摘要
生物大分子和环境中其他小分子的相互作用，大体包括非键相互作用和化学反应两类，对大分子的结构性能、溶解性以及化学性质有着深刻的影响。本论文针对这两类相互作用，对于前者侧重于外部环境条件，如温度，离子环境对它的影响；对于后者则主要着眼于其动力学过程，进行了一系列动力学模拟研究。
对氢键主导的大分子而言，它和环境中其他分子的相互作用以氢键相互作用为主。以纤维素和尿素分子在尿素碱溶液中的相互作用为例，研究此相互作用对氢键主导大分子结构及溶解性能的影响。本论文中，我们的结果展现了尿素分子对纤维素长链的包合作用及它的温度性质，进一步揭示他们之间单一的氢键形成方式，证明尿素分子独特的共轭键结构是其对纤维素包合作用的来源。这些发现有助于理解纤维素溶解于尿素碱溶液中的溶解机理及尿素分子在纤维素溶解过程中的作用并且加深了对氢键主导大分子和极性小分子相互作用的认识。
除了氢键相互作用，非键作用的另一重要方面是静电相互作用。本论文的第三章，我们使用拉伸分子动力学研究了凝血酶适配体在二价镁离子的稳定作用下的四倍体结构。给予这个结构一个外力，实现了在分子动力学模拟的时间尺度内对适配体和金属离子之间静电相互作用的研究。我们的结果发现二价镁离子和凝血酶适配体间静电相互作用强烈，但当周围环境中有对适配体四倍体结构影响巨大的钾离子存在时，这一静电作用有被压制的趋势。在外力作用下，不同离子环境中的四倍体结构呈现不同的展开路径。
对于大分子化学反应的研究，我们更侧重于它的动力学方面。本论文第四章中，我们使用布朗动力学研究了将蛋白质的结构转变和蛋白质配体结合综合考虑下蛋白质和配体分子结合速率常数的计算。在模拟中，我使用了Zhou提供的dual-transition-rates模型，并将反应区域限制在小角度范围内。这使得我们的模型更加趋近于现实条件——蛋白质配体分子的定点结合。模拟结果验证了Zhou的理论推导：当体系中存在一个外势，使得蛋白质在配体分子接近时倾向于和配体分子结合的闭合态结构而在配体分子远离时倾向于不能结合的开放态结构，对于反应区域是蛋白质分子外的整个球壳的情况，蛋白质和配体分子的结合速率常数有精确的分析解；但对于小角度反应区域，只能使用结构转变速率极快和极慢两个极限条件下的结合速率常数来逼近近似，这一近似在反应区域角度越小的情况下越适用。
本论文第五章节，我们依然使用布朗动力学研究了通过柔性链链接的两个蛋白质子区域和配体分子的结合动力学。在这个模型中，我们使用蠕虫链模型模拟蛋白质中的柔性链，并改变蠕虫链链长或持续长度（柔性）以研究柔性链性质对结合速率常数的影响。我们发现对于任意固定链长，改变蠕虫链模型的持续长度（柔性）或者对任意持续长度，改变蠕虫链模型的链长，都能找到一种情况使得蛋白质和配体分子的结合速率常数达到极大值。
The interaction between biomacromolecules and other molecules in theenvironment, containing non-bonded interaction and chemical reaction, plays a verysignificant role in the conformational stability, solubility and chemical properties ofthe macromolecules. We focus on these two kind interactions by means of dynamicssimulations. For the former, ambient conditions as temperature and ions conditionare considered and for the later, the dynamics process is the focus.
The hydrogen bonding interaction is the main part of interactions betweenhydrogen bond dominated macromolecules and other molecules. Its effect on theconformational stability and solubility of macromolecules is investigated by takingthe interaction of cellulose and urea in urea/alkali solvent mixture as an emample.The results display an inclusion complex is formed between them and itstemperature properties. We also find there is only one dominative hydrogen bondingpattern which proves the conjugated bond in urea should be the driving force for theinclusion complex. These finding is very helpful to understand the mechanism ofdissolution of cellulose in urea/alkali solvent mixture and the role that urea playsduring the process.
The other part of non-bonded interaction is electrostatic interaction. TheG-quadruplex formed by thrombin-binding aptamer (TBA) with Mg2+existing isstudied in the section three. A force is added to this system which allows us to studythe electrostatic interaction between DNA aptamer and metal ions by MolecularDynamics simulations. The results show the electrostatic interaction between TBAand Mg2+is strong, however, when there are K+ions around them, it becomes weaker.With the function of the additional force, the G-quadruplex structures with differentmetal ions around them display different unfolding ways.
For chemical reaction, we focus on the dynamics process of it. The kinetics ofprotein-ligand binding coupled to conformational change is studied by BrownianDynamics simulations in the Section four. During the simulation,dual-transition-rates model from Zhou is used, and is made more realistic byrestricting the reactive region to a patch. The simulation results show that, for anenergy surface that switches from favoring the nonreactive conformation while theligand is away to favoring the reactive conformation while the ligand is near, the slow limit and fast limit of binding rate constants become close and, thus, providetight bounds to the binding rate constant. They are in excellent agreement with theanalytical theory from Zhou.
Receptor-binding rate constants of disordered ligands and the protein linkedwith a flexible linker are also investigate by means of Brownian Dynamics inSection five. In the simulation model, we consider the flexible linker of the proteinas a worm-like chain and find that the binding rate constant of the disordered ligandscould reach a maximum by changing the linker contour length or flexibility.
引文
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