单个碱基对的热力学与动力学

发布时间：2019-06-19 02:45

【摘要】：RNA是生物体中一种非常重要的生物大分子,它结构多样,功能丰富,在生命的遗传和进化方面扮演着非常重要的角色,比如,遗传信息的保存,转录,翻译,调控和复制等等。然而,RNA分子要实现这些生物功能,必须从单链结构折叠成二级结构或更为复杂的三级结构,在这些功能结构折叠的过程中,单个碱基对的打开与闭合是非常重要而且是必经的过程,并且功能结构的形成往往是动力学控制,并依赖于碱基对的打开与闭合的速率。所以,深入理解单个碱基对的开关特性是进一步探索RNA分子更多生物功能的基础和关键。由于碱基对在常温下很难打开,所以,本文我们采用在融解温度附近的高温分子动力学模拟计算方法,研究了单个碱基对的打开与闭合的热力学性质和动力学机制,以及溶液中离子浓度和不同近邻碱基对单个碱基对的热力学和动力学的影响。主要的研究内容如下：(1)单个碱基对的热力学和动力学当离子浓度为0.5M时,根据模拟温度分别为390K,400K,410K,420K和430K的模拟轨迹,建立了从动力学模拟轨迹来表征碱基对处于打开态,闭合态和过度态的方法,得到了末端单个碱基对AU的热力学参数及开关动力学。在热力学方面,根据模拟轨迹在平衡状态时打开与闭合的平衡几率分布,得到了打开态与闭合态之间的焓变和熵变,和实验上最近邻模型参数吻合的非常好。在动力学方面,得到了闭合态,打开态和过渡态的平均寿命,以及碱基对的打开速率,闭合速率和转变路径速率。研究结果显示,闭合态平均寿命是与温度呈现较强的关联性,而打开态和过渡态的平均寿命则与温度呈现较弱的关联性。另外,闭合态与打开态之间的转变路径时间也与温度呈现较弱的关联性,并且对跃迁的能量势垒的高度不敏感。通过分析,研究结果表明,RNA分子结构中单个碱基对从闭合到打开的过程中,克服的自由能势垒是碱基对之间的氢键相互作用和与邻近碱基之间的堆积相互作用所引起的焓的增加,而从打开到闭合的过程中,克服的自由能势垒是磷酸骨架扭转角的限制和溶剂粘性等等所引起的熵的减小。这进一步说明一维自由能势能面是可以精确描述碱基对的打开与闭合的动力学,并且这个动力学是布朗运动,扩散常数展现出了超阿列纽斯特性。(2)离子浓度对单个碱基对的热力学和动力学的影响在第一研究工作的基础之上,又分别研究了离子浓度为0.1M和0.05M时碱基对AU的热力学性质和开关动力学机制,根据模拟温度分别为390K,400K,410K和420K的模拟轨迹,得到了碱基对AU在不同离子浓度下的热力学参数及开关特性,并深入分析了离子浓度对碱基对热力学和动力学的影响。在热力学方面,得到了不同离子浓度下碱基对在打开与闭合之间的焓变和熵变,发现溶液中离子浓度的改变对碱基对的焓变没有影响,而熵变随着离子浓度的减小而增大,和实验上得出的结论相一致。在动力学方面,根据闭合态,打开态和过渡态的平均寿命,发现闭合态和过度态的平均寿命不随离子浓度的变化而变化,而打开态的平均寿命随着离子浓度的减小而增大,与实验上观测的结果相一致。研究结果表明,在打开过程中,由于碱基对克服的焓变是一样的,所以,打开速率不随离子浓度的变化而变化；而在闭合过程中,由于描述一维自由能势能面的粗糙程度受离子浓度的影响,当离子浓度越小时,势能面越粗糙,存在的构象陷阱态越多,所以,闭合速率随着离子浓度的减小而变慢,和实验上的结论相一致。(3)近邻碱基对单个碱基对的热力学和动力学的影响当溶液中的离子浓度均为0.5M时,研究了末端单个碱基对GC(5'-GG…3'-CC…)和CG(5'-CA…3'-GU…)在不同近邻碱基下的热力学和动力学。研究结果表明,最近邻碱基不仅影响热力学参数,即碱基对开关时的焓变和熵变,而且在动力学方面影响碱基对在各个构象态的平均寿命和它们之间转换速率。另外,不同的最近邻碱基影响势能面的粗糙程度,与实验上观测的结果相一致。
[Abstract]:RNA is a very important biological macromolecule in the organism, its structure is diverse, the function is rich, plays a very important role in the genetics and evolution of life, such as the preservation, transcription, translation, regulation and replication of the genetic information, etc. However, in order to achieve these biological functions, the RNA molecule must be folded from a single-stranded structure into a secondary structure or a more complex tertiary structure, in which the opening and closing of a single base pair is very important and a required process in the course of the folding of these functional structures, And the formation of functional structures is often dynamic control and depends on the rate of opening and closing of base pairs. Therefore, in-depth understanding of the switching characteristics of a single base pair is the basis and the key to further explore the more biological function of the RNA molecule. Since the base pair is very difficult to open at normal temperature, we use the high-temperature molecular dynamics simulation method near the melting temperature to study the thermodynamic and dynamic mechanism of the opening and closing of a single base pair. And the effect of the ionic concentration in the solution and the thermodynamics and kinetics of a single base pair of different neighbor base pairs. The main contents of the study are as follows: (1) The thermodynamics and kinetics of a single base pair, when the ion concentration is 0.5M, establishes a simulation track of 390K, 400K, 410K, 420K and 430K, respectively, according to the simulated temperature, and establishes a dynamic simulation track to characterize the base pair in an open state, The thermodynamic parameters and the switching dynamics of the single base pair AU are obtained by the method of closed state and over-state. In the thermodynamic aspect, the equilibrium probability distribution of the open and closed states is obtained according to the simulation track in the equilibrium state, and the phase change and the entropy change between the open state and the closed state are obtained, and the parameters of the nearest neighbor model in the experiment are in good agreement with each other. In the kinetic aspect, the average life of the closed state, the open state and the transition state, and the opening rate, the closing rate and the