Transconformations of the SERCA1 Ca-ATPase: a normal mode study

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

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.

New molecular determinants controlling the accessibility of ouabain to its binding site in human Na,K-ATPase alpha isoforms

Inhibition of Na,K-ATPase alpha2 isoforms in the human heart is supposed to be involved in the inotropic effect of cardiac glycosides, whereas inhibition of alpha1 isoforms may be responsible for their toxic effects. Human Na,K-ATPase alpha1 and alpha2 isoforms exhibit a high ouabain affinity but significantly differ in the ouabain association and dissociation rates. To identify the structural determinants that are involved in these differences, we have prepared chimeras between human alpha1 and alpha2 isoforms and alpha2 mutants in which nonconserved amino acids were exchanged with those of the alpha1 isoform, expressed these constructs in Xenopus laevis oocytes, and measured their ouabain binding kinetics. Our results show that replacement of Met119 and Ser124 in the M1-M2 extracellular loop of the alpha2 isoform by the corresponding Thr119 and Gln124 of the alpha1 isoform shifts both the fast ouabain association and dissociation rates of the alpha2 isoform to the slow ouabain binding kinetics of the alpha1 isoform. The amino acids at position 119 and 124 cooperate with the M7-M8 hairpin and are also responsible for the small differences in the ouabain affinity of the ouabain-sensitive alpha1 and alpha2 isoforms. Thus, we have identified new structural determinants in the Na,K-ATPase alpha-subunit that are involved in ouabain binding and probably control, in an alpha isoform-specific way, the access and release of ouabain to and from its binding site.