生物小分子及模型分子在溶液中的相互作用及质子转移研究
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摘要
质子转移在众多化学反应和生命过程中发挥了重要的作用，生物分子内的质子转移造成的互变异构现象是生物体发生点突变的起因之一。众所周知，生物分子大都是在溶液尤其是水溶液中才具有特定的生理活性，因此对生物分子质子转移反应的研究不能脱离对其自身所处环境的考量，即需要了解生物分子在溶液中的相互作用。相互作用是生物分子体系中普遍存在的一类重要作用，在分子组装、分子识别及决定结构—功能—活性关系等方面有着及其重要的作用，其本身就是一个非常有趣的命题。本论文拟从简单的生化模型小分子出发，从研究其在水溶液中的弱相互作用开始进一步探讨其发生的质子转移反应，再从体系上扩展到复杂的生物碱基鸟嘌呤分子，采用分子动力学模拟、量化计算、核磁共振实验等手段对生化模型分子和生物小分子在水溶液中的相互作用和质子转移反应进行了多角度的研究。
由于生物分子普遍含有羰基，论文首先对最简单的羰基体系丙酮的水溶液进行了研究。我们采取全原子OPLS-AA力场对该体系进行了分子动力学模拟，发现羰基侧甲基与水分子间存在着明显的C-H…O弱相互作用，并结合核磁共振波谱研究了体系中的氢键网络结构；之后引入相对氢键度η_(rel)和过量相对氢键度η~E_(rel)的概念，将NMR数据、MD结果与溶液宏观的传递性质归一化到无量纲的参数之下，并对其在全浓度范围内的变化趋势进行了研究，我们发现：由三者分别得出的η~E_(rel)随浓度变化趋势完全一致，并且都在x_A≈0.3左右出现非理想性最强的特殊点，同时溶液中强氢键与C-H…O弱相互作用的浓度依数性表明两者相互关联、互为影响。
在丙酮水溶液相互作用研究的基础上选取了最简单的肽键模型分子甲酰胺的水溶液进行了计算研究。通过量化计算发现溶剂水分子可以在甲酰胺周围三个不同的空间位置分别与之缔合形成稳定的团簇，羰基侧的C-H…O弱相互作用不可被忽略，MD模拟也证实了该观点；全浓度溶液的模拟表明甲酰胺在稀浓度区可以促进水局部结构增强，之后，两者的交叉缔合将逐渐被甲酰胺自身的线状缔合代替。
在明晰了甲酰胺与水分子相互作用的基础上，采用量化计算的方法研究了水分子对甲酰胺质子转移的影响，我们发现与甲酰胺形成团簇的三种水分子在质子转移过程中担任了两种截然不同的角色：缔合在质子转移路径上的水分子(W2)不仅充当质子传递的桥梁，使活化能大大降低，在热力学上也使该过程更加可行，这类水分子可称为位于“催化位”；而另外两种水分子(W1和W3)则恰好相反，不仅使反应活化能提高，反应自由能变也增大，即反应在动力学和热力学两方面都更加不利于进行，这类水分子可称为位于“保护位”。在多水合团簇中，不同性质的水分子将共同作用于中心分子。以上结论在气态和考虑了溶液连续介质影响的计算中都成立，并且在连续介质中催化位水作用增强，保护位水作用却被削弱。我们尝试从质子转移前后分子的结构改变、电荷分布以及水与甲酰胺互变异构体之间的相互作用、NBO分析等方面考察水分子出现两种功效的内在原因。之后对甲酰胺的衍生物、结构更加复杂的甘氨酰胺(N端氨基酸的模型分子)的质子转移进行了类似的研究，同样发现了不同区域的水分子对该反应发挥的催化、保护特性。在甲酰胺的催化位上，我们研究了一系列在结构上能充当氢桥的小分子，发现在它们参与催化的质子转移反应中，活化能的大小与分子自身的DPE+PA值成线性关系，据此可以推测反应达到过渡态是氢桥分子同时从甲酰胺得到质子和自身脱去质子的协同过程。
鸟嘌呤是生命基础碱基中结构最复杂的一种，异构体数量多达36个，其中任意两个异构体之间的反应都可被视为质子转移反应，我们将这个复杂的反应网络按照质子转移发生的位置分成了7类，并分别予以研究。研究发现异构体中稳定性排序靠前的无论在单体能量还是在生成过程中正逆反应能垒对比上，都是具有优势的；质子转移进行的方向选择性和分子的骨架结构有关，具体来说是由发生质子转移部分直接相连的结构部分决定的；反应发生的能垒与质子迁移距离之间存有线性关系，长程的质子转移将需要克服较高的反应能垒，反之亦然；异构体中酮式始终比对应的烯醇式稳定，胺式基本上比对应的亚胺式稳定，这与实验结果相符。鸟嘌呤含有类似甲酰胺的结构部分，我们因此选取了生物体中最常出现的9-H-keto-Guanine研究了水分子对其质子转移反应的影响，发现了与甲酰胺可以相互印证的一些结论：W1仍阻碍质子转移的进行，保护了碱基的正常构型；W2使反应能减小，并且大幅度降低反应能垒，促进烯醇式鸟嘌呤的生成。最后，我们选取乙酰丙酮作为模型，克服了其它生物分子和模型分子烯醇式含量过少或者溶解度过低的不利因素，使用NMR实验手段验证了质子转移过程中催化位的水分子能明显加速反应的进行速率。
本论文通过计算机模拟、量化计算和实验研究了生物小分子和模型分子在水溶液当中的相互作用并以此为基础研究了溶液水分子对中心分子质子转移反应的影响，总结了一些体系中弱相互作用和分子微观结构变化间存在的内在联系，为进一步研究生物大分子体系中的相互作用、结构性质以及基因突变等打下了一定的基础。
