COUPLED FOLDING AND BINDING PROCESSES: COMPUTER SIMULATIONS OF THE LACTOSE REPR

耦合折叠和结合过程：乳糖 REPR 的计算机模拟

• 批准号: 7956334
• 负责人: DAVID BARR
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956334
• 关键词: Algorithms; Automobile Driving; Binding; Biochemical; Biomedical Research; Charge; Computational Science; Computer Retrieval of Information on Scientific Projects Database; Computer Simulation; Coupled; Coupling; DNA; DNA Binding; DNA Sequence; Funding; Grant; High Performance Computing; Institution; Lac Repressors; Lactose; Light; Methods; Motion; Process; Protein Binding; Proteins; Repressor Proteins; Research; Research Personnel; Resources; Rest; Sequence-Specific DNA Binding Protein; Source; System; Thermodynamics; United States National Institutes of Health; Water; Weight; insight; interest; molecular dynamics; protein folding; research study; simulation

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The lac repressor protein is of great biochemical interest because regions of the protein fold as the protein binds a specific DNA sequence and bends the DNA (see attached picture). These coupled protein-folding DNA-binding processes, though common in sequence-specific DNA-binding proteins, prove quite challenging to study. Computational science provides a unique approach to studying this problem by allowing researchers to decouple these two processes and study them independently of each other (impossible in traditional biochemical experiments). I am performing molecular dynamics simulations of the lac repressor protein in its folded and unfolded, bound and unbound states. Specifically, in this project I will use the CHARMM package to perform replica exchange simulations to explore the conformational space of the unfolded lac protein bound to non-specific DNA. Although the system is large (61637 atoms, owing to the need to include explicit water and counterions to offset the charge of the DNA), we have developed advanced biasing algorithms to increase the computational efficiency of these simulations. (H. Kamberaj and A. van der Vaart, JCP, 127, 2007) Thermodynamic information about the system will be obtained from these simulations using the Weighted Histogram Analysis Method and will provide insight into the coupling of folding and binding. In addition, covariance matrices of fluctuations will elucidate the coupling of the motion of the unfolded region to the rest of the protein; these results will be compared to the results of the folded protein bound to specific DNA and will shed light on the molecular interactions that may be responsible for driving local folding upon binding the specific DNA operator.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 lac 阻遏蛋白具有重大的生化意义，因为当该蛋白结合特定 DNA 序列并使 DNA 弯曲时，该蛋白的区域会折叠（参见附图）。这些耦合的蛋白质折叠 DNA 结合过程虽然在序列特异性 DNA 结合蛋白中很常见，但研究起来相当具有挑战性。计算科学提供了一种独特的方法来研究这个问题，它允许研究人员将这两个过程解耦并相互独立地研究它们（在传统的生化实验中这是不可能的）。我正在对 lac 阻遏蛋白的折叠和未折叠、结合和未结合状态进行分子动力学模拟。具体来说，在这个项目中，我将使用 CHARMM 包执行复制品交换模拟，以探索与非特异性 DNA 结合的未折叠 lac 蛋白的构象空间。尽管系统很大（61637 个原子，因为需要包含明确的水和抗衡离子来抵消 DNA 的电荷），但我们开发了先进的偏置算法来提高这些模拟的计算效率。 （H. Kamberaj 和 A. van der Vaart，JCP，127，2007）有关系统的热力学信息将从使用加权直方图分析方法的这些模拟中获得，并将提供对折叠和结合耦合的深入了解。此外，波动的协方差矩阵将阐明未折叠区域的运动与蛋白质其余部分的耦合；这些结果将与结合特定 DNA 的折叠蛋白的结果进行比较，并将揭示分子相互作用，这些相互作用可能负责在结合特定 DNA 操纵子时驱动局部折叠。