王 骏
论文题目：蛋白质折叠和蛋白质组成复杂性简化的研究
作者简介：王 骏，男，1975年11月出生，1998年09月师从于南京大学王炜教授，于2001年06月获博士学位。
摘 要
蛋白质体系是分子生物学的重要研究对象之一。考察蛋白质分子在适宜的环境中如何折叠形成特定的功能结构，是有关蛋白质研究中的核心问题之一。近年来，在蛋白质折叠统计图象、折叠结构的特殊性和蛋白质组成成分的简化表述等方面，有了很大的进展，但还存在着很多有待深入研究的基本问题。本论文主要针对蛋白质的氨基酸序列组成的简化和蛋白质折叠的热力学和动力学特性进行了系统的研究，论文分为五大部分：1）在第一章绪言中，对蛋白质和蛋白质折叠相关问题作了简单的综述，对一些与本文关系较为紧密的问题作了论述；2）在第二章中，研究了蛋白质系统的复杂性的简化；3）在第三章中，研究了蛋白质的折叠热力学和动力学、序列和结构的关系、折叠转变（相变）等特性；4）在第四章中，对论文进行了总结，特别是描述了作者对有关蛋白质方面的研究和近年来有关从物理方向的研究理念的一些观念；5）在附录中，详细介绍了在蛋白质折叠研究中所需的数值方法和技巧，包括一些作者自己进行的改进。论文的创新点是：1）针对蛋白质组成复杂性的研究提出了新的刻画方法，并得到蛋白质简化表示的基本物理图像；2）针对蛋白折叠利用模拟计算对折叠过程的热力学相变（基于Lee-Yang相变理论）和动力学相变（基于动力学驰豫）进行了仔细的研究，这些对蛋白质折叠物理图象提供了新的思路和手段。论文主要内容如下：
1）：蛋白质体系复杂性简化：复杂蛋白质的各种特性的研究在很大程度上都是建立在简化模型上的。简化的模型使复杂的体系变得图像清晰。基于简化模型的相关模拟研究的成功充分说明了蛋白质可以用较为简化的模型来刻画和描述。那么，模型简化到什么层次或程度可能和自然界的蛋白质体系相互比拟或在多大程度上还能刻画和描述蛋白质的有关特性？这个问题对于蛋白质体系的理论研究是基本的。针对这个问题，我们从蛋白质体系中的相互作用（氨基酸之间）出发进行了系统的研究。我们提出了基于格点模型和接触型相互作用（Contact Potentials）的简化表述方法，用失配度（Mismatch）参量刻画了简化的有效性；讨论了失配度参量的物理意义和来源以及最优简化表述存在的优越性和物理意义；通过选择相应的代表字母，我们实现了对蛋白质序列的简化表示。结合氨基酸的替代规则和折叠性的要求，我们还讨论了寻找简化表述的方法的有效性；还结合大范围序列空间的构建和分析，对简化方法进行了进一步的探索和研究。针对特定的折叠结构，蛋白质的简化方式的有效性经过了重新的检验。针对最小分组的存在性，我们还从物理的角度对其存在的一些基本约束，如能谱重叠、序列相似性等，进行了讨论和研究。从各个方面的研究来看，我们认为对蛋白质的进行简化表述是合理和必要的，同时保持适当的成分复杂性是又是构造复杂蛋白质体系所不可缺少的基本要求。这部分工作的内容主要安排在第二章内。
2）：蛋白质折叠的动力学和热力学特性：蛋白质折叠的热力学和动力学是蛋白质体系复杂特征的一个重要方面。了解蛋白质的折叠机制，理解蛋白质的快速折叠的来源，是当前相关研究的热点。我们通过一个简化的统计模型勾画出折叠过程的简单图象，通过引入短程相关的协作性特征，在一定程度上刻画了蛋白质动力学对折叠结构的依赖性；并根据统计物理的方法讨论了复温度场中体系的配分函数的零点，并由此分析了体系相变的特征，这不仅重新检验了原有理论，为其提供了理论上的可靠性，而且提供了一条途径，对蛋白质的折叠转变的热力学性质进行更为细致的刻画，为不同模型之间的比较提供了有益的参考。进一步针对Go型格点模型，利用蒙特卡洛（Monte Carlo）方法，研究了蛋白质的折叠动力学的基本特征，特别刻画了体系动力学随着温度变化而产生的转变过程，针对蛋白质随着温度变化而发生的动力学转变进行了仔细地讨论，清楚地勾画出蛋白质体系中动力学转变的图像，并与实验中推论的图象是一致的，其有效性为蛋白质体系随温度变化的性质演变提供了一个简洁的思路；为了有效地检验我们结果的普适性，我们采用一套不同的蒙特卡罗实现方法对同样的问题进行研究，得到了相同的结果。此外非格点模型研究也证实了模型蛋白质体系在不同的温度区域里经历着不同的动力学过程。这样的动力学转变过程是蛋白质体系中一个具有一般性特征的行为。我们还利用对折叠路径的统计分析并定量讨论了折叠过程形成不同折叠方式的物理来源。我们还通过了解一些有关蛋白质折叠的实验，结合实验进行了定性和物理图象上的讨论比较。通过我们的研究，我们发现这种动力学的转变主要来源于体系变性态的失稳。这样的图像为理解蛋白质折叠机制、不同体系的比较提供了有益的参考。这部分内容主要安排在第三章内。
3）：作为以生物客体为对象的研究，物理学和生物学的关系一直是人们思虑的话题。这里我们概述了本文所关心的问题和研究方案和内容，并结合本文的工作对一些物理学方法在生物学中应用的思路进行了讨论。这些安排在第四章中。
4）：最后的附录描述了一些相关的模型和模拟方法，并作了相应的讨论。
Some studies on the protein folding and reduction
of complexity in proteins
ABSTRACT
Proteins are of greatly importance in molecular biophysics. To understand the folding of protein molecules in proper environment and how the specific functions are formed is one of the hot topics in protein researches. Recently, there are some rapid progresses in grasping the picture of free energy landscapes of folding, extracting the speciality of structures of protein folds and exploring the possible composition simplicity of proteins. Meanwhile, many problems are still undiscovered. In this thesis, systematic studies are proceeded on 1) simplification of protein composition and 2) transitions (kinetic and thermodynamic) following the variation of temperature. In this thesis, a novel criterion with “mismatch” is defined and a basic picture of the simplification of protein representations is outlined. The new descriptions on the thermodynamic and kinetic transitions of folding are provided, which enriches the paradigm of protein folding problem.
