COMPUTATIONAL METHODS FOR STUDYING PROTEIN AND DNA DYNAMICS BY ESR & NMR

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。 我们开发了新的模型和软件来分析蛋白质和DNA系统等大分子的ESR和核磁共振数据。在ESR方面，新软件允许同时对不同频率的ESR谱进行拟合，以提高对各种拟合参数的光谱分辨率。它还允许合规者之间的动态交换。当与慢弛豫局部结构(SRLS)模型耦合时，多频率拟合输出连接自旋标记与大分子的系链的局部动力学和有序性以及整个大分子复合体的整体翻滚速率。该方法已被用于研究T4溶菌酶在几个突变位点上的自旋标记的动态性质。目前，我们正在对T4溶菌酶在不同溶剂中更多突变位点和更高频率下的动力学进行更全面的研究。我们正在为试衣程序增加新的功能。这些特征包括(1)用于自旋标记物内部运动的非对称扩散张量和(2)具有所有三个欧拉角的内部扩散倾斜。在这个子项目的第二部分，我们在核磁共振松弛理论的背景下建立了SRLS模型来分析大分子动力学。在蛋白质核磁共振领域广泛使用的无模型(MF)理论的一个重要假设是两种运动模式之间的解耦。整体蛋白质翻滚和局部运动的动力学耦合是我们朝着理解蛋白质动力学迈出的重要一步。这种方法已经成功地应用于几个蛋白质系统的动力学分析，并将用于马里兰大学David Fushman博士的核磁共振研究，以分析双域(双泛素)系统中的整体和域间运动。

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. We have developed new models and software for analyzing the ESR and NMR data from macromolecules such as protein and DNA systems. In the ESR context, the new software allows a simultaneous fit of ESR spectra at different frequencies to enhance the spectral resolution to the various fitting parameters. It also allows for dynamic exchanges between conformers. When coupled with the slowly relaxing local structure (SRLS) model, the multi frequency fit outputs the local dynamics and ordering of the tether connecting the spin label to the macromolecule as well as the overall tumbling rate of the whole macromolecule complex. This approach has been applied to the study of the dynamic properties of T4 lysozyme spin labeled at several mutant sites. Currently we are conducting a more comprehensive study of T4 lysozyme dynamics at more mutant sites and more frequencies in different solvents. We are adding new features to our fitting programs. These features include (1) an asymmetric diffusion tensor for the internal motion of the spin label and (2) an internal diffusion tilt with all three Euler angles. In the second part of this subproject, we have formulated the SRLS model within the context of NMR relaxation theory to analyze macromolecule dynamics. An important assumption of the widely used model free (MF) theory in the protein NMR community is the decoupling between the two modes of motions. The dynamical coupling of the overall protein tumbling and the local motion is an important step forward towards our understanding of the protein dynamics. This approach has been successfully applied to the dynamics analyses of a few protein systems, and will be used in a NMR study by Dr David Fushman, University of Maryland, to analyze the overall and inter-domain motions in dual-domain (di-ubiquitin) system.