Statistical mechanics of DNA-protein interactions and chromosome organization

技术总结该奖项支持生物聚合物和由生物聚合物组成的复合体的统计力学理论的一般领域的理论研究。这项研究的重点将是DNA-蛋白质的相互作用，以及研究大DNA分子组织成折叠和功能染色体的物理机制。PI将使用平衡和非平衡统计力学来描述在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。这项研究将针对三个方面：1.建立单分子微操作实验中拉伸和扭转应力下双链DNA结构的理论模型，其中扭曲的“超螺旋”状态的形成与双螺旋结构重建成交替构象、变性的“L”和“P”-DNA态之间存在着相当复杂的竞争。同样的一般方法将被用来发展“辫状”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.在蛋白质-DNA相互作用的单分子实验中，研究蛋白质沿DNA的自组织，如在体内发生在染色体上，以及在体外发生在蛋白质-DNA相互作用的单分子实验中。一个主要目标将是发展一种最近观察到的“蛋白质交换”动力学的理论，即通过溶液相蛋白质浓度来控制脱落率。PI还将建立在他最近关于核小体动力学模型的工作基础上，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实验中可能通过调节DNA构象波动来影响酶的速率。3.建立建立高阶染色体结构的模型，特别是通过维持染色体蛋白质复合体的结构，并研究这些复合体折叠DNA如何产生染色体的拓扑简化，即在细胞分裂过程中观察到的自发解缠。该奖项还支持研究生培养。生物学家、物理学家、材料科学家、化学家和工程师将对他们在理论凝聚态物质、材料研究和分子生物学边界的高度跨学科研究方面的培训感兴趣。此外，高中和本科生的研究经验将作为该项目教育活动的一部分。该奖项支持理论研究和教育，重点是了解在活细胞中携带所有遗传信息的非常大的DNA分子的基本组织机制。在微米大小的细菌细胞中发现的大“染色体”DNA有数百万个碱基对-毫米长，而在人类细胞中发现的那些有数亿个碱基对-厘米长。组织这些笨重的分子的问题被放大了，因为要求它们被复制并以近乎完美的保真度彼此分离--为了细胞成功分裂。断裂或错误分离的染色体可能会导致细胞死亡，或者更糟糕的是，细胞行为不稳定，可能导致癌症等危及机体的疾病。该奖项的重点是了解DNA分子如何在细胞中通过与双螺旋相互作用的各种蛋白质分子的作用来折叠它，并通过它自己来解开它。“单分子”技术使研究生物分子间相互作用的精确、定量实验成为可能。这些类型的实验被证明是最自然地从统计力学的角度来研究的，统计力学处理原子和分子的随机运动和集体行为。这个项目还将专注于双螺旋单独在机械应力下的表现，因为在这样的实验中可以精确地控制。最后，该项目包括将开发的描述蛋白质-DNA相互作用的单分子研究的模型转移到“试管”中，以描述活细胞中的生物分子行为。该项目的主要目标之一将是试图了解沿DNA的小蛋白质分子如何能够实现大的和潜在的缠绕的DNA分子彼此分离。该奖项支持与PI密切合作的研究生的教育。这个小组所做的工作将是研究生的主要研究培训，这将导致他们的博士论文；他们将被教育从理论凝聚态物理中获取方法，并将它们应用于生物材料和生物问题。此外，较年轻的学生将参与研究项目，使他们在科学培训的早期阶段接触到研究前沿。

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.