ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
Information Génomique & Structurale (UPR CNRS 2589), 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France and 1 Laboratoire de Physique, Ecole Normale Supérieure, 46, allées d'Italie, 69364 Lyon Cedex 07, France
* To whom correspondence should be addressed. Tel: +33491164604; Fax: +33491164549; Email: karsten.suhre{at}igs.cnrs-mrs.fr
Received February 6, 2004; Revised and Accepted March 9, 2004
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.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. I. Friedman, A. Majumdar, and J. T. Stivers Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage Nucleic Acids Res., June 1, 2009; 37(11): 3493 - 3500. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Jerga, D. J. Miller, S. W. White, and C. O. Rock Molecular Determinants for Interfacial Binding and Conformational Change in a Soluble Diacylglycerol Kinase J. Biol. Chem., March 13, 2009; 284(11): 7246 - 7254. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Zhang, B. Klebansky, R. M. Fine, H. Xu, A. Pronin, H. Liu, C. Tachdjian, and X. Li Molecular mechanism for the umami taste synergism PNAS, December 30, 2008; 105(52): 20930 - 20934. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Lu and J. Ma A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography PNAS, October 7, 2008; 105(40): 15358 - 15363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. E. Dobbins, V. I. Lesk, and M. J. E. Sternberg Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking PNAS, July 29, 2008; 105(30): 10390 - 10395. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kniazeff, L. Shi, C. J. Loland, J. A. Javitch, H. Weinstein, and U. Gether An Intracellular Interaction Network Regulates Conformational Transitions in the Dopamine Transporter J. Biol. Chem., June 20, 2008; 283(25): 17691 - 17701. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Luo, T. Xu, C. Hunke, G. Gruber, S. G. Vasudevan, and J. Lescar Crystal Structure of the NS3 Protease-Helicase from Dengue Virus J. Virol., January 1, 2008; 82(1): 173 - 183. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Autin and P. Tuffery PMG: online generation of high-quality molecular pictures and storyboarded animations Nucleic Acids Res., July 13, 2007; 35(suppl_2): W483 - W488. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Razga, J. Koca, A. Mokdad, and J. Sponer Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA Nucleic Acids Res., June 9, 2007; 35(12): 4007 - 4017. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. I. Garzon, J. Kovacs, R. Abagyan, and P. Chacon DFprot: a webtool for predicting local chain deformability Bioinformatics, April 1, 2007; 23(7): 901 - 902. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Deniziak, C. Sauter, H. D. Becker, C. A. Paulus, R. Giege, and D. Kern Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation Nucleic Acids Res., March 12, 2007; 35(5): 1421 - 1431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. W. R. Serohijos, Y. Chen, F. Ding, T. C. Elston, and N. V. Dokholyan A structural model reveals energy transduction in dynein PNAS, December 5, 2006; 103(49): 18540 - 18545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Eyal, L.-W. Yang, and I. Bahar Anisotropic network model: systematic evaluation and a new web interface Bioinformatics, November 1, 2006; 22(21): 2619 - 2627. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Thompson, Z. C. Ryan, J. L. Salisbury, and R. Kumar The Structure of the Human Centrin 2-Xeroderma Pigmentosum Group C Protein Complex J. Biol. Chem., July 7, 2006; 281(27): 18746 - 18752. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-W. Yang, A. J. Rader, X. Liu, C. J. Jursa, S. C. Chen, H. A. Karimi, and I. Bahar oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W24 - W31. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Lindahl, C. Azuara, P. Koehl, and M. Delarue NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W52 - W56. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Jang, J. I. Jeong, and M. K. Kim UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W57 - W62. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I.J. MacRAE, F. LI, K. ZHOU, W.Z. CANDE, and J.A. DOUDNA Structure of Dicer and Mechanistic Implications for RNAi Cold Spring Harb Symp Quant Biol, January 1, 2006; 71(0): 73 - 80. [Abstract] [PDF]
|
|
|
|
|
|
Z. Bu, R. Biehl, M. Monkenbusch, D. Richter, and D. J. E. Callaway Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy PNAS, December 6, 2005; 102(49): 17646 - 17651. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Meier, P. Polzer, K. Diederichs, W. Welte, and P. Dimroth Structure of the Rotor Ring of F-Type Na+-ATPase from Ilyobacter tartaricus Science, April 29, 2005; 308(5722): 659 - 662. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hammel, H.-P. Fierobe, M. Czjzek, S. Finet, and V. Receveur-Brechot Structural Insights into the Mechanism of Formation of Cellulosomes Probed by Small Angle X-ray Scattering J. Biol. Chem., December 31, 2004; 279(53): 55985 - 55994. [Abstract] [Full Text] [PDF]
|
|