Proton transfer is a common and important phenomenon in chemical and biological reactions. Tautomerism of nucleic acid base, which is induced by proton transfer is considered to be one of the origins for the spontaneous point mutation in DNA. As we all know, biomolecules can only properly function in solution, especially in aqueous solution, as a result, when we investigate the proton transfer process of a biomolecule, we must not ignore the effect of the solution surroundings, and that means, we must synchronously study the interactions between the molecules in solution and take them into consideration. Weak interaction plays an essential role in the structures and properties of proteins and nucleic acids as well as in the behavior of many biological systems, and itself is quite an interesting theme for study. In the present work, MD simulation, quantum calculations, NMR experiment are combined to investigate the weak interaction as well as the proton transfer processes of the biochemical model molecules and small biomolecule systems. We will start from the simplest model molecules to the complicated nucleic acid base guanine.
Because carbonyl exists in many biomolecules, we first study aqueous solution of acetone, the simplest molecule contains carbonyl. An all-atom acetone model and a TIP5P water model have been adopted for molecular dynamics simulation. We found a weak contact C-H…O between the methyl group next to carbonyl and water. NMR data show good agreement with the hydrogen bonding network. Twoquantitiesη_(rel) andη_(rel)~E are applied to study the nonideal association mixture. Westudy the transport properties of the system by comparing theη_(rel)~E's of strong hydrogen bond and weak contact based on transport properties, MD simulations together with NMR experimental data and find good agreement of concentration dependence, which exhibits the cooperation effect. The solution shows extreme deviation from ideal mixing in the concentration range x_A≈0.3.
Formamide, despite its simpleness, it contains the essential features of the peptide linkage and often is used as a model. We study the aqueous solution of formamide as well as its enol form formamidic acid by quantum calculations. It is found that there are three different regions for water molecule to form cluster with the central molecule, one of the clusters contains C-H…O interaction, which is found in acetone aqueous solution, again verified in this mixture by MD simulation. By doing the calculation in the whole concentration, we found that formamide in water-rich region can strengthen the local structure of water, and cross-association between water and formamide will be taken place by the linear association of formamide itself as the concentration of formamide grows higher.
