高度保守的蛋白质,在生理条件下以二聚体形式存在,参与一系列细胞内重要的生理过程。有实验证明,在细胞内动力蛋白轻链LC8的二聚体结构可以被蛋白激酶在Ser88位点磷酸化,导致二聚体解离,对哺乳细胞凋亡过程起到抑制作用。但从生化实验里面无法得到磷酸化的细节和对二聚体结构的影响,以及引起二聚体解离的机理。我们采用分子动力学模拟和自由能计算相结合的方法,为磷酸化导致LC8解离的机理提供了原子尺度的解释。
10 ns常规分子动力学模拟结果表明当在Ser88发生突变或磷酸化(S88E/pSer88)时,Ser88附近的残基和一些相互作用受到扰动。突变使原本紧密结合的Ser88和Ser88’由于同性负电荷的引入而互相排斥,原有的较为牢固的氢键作用被打破。同时,由于位于二聚体结合界面负电荷的引入,使蛋白局部极性增加,从而吸引周围溶剂中的水分子靠近表面,为水分子进入疏水结合界面打开了一个通道。从模拟的结果很清晰的看到,在突变体中水分子由C-端Glu88/pS88位置进入结合界面,通过与His55的侧链相互作用,干扰围绕His55周围的氢键网络。由于His55不再包埋在疏水界而内,而是更多的暴露在水环境中,从而导致其侧链pKa值增大,增加它的质子化几率。而以往的研究已经表明His55的质子化能够使二聚体结构失去稳定性。因此我们的研究表明,LC8在Ser88磷酸化导致二聚体结构解离的过程是通过间接调节His55的质子化状态来实现的。
自由能计算给出了由Ser88磷酸化引起二聚体结构稳定性下降的能量数据。S88E体系的⊿⊿GDisso是-6.6kcal/mol,与实验测得的结果(-8.1kcal/mol)符合的较好。我们的计算还给出了实验中难以检测到的pSer88体系的⊿⊿GDisso为-50.8kcal/mol。通过对自由能结果的进一步分析,发现自由能变化主要是由带负电的pSer88静电排斥作用引起,静电自由能变化项占主导作用,与实验结果吻合较好。以上结果都说明,对Ser88进行磷酸化确实会影响LC8二聚体的稳定性,使其更易发生解离。
2.磷酸化调控ZO-1 PDZ2与Cx43结合机理的研究
ZO-1 PDZ2结构域与连接蛋白(Connexin43, Cx43)的相互作用近年来广受关注,因为它们的相互作用在诸如心肌细胞、成纤维细胞和神经元细胞等诸多细胞中起到调节相邻细胞间隙联结(Gapjunction, GJ)的位置、移动和动念连接模式的作用。有研究发现在Cx43靠近C-端的S(-9)位被激酶磷酸化以后,Cx43与ZO-1PDZ2结构域的结合被打断,PDZ2组装Cx43形成六聚体GJ的功能消失,但是机理尚不明确。
我们采用分子动力学模拟的方法对ZO-1 PDZ2结合Cx43体系进行系统的研究,共研究了包括Free From(PDZ2未结合Cx43)、Short Form(PDZ2结合Cx43靠近C-端的9个残基的肽段体系)、Long Form(PDZ2结合Cx43靠近C-端的12个残基的肽段体系)、Long S(-9)(在Long Form基础上对S(-9)进行磷酸化的体系)和Long S(-9,-10)(在Long Form基础上同时对S(-9,-10)进行磷酸化的体系)。
研究结果表明,无论是否结合Cx43肽段以及肽段长短、是否被磷酸化,ZO-1PDZ2二聚体结构都具有较大的柔性,两个单体以两条反平行的β-链相互作用的结合中心为中点,两个单体的相对位置在模拟过程中在一定幅度内振动,单体本身不发生大的构象变化。四个结合肽段体系中,Cx43肽段与PDZ2二聚体有不同的结合强度和结合模式。通过比较X-ray晶体结构(ZO-1 PDZ2结合9个氨基酸Cx43肽段体系,Short Form)和ZO-1 PDZ2结合12个氨基酸Cx43肽段(Long Form)结合情况发现,Short Form体系中,Cx43肽段N-端脱离于PDZ2表面的结合,向自身C-端折叠形成发卡状构象,而Long Form体系中肽段则与PDZ2形成稳定的结合,说明在Short Form中Cx43的N-端增加的三个氨基酸ASS对于稳定Cx43在PDZ2上的结合有不可忽略的重要性。对Long Form体系的S(-9)做磷酸化突变,或者同时磷酸化S(-9)和S(-10)以后,磷酸根的引入使Cx43与PDZ2的结合作用被削弱,在20 ns动力学模拟过程中,肽段与PDZ2没有在固定的结合位点形成稳定的结合作用。我们的模拟结果证明磷酸化确实对Cx43与ZO-1 PDZ2的相互作用起到调节作用,且调节机制主要是缘于磷酸根基团负电荷的引入带来的静电扰动,破坏了Cx43与PDZ2之间原有的氢键和盐桥相互作用导致的。
The reversible phosphorylation of proteins regulates almost all aspects of cell life, and provides a fast and efficient way to regulate protein functions, and it is used to control all basic cellular processes, including metabolism, signaling, motility, growth, proliferation, differentiation, organelle trafficking and membrane transport. Abnormal phosphorylation is a cause or consequence of many diseases. In many cases, phosphorylation regulates conformation changes of proteins and results in switch-like changes in protein function.
