RMSD

Conformational ensemble of Digoxin and Digitoxin, the two prominent cardiac glycosides was developed by employing force fields based geometry optimization and energy minimization methods to find lowest energy conformers. The interamolecular energies of each lowest energy conformer obtained by various approaches were computed. The torsional space explored by the lowest energy conformers were calculated by measuring its rotatable bonds angle. Root mean squared deviation (RMSD) over all atoms in conformational space interspersed over lowest energy conformers was estimated to study the confidence of obtaining lowest energy conformers over converged iterations. We emphasized the role of force-fields and multiple steps of iterations for conformational space exploration in determining the lowest energy conformers.

Codakine is a new Ca(2+)-dependent mannose-binding C-type lectin (MBL) isolated from the gill tissue of the tropical clam, Codakia orbicularis. Bioinformatic analyses with the BLAST program have revealed similarities with marine lectins involved in immunity whose three-dimensional (3D) structures were unknown up until recently. In this article, we present bioinformatic analyses of marine lectins that are homologous to codakine, in particular lectins from the sea worm Laxus oneistus, named mermaid. These lectins are involved in the symbiotic association with sulphur-oxidizing bacteria which are closely related to the C. orbicularis gill symbiont. Using homology modelling, folding that is characteristic of C-type lectins was observed in all the marine Ca(2+)-dependent lectins studied, with conservation of random coiled structures of the carbohydrate recognition domain (CRD) and Ca(2+)-binding sites. Like codakine, the marine lectins analysed contain a signal peptide commonly found in secreted and transmembrane proteins. The majority of the predictive 3D models established from the lectins exhibit a common feature, namely the involvement in invertebrate and vertebrate immunity (dendritic cell receptor, macrophage receptor, etc.). These bioinformatic analyses and the literature data support the hypothesis that codakine, like the L. oneistus mermaids, is probably involved in the cellular mediation of symbiosis and defence against pathogenic microorganisms.

The physiological transient complex between cytochrome f (Cf) and cytochrome c6 (Cc6) from the cyanobacterium Nostoc sp. PCC 7119 has been analysed by NMR spectroscopy. The binding constant at low ionic strength is 8±2mM−1, and the binding site of Cc6 for Cf is localized around its exposed haem edge. On the basis of the experimental data, the resulting docking simulations

Growth factor receptor-bound protein 2 (Grb2) plays an essential role in the Ras-MAPK signalling pathway which is an important target for anti-cancer drug design. The precise mechanisms by which effective and selective ligands can bind to the Src homology 2 (SH2) domain of ...