After knowing the interaction between formamide and water molecule, we move on to the investigation on its proton transfer process. Water molecules in the vicinity of formamide can be classified into two groups according to the different effects on the proton transfer process of formamide: water in two of them (W1 and W3) can protect formamide from tautomerizing, while in the third one (W2) works oppositely. For a multi-hydrated cluster, it will be an integrated effect of all the hydrated water. Above results are obtained in gas phase as well as in SCIPCM solution model, however, comparing with the situation in gas phase, the protective effects induced by W1 and W3 become smaller, and the assistant effect becomes more obvious. We tried to explain the differentia of the two kinds of water molecule by using the structural variation and potential electronic surface change during the transition, intermolecular interaction between the water and solvent as well as NBO analysis. The same conclusion can be drawn out in the study of Glycinamide, a derivative of formamide, the simplest and appropriate model compound for N-terminal amino acids. At last, a series of small molecules, which can deliver the hydrogen bond in the proton transfer process, are put in the assistant region. Activation energy of the reaction and DPE+PA value of the assistant molecule show a linear relationship, by which we may presume that the assistant molecule get the hydrogen bond from formamide and send out its own hydrogen at the same time in forming the transition state.
Guanine is the most sophisticated nucleic acid base. There are 36 possible tautomers, any one of which can be produced by proton transfer from another tautomer. We investigate the complex network by dividing them into seven groups. We found that the relative stability of the tautomers is reasonable both on thermodynamics and dynamics, the unstable tautomer has biggerΔE as well as higher energy barrier in the forming process; reaction direction between two transferable tautomers will be greatly influenced by the geometric property of the remaining part just next to the location where the transition happens; longer proton transfer distance is corresponding to higher activation energy, the vice versa; for transferable isomers with the same framework, keto form is more stable than the enol form, and the amino form is more stable than the imino one, the validity of this conclusion can be checked among the 36 tautomers, and agree with the experiment work. There is a segment quite like formamide in the structure of guanine, so we investigated the water's effect on the tautomerism of 9-H-keto-Guanine, we obtained accordant result: W1 can protect guanine from tautomerizing to the rare enol form, W2 can promote the tautomersim. At last, we study the tautomerization of acetylacetone by NMR, because enol form of this molecule can be actually tested in common surroundings and it does not have the solubility problem, both of which are quite annoying issues for the study of nucleic acid base.
