Suhre Karsten, Sanejouand Yves-Henri
Information Génomique & Structurale (UPR CNRS 2589), 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W610-4. doi: 10.1093/nar/gkh368.
Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.
正常模式分析（NMA）是预测给定大分子可能运动的强大工具。最近研究表明，已知蛋白质运动的一半最多可通过使用两个低频正常模式来建模。NMA的应用涵盖结构生物学的广泛领域，例如研究配体结合时蛋白质的构象变化、膜通道的打开和关闭、核糖体的潜在运动以及病毒衣壳的成熟。NMA另一个新兴领域与通过X射线晶体学确定蛋白质结构有关，其中正常模式扰动模型用作通过分子置换（MR）进行衍射数据定相的模板。在此，我们展示了ElNémo，这是一个弹性网络模型的网络界面，它提供了一个快速且简单的工具，用于计算、可视化和分析大型大分子的低频正常模式，并生成大量不同的起始模型用于MR。由于ElNémo中实现了“旋转-平移-块”（RTB）近似，实际上可处理的蛋白质大小没有上限。输入蛋白质数据库（PDB）格式的蛋白质结构后，ElNémo会计算其100个最低频率模式，并生成一组全面的描述性参数和可视化结果，例如运动的集体程度、残基均方根位移、距离波动图以及观测到的和正常模式衍生的原子位移参数（B因子）之间的相关性。可生成任意数量的用于MR的正常模式扰动模型以供下载。如果同一（或同源）蛋白质的两个构象可用，ElNémo会识别对相应蛋白质运动贡献最大的正常模式。可通过http://igs-server.cnrs-mrs.fr/elnemo/index.html免费访问该网络服务器。