Simplified models are the basis of the physical studies on proteins. The minimalist models may induce a clear picture of the complex system, and the success using the simple models affirms the possibility of simplification for protein systems. The question is, what kinds of models may be proper while comparing with real systems of proteins, which is important for theoretical understanding of proteins. We provide a systematic approach to the simplification problem. Based on the approximation with lattice models and contact-form potentials, a mismatch characteristic is proposed to depict the effectiveness of residue substitution. The physical meaning of “mismatch”, as well as that of the best reduction of residue, is discussed. The simplification of proteins is realized by substituting residues with the representatives of their corresponding groups. The validity of our proposed grouping schemes is tested for well-designed model protein sequences. By mapping the sequences into a large space, we obtained some insights on the reduction for protein sequences rather than just residues. The mapping between reduced sequences and the 20-letter sequences is also investigated. Besides these, we also discussed the overlapping of levels and the similarity between sequences for the cases with different compositions. With these proof, we believe that the simplification of protein representation do exists, and that suitable compositional complexity is the fundamental requirement to re-build real protein systems. This part of works is arranged in the Chapter 2.
To understanding folding thermodynamics and kinetics is the basic part to know proteins. The energetic and structural ingredients are essential for folding processes. With a simple statistical model, the thermodynamics and kinetics are outlined, which shows the effects of entropy and frustration to folding behavior. We also introduce a short-range correlation between residues to simulate the cooperativity. The dependence of the folding kinetics on the native bond maps provides some insights on the effects of native structures to folding rate. The folding transition is studied from the zeros of partition function on the complex temperature plane. It gives a more detailed description on the properties of the folding transition, with a better theoretical reliance. Some comparisons between different models are also discussed. Then, the kinetic transition of protein systems is analyzed in details. Not only the kinetic transition is clearly shown, but also the nature of this transition is also analyzed in-depth. As a result, the kinetic transition is attributed to a downhill kinetics, which is associated with the un-stablization of denatured states. Our predictions have their good consistence with the simulation results. Different realization of Monte Carlo method and off-lattice modeling are all shown the universality of the kinetic transition. These pictures offer us some interesting knowledge for folding mechanism and comparison between different models. This part of work is arranged in Chapter 3.
At last, my main results and thought on the works in this thesis are concluded in the last chapter, Chapter 4.
In Appendix, details of modeling and simulation methods are proposed.
