Statistical mechanics of DNA-protein interactions and chromosome organization

DNA-蛋白质相互作用和染色体组织的统计力学

• 批准号: 1206868
• 负责人: John Marko
• 金额: $ 33万
• 依托单位: Northwestern University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1206868&HistoricalAwards=false
• 关键词: Statistical; mechanics; DNA; protein; interactions

TECHNICAL SUMMARYThis award supports theoretical research in the general area of statistical-mechanical theories of biopolymers and complexes composed of biopolymers. The focus of the research will be on DNA-protein interactions and studies of physical mechanisms underlying the organization of large DNA molecules into folded and functional chromosomes. The PI will use equilibrium and non-equilibrium statistical mechanics to describe single-molecule biological physics experiments carried out in vitro, and to develop models for chromosome dynamics in vivo. The research will be aimed at three thrusts:1. Developing theoretical models for the structure of double-stranded DNA under tensile and twisting stress as studied in single-molecule micromanipulation experiments, where there is a rather complex competition between formation of writhed "supercoiled" states, and structural reconstructions of the double helix into alternative conformations, denatured "L"- and "P"-DNA states. The same general methods will be used to develop theories of "braided" double helix DNAs, which are key substrates being used for studying DNA topoisomerases. 2. Studying the self-organization of proteins along DNA, as occurs in vivo in chromosomes, and in vitro in single-molecule experiments on protein-DNA interactions. A major objective will be development of a theory for recently observed "protein exchange" dynamics, whereby off-rates are controlled by solution-phase protein concentration. The PI will also build on his recent work on models of nucleosome dynamics, including effects of post-translational modification of nucleosomes, and competition of nucleosomes with transcription factors. The PI will examine the role played by boundary conditions on chromosomal domains, and in single-DNA experiments on DNA conformational fluctuations that may affect enzyme rates through modulation of DNA conformational fluctuations. 3. Developing models to establish higher-order chromosome structure, especially by the action of Structural Maintenance of Chromosome protein complexes, and studying how the folding of DNA by those complexes can generate the topological simplification of chromosomes, their spontaneous disentanglement, that is observed to occur during cell division.The award also supports graduate student training. Their training, in highly interdisciplinary research at the boundaries of theoretical condensed matter and materials research and molecular biology, will be of interest to biologists, physicists, materials scientists, chemists and engineers. In addition, high school and undergraduate research experiences will be provided as part of the educational activities of the project. NONTECHNICAL SUMMARYThis award supports theoretical research and education focused on the understanding of the fundamental mechanisms that underlie the organization of the very large DNA molecules that carry all genetic information in living cells. The large "chromosome" DNAs found in micron-sized bacterial cells are millions of base pairs - millimeters - in length, while those found in human cells are hundreds of millions of base pairs - centimeters - in length. The problem of organizing these unwieldy molecules is magnified by the requirement that they be replicated and separated from one another with near-perfect fidelity - for a cell to successfully divide. Broken or erroneously segregated chromosomes can lead to death of a cell, or worse, erratic cell behavior that can lead to organism-endangering diseases such as cancer. This award is focused on understanding how DNA molecules can be organized in the cell, by the action of a variety of protein molecules that interact with the double helix so as to fold it up, and to pass it through itself to disentangle it. "Single-molecule" technologies have made possible precise, quantitative experiments to study interactions of biological molecules. These types of experiments turn out to be most naturally studied from the point of view of statistical mechanics which deals with the random motion and collective behaviors of atoms and molecules. This project will also focus on how the double helix alone behaves when placed under mechanical stress, as can be precisely controlled in such experiments. Finally, this project includes work on transferring the models developed to describe single-molecule studies of protein-DNA interactions in the "test tube" to describe biomolecule behavior in living cells. One of the overarching objectives of the project will be to try to understand how the small protein molecules along a DNA are able to effect separation of large and potentially entangled DNA molecules from one another.This award supports the education of graduate students working closely with the PI. The work done by this group will be the main research training of the graduate students which leads to their Ph.D. theses; they will be educated to take methods from theoretical condensed matter physics and to apply them to problems of biological materials and biology. In addition, younger students will be involved in the research project, exposing them to research frontiers at an early stage in their scientific training.

