Browsing by Subject "Molecular modeling"

Now showing 1 - 3 of 3
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    Chitosan as stabilizing agent for negatively charged nanoparticles
    (Elsevier, 2016-12-24) Collado-González, Mar; García Montalbán, Mercedes; Peña-García, Jorge; Pérez-Sánchez, Horacio; Víllora Cano, Gloria; Díaz Baños, F. Guillermo; Biología Celular e Histología
    Chitosan is a biocompatible polysaccharide with positive Z potential which can stabilize negative charged nanoparticles. Silk fibroin nanoparticles and citrate gold nanoparticles, both with negative Z potential, but they form aggregates at physiological ionic strength. In this work, we study the behavior of chitosan in solution when the ionic strength of the medium is increased and how the concentration of chitosan and the proportion of the two components (chitosan and AuNP or SFN) significantly affect the stability and size of the nanocomposites formed. In addition to experimental measurements, molecular modeling were used to gain insight into how chitosan interacts with silk fibroin monomers, and to identify the main energetic interactions involved in the process. The optimum values for obtaining the smallest and most homogeneous stable nanocomposites were obtained and two different ways of organization through which chitosan may exert its stabilizing effect were suggested.
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    Competing lipid-protein and protein-protein interactions determine clustering and gating patterns in KcsA
    (American Society for Biochemistry and Molecular Biology, 2015-09-02) Molina Gallego, María Luisa; Giudici Besseghini, Ana Marcela; Poveda Larrosa, José Antonio; Fernández Ballester, Gregorio; Montoya Díaz, Estefanía; Renart Pérez, María Lourdes; Fernández Carvajal, Asia María; Encinar Hidalgo, José Antonio; Riquelme Pino, Gloria; Morales Calderón, Andrés; González Ros, José Manuel; Bioquímica y Biología Molecular B e Inmunología
    There is increasing evidence to support the notion that membrane proteins, instead of being isolated components floating in a fluid lipid environment, can be assembled into supramolecular complexes that take part in a variety of cooperative cellular functions. The interplay between lipid-protein and protein-protein interactions is expected to be a determinant factor in the assembly and dynamics of such membrane complexes. Here we report on a role of anionic phospholipids in determining the extent of clustering of KcsA, a model potassium channel. Assembly/disassembly of channel clusters occurs, at least partly, as a consequence of competing lipid-protein and protein-protein interactions at nonannular lipid binding sites on the channel surface and brings about profound changes in the gating properties of the channel. Our results suggest that these latter effects of anionic lipids are mediated via the Trp67–Glu71–Asp80 inactivation triad within the channel structure and its bearing on the selectivity filter.
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    Intraresidual correlated motions in peptide chains
    (American Chemical Society, 2019-10-31) Bastida, Adolfo; Carmona García, Javier; Zúñiga, José; Requena, Alberto; Cerezo, Javier; Química Física
    We investigate the interresidual and intraresidual correlations between dihedral displacements of adjacent residues within model polyalanine peptides by analyzing extensive molecular dynamics trajectories. Correlations are evaluated individually at different residue conformations covering the whole (ϕi ,ψi )-space. From these, we draw maps that unveil an unprecedented strong intramolecular correlation displaying opposite (correlated/anticorrelated) behaviors at different conformations. Both interresidual and intraresidual correlations arise from the propensity of the peptide to minimize the overall atomic displacements.