Transition Structures and the Evolution of Protein Folds

蛋白质结构聚集成折叠家族，充当进化模板，其中骨架结构被循环利用，以创造具有不同功能的蛋白质。蛋白质进化的理论模型提出，在序列空间中存在一个“神经网络”，它将编码相同折叠的不同序列互联在一起。在这样的网络中，点突变或微小的插入/缺失改变的连续路径连接所有组分序列。这些网络可能相当大，因为许多不同的序列可以编码相同的折叠。蛋白质进化中的一个基本问题是不同的神经网络之间如何以及多久发生一次交换，从而导致从一个折叠到另一个折叠的进化。在进化过程中，由少量突变诱导的新表型特征必须与突变可能导致的对重要功能的有害影响进行平衡。有证据表明，分子进化可能是由生物分子作为不同折叠之间的桥梁而呈现出多种构象的能力所引导的。在这种情况下，进化中的蛋白质最初可以提高对新功能的适应性，而不会失去原来的功能。桥联状态允许蛋白质探索新的结构和功能，而部分结构集合保持初始构象并起到保险的作用。特别令人感兴趣的是罕见的桥或过渡序列，它们以不同的概率折叠成不同的非重叠结构。蛋白质的稳定性通常被认为是一种独特的天然状态和一系列未折叠状态之间的两种状态的转变。然而，设计和诱变实验表明，替代折叠的自由能差异可能比通常想象的要小得多，导致进化速度对替代构象之间的自由能差异敏感。这项研究的中心是蛋白质折叠如何随着时间的推移而变化，替代折叠的存在如何影响蛋白质进化的速度，以及如何从现有的蛋白质进化出新的蛋白质功能。重点描述了所选择的蛋白质序列的构象空间、进化路径、连接和性质，这些蛋白质序列原则上可以稳定地采用两个不同的折叠，或者存在于一个折叠中，但距离不同的折叠有1到3个突变。将考虑显示非常高的序列一致性但显示不同折叠和功能的特定蛋白质系统，例如基于P22Arc抑制物同源二聚体中极性和非极性氨基酸模式的交替折叠；以及基于链球菌细胞壁蛋白G的GA和GB结构域的工程蛋白。原子分子动力学技术对这些蛋白质系统的研究将得到不同蛋白质家族的分子进化分析的补充，特别是那些先前已经研究过三级结构对进化影响的蛋白质家族，而没有考虑替代蛋白质折叠对进化速率的潜在作用。一种新的进化推断程序可以定量评估交替褶皱的进化影响，这将有助于这些研究。然后，通过推理过程确定的最有趣的假定祖先蛋白质将被用原子建模技术进行更详细的研究，该技术将检查所有相关的结构特征。这个项目将促进分子模拟和进化研究社区之间的互动，这两个社区传统上基本上是相互孤立的。这主要是一个以学生/博士后为基础的研究项目，将促进北卡罗来纳州立大学生物信息学和物理学之间的教育联系。更大的计算生物分子社区将受益于为琥珀包免费提供的软件的继续开发，以及通过开发新的进化推断软件。此外，PI将开发新的研究生课程，促进留住和招收少数族裔学生，在北卡罗来纳州立大学开发生物物理学选项，为学生提供国际研究经验(主要通过在日本的合作)，并为所有教育水平的学生和研究伙伴提供全面和丰富的环境。

Protein structures cluster into families of folds that act as evolutionary templates, where the backbone structures are recycled to create proteins with different functions. Theoretical models of protein evolution propose the existence of a "neutral network" in sequence space that interconnects the different sequences encoding the same fold. In such networks, continuous paths of point mutations or small insertion/deletion changes connect all component sequences. These networks can be quite large, since many different sequences can encode the same fold. A fundamental question in protein evolution is how and how often exchanges between different neutral networks occur, leading to evolution from one fold to another. During evolution, the induction of new phenotypic traits by a small number of mutations has to be balanced against the deleterious effects on vital functions that mutations can cause. There is evidence that molecular evolution may be steered by the ability of biomolecules to take on numerous conformations as a bridge between different folds. Under this scenario, an evolving protein can initially attain increased fitness for a new function without losing its original function. Bridge states allow proteins to explore new structures and functions while part of the structural ensemble retains the initial conformation and function as insurance. Of particular interest are rare bridge or transition sequences that fold with different probabilities into distinct non-overlapping structures. Protein stability is generally viewed in terms of a two-state transition between a unique native state and an ensemble of unfolded ones. However, design and mutagenesis experiments suggest that the difference in free energy of alternative folds may be much smaller than typically envisioned, leading to evolutionary rates that are sensitive to the free energy differences between alternative conformations. This research centers on how protein folds change over time, on how the existence of alternative folds affects the rates of protein evolution, and on how new protein functionality can evolve from an already existing protein. Emphasis is given to the characterization of the conformational space, evolutionary pathways, connections, and properties of select protein sequences that, in principle, can stably adopt two different folds, or exist in one fold but are 1 to 3 mutations away from a different fold. Specific protein systems that show a very high sequence identity but display different folds and functions will be considered, such as alternate folds based on the patterning of polar versus non-polar amino acids in the P22 Arc repressor homodimer; and engineered proteins based on the GA and GB domains of the cell wall Protein G of Streptococcus bacteria. The study of these protein systems by atomistic molecular dynamic techniques will be complemented by molecular evolution analyses of diverse protein families, especially those for which the evolutionary impact of tertiary structure has previously been investigated without regard to the potential role of alternative protein folds on evolutionary rates. A novel evolutionary inference procedure that can quantitatively assesses the evolutionary influence of alternative folds will facilitate these investigations. The most interesting of putative ancestral proteins that are identified by the inference procedure will then be studied in more detail with atomistic modeling techniques that will examine all relevant structural characteristics. This project will foster interaction between the molecular simulation and evolution research communities, which have traditionally been largely isolated from each other. This is primarily a student/postdoc based research project, which will foster educational ties between NC State Bioinformatics and Physics. The larger computational biomolecular community will benefit through the continued development of freely available software for the AMBER package, as well as through the development of new evolutionary inference software. In addition, The PI will develop new graduate courses, foster the retention and recruitment of minority students, develop the Biophysics option at NC State, provide international research experience to students (mainly via a collaboration in Japan), and provide for a well-rounded and rich environment for students and research partners at all educational levels.