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.

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。 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定位该位点。为了在短时间内找到正确的位点，蛋白质在3D扩散和沿着DNA的1D滑动之间交替。1D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定时很重要。蛋白质能以多快的速度沿着DNA沿着？最近的研究，通过核磁共振光谱解决了结构的二聚乳糖阻遏物（LacI）键的非特异性区域的DNA。有人认为，蛋白质在与这种构象的非特异性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沿着滑动的速度。具体来说，我们想解决以下关于蛋白质-DNA滑动的问题。(1)了解一个蛋白质是沿着沿着DNA扩散还是沿着沿着螺旋运动的主要格罗夫扩散;（2）估计扩散的自由能势垒的高度，并使用这个估计来计算扩散速率;（3）测试势垒是否依赖于序列。首先，使用NAMD，很好地检查蛋白质（LacI，PDB：1 OSL）是否能够在外力下沿着DNA移动。我们将研究两种可能性：（1）沿着沿着DNA的直线运动和（2）沿着沿着DNA的主要格罗夫的螺旋运动。为了比较这两种可能性（直线与螺旋），我们将设置模拟，其中在直线或螺旋方向上向蛋白质施加相同的力，并测量蛋白质位移的速率。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的序列，并使用上述技术测量作为序列的函数的扩散的势垒和速率。为了达到这些目标，将使用NAMD计划中实施的不同模拟技术。其中包括等速模拟、恒力模拟和自适应偏置力模拟。该项目试验部分所需的计算机时间估计为30，000 SU。