ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

Abstract

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.

Figure 1

An example of a typical ElNémo output that is available for every run through the result page (top left). The normal mode analysis page (top right) displays the different properties of the first 100 lowest-frequency modes, i.e. their frequency, degree of collectivity of movement, mean square displacement 〈R²〉, overlap (if two conformations are available) and its corresponding amplitude. Three-dimensional animations from three orthogonal viewpoints are available in large and small sizes. Comparison of a normal mode perturbed structure and a second conformation in terms of RMSD and number of residues that are closer than 3 Å can be done (bottom right). Analysis of distance fluctuations between all CA atoms is presented in the form of a cross-plot, where red and blue dots indicate those residues for which the pairwise distance changes most significantly in the movement defined by a given mode. The result page also allows submission of normal mode calculations for new modes with varying amplitude ranges. The resulting normal mode perturbed models in PDB format can be downloaded for further processing (e.g. using VMD (28) to visualize the protein movements as presented on the ElNémo example page) or as templates for MR.