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.

Structure of the full-length HCV IRES in solution

“…5c). The lowest and second lowest frequency modes calculated by normal mode analysis 42 corresponded to similar motions in the molecule than the first and second PC, as typically found with other biomolecules 43 .…”

“…In a second step, in order to expand the sampled conformational space, the best fitting model of each MD simulation was submitted to normal mode calculation (NMA) using the elNémo web-server 42 . For each of these 6 models, 40 structures were extracted (using an amplitude of motion equal to ± 1000 and a step of 50) from each of the five lowest frequency normal modes, yielding 1,200 additional models ( Supplementary Fig.…”

“…To improve the conformation sampling generated by this motion, starting from the best model selected after the last four ESMD with AMBER99, we used the elNémo webserver 42 with a large amplitude of motion (±2,000) and selected five snapshots from the lowest frequency mode of motion (4 Â 5 ¼ 20 models). These models were energy-minimized in GROMACS and were used to generate additional models by randomly rotating domain II around a pivot point located in a single-stranded region at the intersection between domains II and III (nucleotides 119-124).…”

Architecture of the yeast Elongator complex

“…For subsequent steps, we took the top scoring fit of Elp1‐CTD, since the fit was unambiguous for this domain, and 10,000 top scoring fits for other domains. The fit Elp1‐CTD was additionally optimized with crude flexible fitting by generating a series of conformations Normal Mode Analysis and selecting the conformation optimally fitting the EM map (using the ElNemo 66 server). Then, we generated 10,000 configurations of all Elp1, Elp2, and Elp3 domains by recombining the above fits using simulated annealing Monte Carlo optimization.…”

Conformational dynamics of supramolecular protein assemblies

“…While several data banks and servers [22][23][24][25][26][27] exist to disseminate publically the conformational dynamics of protein structures deposited in the PDB, similar data banks do not exist at present for the EMDB. Such a data bank would support both further computational analyses to gain insight into the biological function of high molecular weight protein assemblies lacking atomic structure, as well as potentially serve as a basis set for classification in singleparticle reconstruction [28].…”