Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic 3010, Australia.
BMC Bioinformatics. 2011 Oct 27;12:421. doi: 10.1186/1471-2105-12-421.
Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR) relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary.
The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program.
NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.
蛋白质是具有从皮秒到超过秒的运动范围的动态分子。然而，许多蛋白质功能似乎发生在微秒到毫秒的时间尺度上，因此人们对这些运动在催化和分子相互作用中的重要性进行了激烈的研究。核磁共振（NMR）弛豫色散实验用于测量微秒到毫秒时间尺度内离散核的运动。从这些实验中提取关于构象/化学交换、交换状态的分布和化学位移差异的信息。为了确保正确提取这些参数，需要对这些实验进行准确和仔细的分析。
本文介绍的软件旨在自动分析弛豫色散数据并提取上述参数。它是用 Python 编写的，可在多个平台上使用，具有最高的性能。可以使用 Levenberg-Marquardt 最小化算法拟合实验数据到不同的模型，并使用不同的统计检验来选择最佳模型。为了演示该程序的功能，对合成数据和 NMR 数据进行了分析。使用标准程序，可以在最小的用户干预下对这些数据进行分析，包括生成图形和彩色编码结构。
NESSY 是一种易于使用的开源软件，可用于分析 NMR 弛豫数据。本文展示了其稳健性和标准程序。