From the nineties of the 20th century, with the development of computer science as well as the human genome project implementation, bioinformatics has been developed rapidly. Protein is an indispensable research object in bioinformatics, therefore, computer simulation of proteins has become a well-established and important research area. Via molecular modeling can build the three-dimensional model of proteins, to research the structure characteristics of the macromolecules, analyze the interaction between the protein and substrate, and describe protein biochemistry functions, thus molecular simulation has already become a powerful tool for biology experiments and drug design. Besides the conventional molecular dynamics simulation, the steered molecular dynamics simulation method became a good complement to it through modifying the energy function to effectively reduce the height of barriers separating low-energy states. In this thesis, we have carried out molecular simulation technology combined with steered molecular dynamics simulation and free energy calculations to study protein conformation changes and protein-inhibitor interactions induced by phosphorylation. The computer simulations of the protein and substrate interactions may understand some problems that can not been solved in the experiment. The simulation results can support the further studies on them and direct the design of new inhibitors and drugs. The main results are summarized as follows:
1. Mechanism of Ser88 phosphorylation induced dimer dissociation in dynein light chain LC8.
Dynein light chain LC8 is a highly conserved, dimeric protein involving in a variety of essential cellular events. Phosphorylation at Ser88 was found to promote mammalian cell survival and regulate the dimer to monomer transition at physiological pH condition. Combining molecular dynamics (MD) simulation and free energy calculation methods, we explored the atomistic mechanism of the phosphorylation induced dimer dissociation. The MD simulation revealed that phosphorylation/phosphomimetic mutation at Ser88 opens an entrance into the dimer interface for water molecules, which disturbs the hydrogen bond network around His55 and is expected to raise the pKa value and protonation ratio of His55 as well. The free energy calculations showed that S88E mutation destabilized the dimer by 6.6 kcal/mol, in good agreement with the experimental value of 8.1 kcal/mol. The calculated destabilization upon phosphorylation is 50.8 kcal/mol, showing that phosphorylation definitely prevents dimer formation at physiological condition. Further analysis of the calculated free energy changes demonstrated that the electrostatic contribution dominates the impact of phosphorylation on dimer dissociation.
2. Mechanism of phosphorylation regulated interaction between ZO-1 PDZ2 and Cx43.
The interactions of connexins (especially connexin43, Cx43), the most abundant connexin in mammals) with the second PDZ domain of ZO-1 received particular attention in recent years in the context of GJ formation and regulation. Accumulating evidence indicates that ZO-1 actively participates in the dynamic remodeling of GJs in a number of cellular systems, including cardiomyocytes, fibroblasts and neurons. There are evidences that the phosphorylation of connexin on the carboxyl terminal domain may regulate, or are correlated, with gap junction turnover, but the regulating mechanism is not clear yet. With molecular dynamics simulation, we explore the atomics mechanism of S(-9)/S(-10) phosphorylation regulated Cx43 binding with ZO-1 PDZ2 domain. The MD simulation shows that two monomers of PDZ2 domain have good flexibility and fluctuates toward each other during simulation whether binding with Cx43 or not. Cx43 with 12 residues shows better binding affinity than 9 residues peptide with PDZ2, while the latter forms 'hair-pin' during simulations. While S(-9) or S(-9,-10) was phosphorylated, the interaction between Cx43 peptide and PDZ2 was interrupted or weakened. Because the phosphate carries a -2 charge and the resulting large electrostatic perturbation modulates the energy landscapes governing protein-protein interaction. Hydrogen bonds formed by S(-9), S(-10) from Cx43 and E210, E238 from PDZ2 were disrupted because of phosphorylation. Long-Form Cx43 (with 12 residues) has the best binding affinity with PDZ2, in good agreement with experiment data.
引文
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