To sum up, computer simulation, quantum calculation and experiment are combined to investigate the biochemical model molecules and small biomolecules in solution, some rules on the interaction and the structure variation in solution are discovered. We expect it can provide a base for the future development of the research on the tautomerism of other biomolecules and related gene mutation.
由于生物分子普遍含有羰基，论文首先对最简单的羰基体系丙酮的水溶液进行了研究。我们采取全原子OPLS-AA力场对该体系进行了分子动力学模拟，发现羰基侧甲基与水分子间存在着明显的C-H…O弱相互作用，并结合核磁共振波谱研究了体系中的氢键网络结构；之后引入相对氢键度η_(rel)和过量相对氢键度η~E_(rel)的概念，将NMR数据、MD结果与溶液宏观的传递性质归一化到无量纲的参数之下，并对其在全浓度范围内的变化趋势进行了研究，我们发现：由三者分别得出的η~E_(rel)随浓度变化趋势完全一致，并且都在x_A≈0.3左右出现非理想性最强的特殊点，同时溶液中强氢键与C-H…O弱相互作用的浓度依数性表明两者相互关联、互为影响。
在丙酮水溶液相互作用研究的基础上选取了最简单的肽键模型分子甲酰胺的水溶液进行了计算研究。通过量化计算发现溶剂水分子可以在甲酰胺周围三个不同的空间位置分别与之缔合形成稳定的团簇，羰基侧的C-H…O弱相互作用不可被忽略，MD模拟也证实了该观点；全浓度溶液的模拟表明甲酰胺在稀浓度区可以促进水局部结构增强，之后，两者的交叉缔合将逐渐被甲酰胺自身的线状缔合代替。
在明晰了甲酰胺与水分子相互作用的基础上，采用量化计算的方法研究了水分子对甲酰胺质子转移的影响，我们发现与甲酰胺形成团簇的三种水分子在质子转移过程中担任了两种截然不同的角色：缔合在质子转移路径上的水分子(W2)不仅充当质子传递的桥梁，使活化能大大降低，在热力学上也使该过程更加可行，这类水分子可称为位于“催化位”；而另外两种水分子(W1和W3)则恰好相反，不仅使反应活化能提高，反应自由能变也增大，即反应在动力学和热力学两方面都更加不利于进行，这类水分子可称为位于“保护位”。在多水合团簇中，不同性质的水分子将共同作用于中心分子。以上结论在气态和考虑了溶液连续介质影响的计算中都成立，并且在连续介质中催化位水作用增强，保护位水作用却被削弱。我们尝试从质子转移前后分子的结构改变、电荷分布以及水与甲酰胺互变异构体之间的相互作用、NBO分析等方面考察水分子出现两种功效的内在原因。之后对甲酰胺的衍生物、结构更加复杂的甘氨酰胺(N端氨基酸的模型分子)的质子转移进行了类似的研究，同样发现了不同区域的水分子对该反应发挥的催化、保护特性。在甲酰胺的催化位上，我们研究了一系列在结构上能充当氢桥的小分子，发现在它们参与催化的质子转移反应中，活化能的大小与分子自身的DPE+PA值成线性关系，据此可以推测反应达到过渡态是氢桥分子同时从甲酰胺得到质子和自身脱去质子的协同过程。
鸟嘌呤是生命基础碱基中结构最复杂的一种，异构体数量多达36个，其中任意两个异构体之间的反应都可被视为质子转移反应，我们将这个复杂的反应网络按照质子转移发生的位置分成了7类，并分别予以研究。研究发现异构体中稳定性排序靠前的无论在单体能量还是在生成过程中正逆反应能垒对比上，都是具有优势的；质子转移进行的方向选择性和分子的骨架结构有关，具体来说是由发生质子转移部分直接相连的结构部分决定的；反应发生的能垒与质子迁移距离之间存有线性关系，长程的质子转移将需要克服较高的反应能垒，反之亦然；异构体中酮式始终比对应的烯醇式稳定，胺式基本上比对应的亚胺式稳定，这与实验结果相符。鸟嘌呤含有类似甲酰胺的结构部分，我们因此选取了生物体中最常出现的9-H-keto-Guanine研究了水分子对其质子转移反应的影响，发现了与甲酰胺可以相互印证的一些结论：W1仍阻碍质子转移的进行，保护了碱基的正常构型；W2使反应能减小，并且大幅度降低反应能垒，促进烯醇式鸟嘌呤的生成。最后，我们选取乙酰丙酮作为模型，克服了其它生物分子和模型分子烯醇式含量过少或者溶解度过低的不利因素，使用NMR实验手段验证了质子转移过程中催化位的水分子能明显加速反应的进行速率。
本论文通过计算机模拟、量化计算和实验研究了生物小分子和模型分子在水溶液当中的相互作用并以此为基础研究了溶液水分子对中心分子质子转移反应的影响，总结了一些体系中弱相互作用和分子微观结构变化间存在的内在联系，为进一步研究生物大分子体系中的相互作用、结构性质以及基因突变等打下了一定的基础。
Proton transfer is a common and important phenomenon in chemical and biological reactions. Tautomerism of nucleic acid base, which is induced by proton transfer is considered to be one of the origins for the spontaneous point mutation in DNA. As we all know, biomolecules can only properly function in solution, especially in aqueous solution, as a result, when we investigate the proton transfer process of a biomolecule, we must not ignore the effect of the solution surroundings, and that means, we must synchronously study the interactions between the molecules in solution and take them into consideration. Weak interaction plays an essential role in the structures and properties of proteins and nucleic acids as well as in the behavior of many biological systems, and itself is quite an interesting theme for study. In the present work, MD simulation, quantum calculations, NMR experiment are combined to investigate the weak interaction as well as the proton transfer processes of the biochemical model molecules and small biomolecule systems. We will start from the simplest model molecules to the complicated nucleic acid base guanine.
