MOLECULAR DYNAMICS SIMULATIONS OF PROTEIN-DNA SLIDING

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 蛋白质对DNA上特定位点的识别和结合是调控基因表达、重组、复制等过程的核心。为了结合DNA上的特定位置，蛋白质首先必须在同一DNA分子中存在的大量可选序列中定位该位置。为了在短时间内找到正确的位置，蛋白质在三维扩散和沿着DNA滑动的一维之间交替。一维滑动的速度决定了整个搜索过程的速度，因此对基因表达的时间选择很重要。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二聚体乳糖抑制物(LacI)与DNA的非特异性区域的结合结构。有人提出，当蛋白质与这种构象中的非特异性DNA结合时，它能够滑动。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。具体地说，我们想要解决以下关于蛋白质-DNA滑动的问题。(1)了解沿DNA扩散的蛋白质是直线运动还是沿主树林螺旋运动；(2)估计扩散的自由能屏障的高度，并使用该估计来计算扩散速度；(3)测试屏障是否与序列有关。首先，使用NAMD，我们将检查蛋白质(LacI，PdB：1OSL)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DNA直线运动和(2)沿DNA大树林的螺旋运动。为了比较这两种可能性(直线和螺旋)，我们将建立模拟，其中在直线或螺旋方向对蛋白质施加相同的力，并测量蛋白质置换的速度。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函数的扩散障碍和扩散速率。为了达到这些目标，将使用在NAMD程序中实现的不同的仿真技术。其中包括恒定速度模拟、恒定力模拟和自适应偏向力模拟。该项目试验部分所需的计算机时间估计为30,000 SU。

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.