transition path rate of the base pair are obtained. The results show that the average life of the closed state is strongly related to the temperature, and the average life of the open state and the transition state exhibits a weak correlation with the temperature. In addition, the transition path time between the closed state and the open state also exhibits a weak correlation with the temperature and is not sensitive to the height of the energy barrier of the transition. Through the analysis, the results show that the free energy barrier against which the single base pair in the RNA molecular structure is closed to the opening is an increase in the hydrogen bond interaction between the base pairs and the interaction of the accumulation of the adjacent bases, In the process of opening to closing, the free energy barrier to be overcome is the reduction of the entropy caused by the restriction of the twist angle of the phosphoric acid skeleton and the viscosity of the solvent, and the like. This further shows that the one-dimensional free energy potential surface can accurately describe the dynamics of the opening and closing of base pairs, and the kinetics is the Brownian motion, and the diffusion constant exhibits the super-Arrhenius character. (2) The effect of the ion concentration on the thermodynamics and kinetics of a single base pair is based on the first study, and the thermodynamic properties and the switching dynamics of the base pair AU when the ion concentration is 0.1M and 0.05M are respectively studied, and the simulation temperature is 390K and 400K, respectively. The thermodynamic parameters and switching characteristics of base pair AU at different ion concentrations are obtained, and the effect of ion concentration on the thermodynamics and dynamics of base pair is analyzed. In the thermodynamic aspect, the evolution and entropy change of base pair under different ion concentration on the opening and closing are obtained, and the change of the ion concentration in the solution has no effect on the change of the base pair, and the entropy change is increased with the decrease of the ion concentration, and the result is consistent with the conclusion. In the dynamic aspect, the average life of the closed state and the transition state is found to not change with the change of the ion concentration according to the average life of the closed state, the open state and the transition state, and the average life of the open state increases with the decrease of the ion concentration, and is consistent with the results observed in the experiment. The results show that, during the opening process, the opening rate does not change with the change of the ion concentration, and the degree of roughness of the one-dimensional free energy potential surface is affected by the ion concentration during the closing process. The more the ion concentration is, the more rough the potential energy surface, the more the formation trap state, so the closing rate becomes slower with the decrease of the ion concentration, and is in line with the experimental conclusion. (3) The effect of the thermodynamics and kinetics of the single base pair of the nearest neighbor base pair is that when the concentration of the ions in the solution is 0.5M, the single base pair GC (5 '-GG.) at the end is studied. 3 '-CC... ) And CG (5 '-CA... 3 '-GU... ) Thermodynamics and kinetics at different neighbor bases. The results show that the nearest base not only affects the thermodynamic parameters, that is, the evolution and entropy of the base pair switches, but also the average life of the base pairs in the various conformations and the conversion rate of the base pairs in the dynamics. In addition, the different nearest neighbor bases affect the degree of roughness of the potential energy surface, which is consistent with the results observed in the experiment.
【学位授予单位】：武汉大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q615

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