Because carbonyl exists in many biomolecules, we first study aqueous solution of acetone, the simplest molecule contains carbonyl. An all-atom acetone model and a TIP5P water model have been adopted for molecular dynamics simulation. We found a weak contact C-H…O between the methyl group next to carbonyl and water. NMR data show good agreement with the hydrogen bonding network. Twoquantitiesη_(rel) andη_(rel)~E are applied to study the nonideal association mixture. Westudy the transport properties of the system by comparing theη_(rel)~E's of strong hydrogen bond and weak contact based on transport properties, MD simulations together with NMR experimental data and find good agreement of concentration dependence, which exhibits the cooperation effect. The solution shows extreme deviation from ideal mixing in the concentration range x_A≈0.3.
Formamide, despite its simpleness, it contains the essential features of the peptide linkage and often is used as a model. We study the aqueous solution of formamide as well as its enol form formamidic acid by quantum calculations. It is found that there are three different regions for water molecule to form cluster with the central molecule, one of the clusters contains C-H…O interaction, which is found in acetone aqueous solution, again verified in this mixture by MD simulation. By doing the calculation in the whole concentration, we found that formamide in water-rich region can strengthen the local structure of water, and cross-association between water and formamide will be taken place by the linear association of formamide itself as the concentration of formamide grows higher.
After knowing the interaction between formamide and water molecule, we move on to the investigation on its proton transfer process. Water molecules in the vicinity of formamide can be classified into two groups according to the different effects on the proton transfer process of formamide: water in two of them (W1 and W3) can protect formamide from tautomerizing, while in the third one (W2) works oppositely. For a multi-hydrated cluster, it will be an integrated effect of all the hydrated water. Above results are obtained in gas phase as well as in SCIPCM solution model, however, comparing with the situation in gas phase, the protective effects induced by W1 and W3 become smaller, and the assistant effect becomes more obvious. We tried to explain the differentia of the two kinds of water molecule by using the structural variation and potential electronic surface change during the transition, intermolecular interaction between the water and solvent as well as NBO analysis. The same conclusion can be drawn out in the study of Glycinamide, a derivative of formamide, the simplest and appropriate model compound for N-terminal amino acids. At last, a series of small molecules, which can deliver the hydrogen bond in the proton transfer process, are put in the assistant region. Activation energy of the reaction and DPE+PA value of the assistant molecule show a linear relationship, by which we may presume that the assistant molecule get the hydrogen bond from formamide and send out its own hydrogen at the same time in forming the transition state.
Guanine is the most sophisticated nucleic acid base. There are 36 possible tautomers, any one of which can be produced by proton transfer from another tautomer. We investigate the complex network by dividing them into seven groups. We found that the relative stability of the tautomers is reasonable both on thermodynamics and dynamics, the unstable tautomer has biggerΔE as well as higher energy barrier in the forming process; reaction direction between two transferable tautomers will be greatly influenced by the geometric property of the remaining part just next to the location where the transition happens; longer proton transfer distance is corresponding to higher activation energy, the vice versa; for transferable isomers with the same framework, keto form is more stable than the enol form, and the amino form is more stable than the imino one, the validity of this conclusion can be checked among the 36 tautomers, and agree with the experiment work. There is a segment quite like formamide in the structure of guanine, so we investigated the water's effect on the tautomerism of 9-H-keto-Guanine, we obtained accordant result: W1 can protect guanine from tautomerizing to the rare enol form, W2 can promote the tautomersim. At last, we study the tautomerization of acetylacetone by NMR, because enol form of this molecule can be actually tested in common surroundings and it does not have the solubility problem, both of which are quite annoying issues for the study of nucleic acid base.
To sum up, computer simulation, quantum calculation and experiment are combined to investigate the biochemical model molecules and small biomolecules in solution, some rules on the interaction and the structure variation in solution are discovered. We expect it can provide a base for the future development of the research on the tautomerism of other biomolecules and related gene mutation.
引文
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