该奖项支持生物聚合物和由生物聚合物组成的复合物的物理力学理论的一般领域的理论研究。研究的重点将是DNA-蛋白质相互作用和研究大DNA分子组织成折叠和功能性染色体的物理机制。PI将使用平衡和非平衡统计力学来描述体外进行的单分子生物物理实验，并开发体内染色体动力学模型。本研究将针对三个方面：1。 发展理论模型的双链DNA的结构在拉伸和扭转应力下的研究，在单分子显微操作实验中，有一个相当复杂的竞争之间的形成扭曲的“超螺旋”状态，和结构重建的双螺旋到替代构象，变性的“L”和“P”-DNA状态。 同样的一般方法将用于发展“编织”双螺旋DNA的理论，这是用于研究DNA拓扑异构酶的关键底物。 2. 研究蛋白质沿着DNA的自组织，如体内染色体中发生的，以及体外蛋白质-DNA相互作用的单分子实验。一个主要的目标将是最近观察到的“蛋白质交换”动力学理论的发展，其中关闭率控制的溶液相蛋白质浓度。PI还将建立在他最近对核小体动力学模型的研究基础上，包括核小体翻译后修饰的影响，以及核小体与转录因子的竞争。PI将研究染色体结构域上的边界条件所起的作用，以及在DNA构象波动的单DNA实验中可能通过DNA构象波动的调制影响酶速率。 3.通过染色体蛋白质复合物的结构维持作用，开发建立染色体高阶结构的模型，研究这些复合物对DNA的折叠如何产生染色体的拓扑简化，以及在细胞分裂过程中观察到的染色体自发解缠结。该奖项还支持研究生培养。他们的培训，在理论凝聚态和材料研究和分子生物学的边界高度跨学科的研究，将感兴趣的生物学家，物理学家，材料科学家，化学家和工程师。此外，高中和本科研究经验将作为该项目教育活动的一部分提供。和/或#8195;非技术性总结该奖项支持理论研究和教育，重点是理解活细胞中携带所有遗传信息的非常大的DNA分子组织的基本机制。 在微米大小的细菌细胞中发现的大型“染色体”DNA长度为数百万个碱基对（毫米），而在人类细胞中发现的DNA长度为数亿个碱基对（厘米）。 组织这些笨拙的分子的问题被放大了，因为它们需要以近乎完美的保真度进行复制和彼此分离-为了细胞成功分裂。 断裂或错误分离的染色体可能导致细胞死亡，或者更糟的是，不稳定的细胞行为可能导致危及生物体的疾病，如癌症。 该奖项的重点是了解DNA分子如何在细胞中组织起来，通过各种蛋白质分子的作用，与双螺旋相互作用，使其折叠起来，并使其通过自身解开它。“单分子”技术使研究生物分子相互作用的精确定量实验成为可能。从统计力学的角度研究这些类型的实验是最自然的，统计力学研究的是原子和分子的随机运动和集体行为。该项目还将重点关注双螺旋在机械应力下的单独行为，因为在这样的实验中可以精确控制。 最后，该项目包括将为描述“试管”中蛋白质-DNA相互作用的单分子研究而开发的模型转移到描述活细胞中生物分子行为的工作。 该项目的首要目标之一将是试图了解小蛋白质分子沿着DNA是如何能够影响大的和潜在的纠缠DNA分子彼此分离的。该奖项支持与PI密切合作的研究生的教育。 该小组所做的工作将是研究生的主要研究培训，从而获得博士学位。论文;他们将接受教育，从理论凝聚态物理学的方法，并将其应用到生物材料和生物学的问题。 此外，年轻的学生将参与研究项目，使他们在科学训练的早期阶段接触研究前沿。