Mesoscale modeling of protein-DNA assemblies

该项目将专注于设计一种新的计算程序，用于测定和分析蛋白质-DNA组装的结构，其中DNA弹性能、带电残基的静电斥力和蛋白质-DNA结合能是组装能量的主要组成部分。该程序将包括用于计算DNA构型的快速新算法，测定DNA片段和多肽链的自由能，以及分析蛋白质-DNA结合状态。在该项目中，该程序将应用于研究大肠杆菌中lac操纵子的转录，包括由lac抑制因子诱导的DNA环的结构，解释互操作符距离对抑制效率的影响，确定环与RNA聚合酶之间的相互作用，研究LacR和CAP结合的协同性，并模拟上游启动子区域与RNA聚合酶结合的aCTD结构域的结构。本项目开发的方法将适用于在DNA复制、重组或染色质重塑过程中形成的其他复杂蛋白质-DNA组装的建模。该项目的目标是开发一个计算机程序，为分子生物学家提供一种工具，他们可以用它来创建细胞内成分的结构模型，从而详细探索细胞的内部工作。该项目将现代计算机技术与生物大分子物理特性的前沿知识结合起来，通过允许生物学家在计算机上测试关于细胞功能的假设，该项目将节省时间和昂贵的实验资金。该计划将通过加强实验结果的解释，进一步减少当前实验技术的局限性。在项目过程中获得的关于大肠杆菌的具体信息将使我们了解大肠杆菌或任何其他细菌的基因如何影响其在不利条件下的生存，例如在细菌感染期间发生的情况。

The project will focus on the design of a novel computational procedure for determination and analysis of the structure of protein-DNA assemblies, in which the DNA elastic energy, the electrostatic repulsion of charged residues, and the protein-DNA binding energy are the main components of the assembly energetics. The procedure will include fast new algorithms for calculation of DNA configurations, determination of the free energy of DNA segments and polypeptide tethers, and analysis of protein-DNA binding states. In the project the procedure will be applied to the study of the transcription of the lac operon in E. coli, including the structure of DNA loops induced by the Lac repressor, explanation the effect of interoperator distance on efficiency of repression, determination of the interaction between the loop and RNA polymerase, investigation of the cooperativity of binding of LacR and CAP, and modeling the structure of the upstream promoter region with bound aCTD domains of the RNA polymerase. The methods developed in this project will be applicable to modeling of other complex protein-DNA assemblies that form during DNA replication, recombination, or chromatin remodeling.The goal of this project is to develop a computer program that will provide molecular biologists with a tool they can use to create structural models of intracellular components and hence explore in detail the inner workings of cells. The program will combine modern computer technology with cutting edge knowledge about the physical properties of biological macromolecules, and by allowing the biologists to test hypotheses about cellular functions on the computer the program will save both time and funding on expensive experiments. The program will further reduce the limitations of current experimental techniques by enhancing the interpretation of experimental results. The specific information to be obtained in the course of the project about E. coli will give us an understanding of how genes of E. coli, or any other bacteria, affect its survival in adverse conditions such as those that occur, for example, during bacterial infection.