COMPUTATIONAL METHODS FOR STUDYING PROTEIN 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来自蛋白质系统的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。当与缓慢松弛局部结构(SRLS)模型相结合时，多频率拟合输出连接探针和蛋白质的系绳的局部动力学和有序性以及整个蛋白质复合体的整体翻滚速率。该方法已被应用于研究T4溶菌酶自旋标记在多个位点的动力学性质。对不同温度下测量的ESR谱的系统分析为拟合参数增加了额外的光谱分辨率。特别关注了不同位置之间的动力学和有序参数的比较。我们已经利用这些结果设计了新的实验，允许有效地分离不同的运动模式。我们还在升级SRLS模型，以包括三种运动模式，这是对复杂蛋白质动力学的更好近似。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模型来分析蛋白质动力学。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理解蛋白质动力学分析的重要一步。该方法已成功地应用于几个蛋白质体系的动力学分析。目前，它正被推广到核磁共振谱密度的交叉项的计算。

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 protein 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. When coupled with the slowly relaxing local structure (SRLS) model, the multifrequency fit outputs the local dynamics and ordering of the tether connecting the probe to the protein as well as the overall tumbling rate of the whole protein complex. This approach has been applied to the study of the dynamic properties of T4 lysozyme spin labeled at several sites. A systematic analysis of the ESR spectra measured at different temperatures adds additional spectral resolution to the fitting parameters. Special focus has been placed on a comparison of the dynamics and ordering parameters amongst different sites. We have used these results to design new experiments, which allow an effective separation of different modes of motions. We are also upgrading the SRLS model to include three modes of motion, which is a better approximation of the complex protein dynamics. In the second part of this subproject, we have formulated the SRLS model within the context of NMR relaxation theory to analyze protein 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 dynamical analysis. This approach has been successfully applied to the dynamics analyses of a few protein systems. It is currently being extended to the calculation of the cross terms of NMR spectral density.