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: 8171873
• 负责人: DAVID BARR
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8171873
• 关键词: Algorithms; Automobile Driving; Binding; Biochemical; Charge; Computational Science; Computer Retrieval of Information on Scientific Projects Database; Computer Simulation; Coupled; Coupling; DNA; DNA Binding; DNA Sequence; Funding; Grant; 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.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 乳糖阻遏蛋白具有很大的生物化学意义，因为当蛋白质结合特定的DNA序列并弯曲DNA时，蛋白质的区域会折叠（见附图）。这些偶联的蛋白质折叠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，允许研究人员解耦这两个过程，并相互独立地研究它们（在传统的生物化学实验中是不可能的）。我正在进行分子动力学模拟乳糖阻遏蛋白在折叠和未折叠，结合和未结合状态。具体来说，在这个项目中，我将使用CHARMM软件包进行副本交换模拟，以探索非特异性DNA结合的未折叠乳糖蛋白的构象空间。虽然系统很大（61637个原子，由于需要包括明确的水和抗衡离子，以抵消DNA的电荷），我们已经开发了先进的偏置算法，以提高这些模拟的计算效率。（H. Kamberaj和A.货车der Vaart，JCP，127，2007）关于系统的热力学信息将使用加权直方图分析方法从这些模拟中获得，并且将提供对折叠和结合的耦合的洞察。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的其余部分的耦合;这些结果将与折叠蛋白质与特定DNA结合的结果进行比较，并将揭示可能负责在结合特定DNA操作子后驱动局部折叠的分子相互作用。