Predicting Protein-DNA Interactions with Structural Models

描述(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。这项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)来计算预测蛋白质-DNA结构和相互作用的工具。我们将开发使用相关蛋白质的实验确定的结构来预测蛋白质和DNA分子之间的复合体的三维结构的方法。我们的新贡献将是开发模拟技术，使DNA复合体中相关蛋白质的三维结构更接近与DNA结合的感兴趣蛋白质的结构。人们普遍认为，缺乏能够完成这一任务的现有技术是蛋白质之间广泛传递结构信息的主要障碍。该项目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--该项目旨在通过实验手段确定一组具有代表性的蛋白质的结构--允许使用高分辨率结构数据来了解未表征蛋白质的结构和功能。这个项目的第二部分的目标是使用我们生成的结构模型来对所讨论的蛋白质的生物功能做出具体的预测。更准确地说，我们建议开发预测特定蛋白质将与哪些特定DNA序列结合的方法。我们将通过建立蛋白质与各种DNA序列的复合体的结构模型来实现这一点，并使用高级力场来评估其与这些不同序列的亲和力。成功将取决于我们用来计算蛋白质与其潜在伙伴之间相互作用能量的力场的准确性。更复杂的是，这些DNA分子的结构可能都略有不同，蛋白质本身可能会以不同的方式在结构上适应不同的序列，以实现最佳匹配。在这个项目的最后一部分，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。这种名为MyoD的蛋白质因其将各种类型的细胞转化为肌肉细胞的非凡能力而被称为骨骼肌发育的“主调节器”。我们将通过建立MyoD与基因组中特定位置之间相互作用的结构模型来研究MyoD在发育过程中发挥关键功能的机制。这些模型将包括帮助将MyoD靶向生物相关部位的伙伴分子。这些研究的最终目标将是预测基因组中MyoD和其他关键调控蛋白发挥作用的位置。 与公共健康相关：这项研究将使我们更好地理解我们的基因决定我们的身体特征的基本调控过程，其中包括疾病易感性。在这个项目中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，以便适当地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.