COMPUTATIONAL METHODS FOR STUDYING PROTEIN DYNAMICS BY ESR & NMR

通过 ESR 研究蛋白质动力学的计算方法

• 批准号: 7602606
• 负责人: Jack H Freed
• 金额: $ 0.62万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7602606
• 关键词: Classification; Communities; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Computing Methodologies; Coupled; Coupling; Data; Frequencies; Funding; Grant; Institution; Measures; Modeling; Motion; Muramidase; Output; Property; Protein Dynamics; Proteins; Rate; Relaxation; Research; Research Personnel; Resolution; Resources; Site; Source; Spin Labels; Structure; System; Temperature; United States National Institutes of Health; density; design; research study; theories

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.

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。 我们开发了新的模型和软件，用于分析蛋白质系统的ESR和NMR数据。 在ESR背景下，新软件允许在不同频率下同时拟合ESR光谱，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，多频拟合输出将探针连接到蛋白质的系链的局部动力学和排序以及整个蛋白质复合物的整体翻滚速率。 这种方法已被应用到T4溶菌酶的动态特性的研究自旋标记在几个网站。 在不同温度下测量的ESR谱的系统分析增加了额外的光谱分辨率的拟合参数。 特别关注已被放置在不同的网站之间的动力学和订购参数的比较。 我们已经使用这些结果来设计新的实验，这使得不同的运动模式的有效分离。 我们还升级了SRLS模型，以包括三种运动模式，这是一个更好的近似复杂的蛋白质动力学。 在这个子项目的第二部分，我们制定了SRLS模型的NMR弛豫理论的背景下，分析蛋白质动力学。 在蛋白质核磁共振研究中广泛使用的无模型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一些蛋白质系统的动力学分析。 目前正将其推广到NMR谱密度交叉项的计算中。