Predicting Protein-DNA Interactions with Structural Models

描述（由申请人提供）：蛋白质和DNA分子之间的相互作用是广泛的遗传和调控过程的核心。该研究项目将改进仅使用蛋白质序列数据（如人类基因组计划产生的数据）计算预测蛋白质-DNA结构和相互作用的工具。我们将开发的方法来预测蛋白质和DNA分子之间的复合物的三维结构使用实验确定的相关蛋白质的结构。我们的新贡献将是模拟技术的发展，可以移动的三维结构的相关蛋白质与DNA的复合物更接近的结构结合到DNA的感兴趣的蛋白质。缺乏现有的技术，可以实现这一任务被广泛认为是一个主要的障碍，蛋白质之间的结构信息的广泛转移。该项目的这一部分的成功完成将大大增加正在进行的结构基因组学项目的影响，这些项目的目的是通过实验手段确定一组代表性蛋白质的结构，使高分辨率结构数据能够用于了解未表征蛋白质的结构和功能。该项目的第二个组成部分的目标是使用我们生成的结构模型对所讨论的蛋白质的生物功能进行具体预测。更准确地说，我们建议开发方法来预测给定蛋白质将与DNA的哪些特定序列结合。我们将通过构建蛋白质与各种DNA序列复合的结构模型，并使用先进的力场评估其对这些不同序列的亲和力来实现这一点。成功与否将取决于我们用来计算蛋白质及其潜在伴侣之间相互作用能量的力场的准确性。作为额外的复杂性，这些DNA分子的结构可能都略有不同，蛋白质本身可能以不同的方式在结构上适应不同的序列，以实现最佳匹配。在本项目的最后一部分，我们将应用这些方法来研究一种具有重要生物学意义的特定蛋白质。这种蛋白质，MyoD，被称为骨骼肌发育的“主调节器”，因为它具有将各种类型的细胞转化为肌肉细胞的非凡能力。我们将通过建立MyoD与基因组中特定位点之间相互作用的结构模型，研究MyoD在发育过程中发挥关键功能的机制。这些模型将包括有助于将MyoD靶向生物学相关位点的伴侣分子。这些研究的最终目标是预测基因组中MyoD和其他关键调节蛋白发挥作用的位点。 公共卫生相关性：这项研究将导致我们对基因决定我们身体特征的基本调控过程的更好理解，其中包括疾病易感性。该项目开发的软件工具将被广泛用于回答有关蛋白质如何与DNA分子相互作用的重要问题，以正确调节我们的细胞过程。

DESCRIPTION (provided by applicant): Interactions between proteins and DNA molecules are central to a wide range of genetic and regulatory processes. This research project will lead to improved tools for computationally predicting protein-DNA structures and interactions using only protein sequence data (such as that generated by the human genome project). We will develop methods for predicting the three-dimensional structures of complexes between proteins and DNA molecules using the experimentally determined structures of related proteins. Our novel contribution will be the development of simulation techniques that can move the three-dimensional structure of the related protein in complex with DNA closer to the structure of the protein of interest bound to DNA. The lack of existing techniques that can achieve this task is widely recognized as a major impediment to the widespread transfer of structural information between proteins. Successful completion of this component of the project would greatly increase the impact of the ongoing structural genomics projects - which aim to determine by experimental means the structures of a representative set of proteins - by allowing high-resolution structural data to be used to understand the structures and functions of uncharacterized proteins. The goal of the second component of this project is to use the structural models we generate to make concrete predictions about the biological functions of the proteins in question. More precisely, we propose to develop methods that will predict which specific sequences of DNA a given protein will bind to. We will go about this by building structural models of the protein in complex with a variety of DNA sequences and evaluating its affinity for these different sequences using advanced force fields. Success will hinge on the accuracy of the force fields we use to calculate the energies of interaction between the protein and its potential partners. As an additional complication, the structures of these DNA molecules may all be slightly different, and the protein itself may adapt structurally to different sequences in different ways to achieve an optimal fit. In the final component of this project, we will apply these methods to study a specific protein of great biological importance. This protein, MyoD, has been called a 'master-regulator' of skeletal muscle development for its remarkable ability to turn cells of a variety of types into muscle cells. We will investigate the mechanisms by which MyoD performs its critical functions during development by building structural models of the interactions between MyoD and specific sites in the genome. These models will include partner molecules that help to target MyoD to biologically relevant sites. The eventual goal of these studies will be to predict the sites in the genome at which MyoD and other key regulatory proteins exert their effect. PUBLIC HEALTH RELEVANCE: This research will lead to an improved understanding of the fundamental regulatory processes by which our genes determine our physical characteristics, among them disease susceptibilities. The software tools developed in this project will be widely used to answer important questions about how proteins interact with DNA molecules in order to properly regulate our cellular processes.