MOLECULAR DYNAMICS SIMULATIONS OF PROTEIN-DNA SLIDING

蛋白质-DNA 滑动的分子动力学模拟

• 批准号: 7601518
• 负责人: Leonid A Mirny
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601518
• 关键词: Address; Binding; Computer Retrieval of Information on Scientific Projects Database; Computers; DNA; DNA Sequence; Diffuse; Diffusion; Free Energy; Funding; Gene Expression; Gene Expression Regulation; Genetic Recombination; Goals; Grant; Height; Institution; Lactose; Learning; Measures; Molecular Conformation; Motion; NMR Spectroscopy; Numbers; Object Attachment; Process; Proteins; Rate; Research; Research Personnel; Resources; Site; Slide; Source; Structure; Techniques; Testing; Time; United States National Institutes of Health; molecular dynamics; programs; 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. Recognition and binding of specific sites on DNA by proteins is central for regulation of gene expression, recombination, replication and other processes. To bind its specific site on DNA a protein first has to locate the site among a very large number of alternative sequences that are present in the same DNA molecule. To find the right site in a short time, the protein alternates between 3D diffusion, and 1D sliding along DNA. The rate of 1D sliding determines the rate of the overall search process, and thus can important for timing of gene expression. How fast can a protein slide along DNA? Recent studies by NMR spectroscopy solved the structure of dimeric lactose repressor (LacI) bond to a non-specific region of DNA. It was suggested that a protein is capable of sliding when bound to non-specific DNA in this conformation. We aim at using Molecular Dynamic to study how fast a protein can slide along DNA. Specifically, we would like to address the following questions about protein-DNA sliding. (1) Learning whether a protein that diffuses along DNA goes straight or along the major grove in a spiral motion; (2) Estimating the height of the free energy barrier for diffusion and using this estimate it to calculate the rate of diffusion; (3) Testing whether the barriers are sequence-dependent. First, using NAMD, well examine whether the protein (LacI, pdb:1OSL) is capable of moving along DNA under external force. We will examine two possibilities: (1) straight motion along DNA and (2) in spiral motion along DNA major grove. To compare these two possibilities (straight vs spiral) we will set up simulations in which an identical force is applied to the protein in straight or spiral direction, and measure the rate of protein displacement. Second, we will estimate the minimal force needed to make the protein move and hence calculate the height of the barrier for two possible scenarios. Third, we will change the sequence of DNA and measure the barriers and rates of diffusion as a function of sequence using techniques described above. In order to reach these goals, different simulation techniques implemented in NAMD program will be used. These include Constant velocity simulations, Constant force simulations, and Adaptive biasing force simulations. The amount of computer time needed for the pilot part of this project is estimated to be 30,000 SUs.

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。子项目及 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。 蛋白质对 DNA 上特定位点的识别和结合对于基因表达、重组、复制和其他过程的调节至关重要。为了结合 DNA 上的特定位点，蛋白质首先必须在同一 DNA 分子中存在的大量替代序列中找到该位点。为了在短时间内找到正确的位点，蛋白质在 3D 扩散和沿 DNA 的 1D 滑动之间交替。一维滑动的速率决定了整个搜索过程的速率，因此对于基因表达的计时很重要。蛋白质沿着 DNA 滑动的速度有多快？最近的核磁共振波谱研究解决了与 DNA 非特定区域键合的二聚乳糖阻遏蛋白 (LacI) 的结构。有人认为，当蛋白质以这种构象与非特异性 DNA 结合时，能够滑动。我们的目标是利用分子动力学来研究蛋白质沿着 DNA 滑动的速度。具体来说，我们想解决以下有关蛋白质-DNA 滑动的问题。 (1) 了解沿着 DNA 扩散的蛋白质是直线运动还是沿着大树林进行螺旋运动； (2) 估计扩散自由能势垒的高度，并使用该估计值来计算扩散速率； (3) 测试屏障是否具有序列依赖性。首先，使用NAMD，我们检查蛋白质（LacI，pdb：1OSL）是否能够在外力作用下沿着DNA移动。我们将研究两种可能性：(1) 沿 DNA 直线运动和 (2) 沿 DNA 主丛螺旋运动。为了比较这两种可能性（直线与螺旋），我们将建立模拟，在直线或螺旋方向上向蛋白质施加相同的力，并测量蛋白质位移速率。其次，我们将估计使蛋白质移动所需的最小力，从而计算两种可能情况下的屏障高度。第三，我们将改变 DNA 序列，并使用上述技术测量作为序列函数的扩散障碍和速率。为了实现这些目标，将使用 NAMD 程序中实现的不同模拟技术。其中包括恒速模拟、恒力模拟和自适应偏置力模拟。该项目试点部分所需的计算机时间估计为 30,000 个 SU。