BIOPHYM

Serrano, Spain
Serrano, Spain

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Jeronimo K.,Biophym | Jeronimo K.,Simon Bolivar University of Venezuela | Cruz V.L.,Biophym | Ramos J.,Biophym | And 6 more authors.
European Polymer Journal | Year: 2014

We have used molecular dynamics simulations to study the process of macromolecular organisation of single chain linear and branched polyethylene on the surface of carbon nanotubes. These systems can be considered as good models for the study of the mechanism of polymer folding at the early stage of crystal formation on carbon nanotubes. The mean-squared radius of gyration, the stem length, the bond orientation order parameter and the radial distribution have been used to describe the organisation process and the structure of the chains at the carbon nanotube surface. When compared to the process of organisation of isolated single chains, interesting results are observed: (i) two different mechanisms of chain organisation give rise to different morphologies; lamellar thickening and lateral crystal growth lead to mono- and multilayered structures, independently of the presence of short chain branching; (ii) lamellar thickening is however hindered, but still present, in the case of polymer chains with short chain branches; (iii) both the stem length and the order parameter increase in the nanocomposites with respect to those obtained for isolated chains under the same conditions; (iii) the reorganisation process of thickening is accelerated by the presence of the carbon nanotubes, which act as nucleating agents; and (iv) the presence of short chain branching in polymer chains delays the onset of nucleation and growth of the crystalline structure, suggesting that the process is quite sensitive to the local chain chemistry. © 2014 Elsevier Ltd. All rights reserved.


Nunez-Ramirez R.,BIOPHYM | Sanchez-Barrena M.J.O.,CSIC - Institute of Physical Chemistry "Rocasolano" | Villalta I.,CSIC - Institute of Natural Resources and Agriculture Biology of Seville | Vega J.F.,BIOPHYM | And 4 more authors.
Journal of Molecular Biology | Year: 2012

The Arabidopsis thaliana Na+/H+ antiporter salt-overly-sensitive 1 (SOS1) is essential to maintain low intracellular levels of toxic Na+ under salt stress. Available data show that the plant SOS2 protein kinase and its interacting activator, the SOS3 calcium-binding protein, function together in decoding calcium signals elicited by salt stress and regulating the phosphorylation state and the activity of SOS1. Molecular genetic studies have shown that the activation implies a domain reorganization of the antiporter cytosolic moiety, indicating that there is a clear relationship between function and molecular structure of the antiporter. To provide information on this issue, we have carried out in vivo and in vitro studies on the oligomerization state of SOS1. In addition, we have performed electron microscopy and single-particle reconstruction of negatively stained full-length and active SOS1. Our studies show that the protein is a homodimer that contains a membrane domain similar to that found in other antiporters of the family and an elongated, large, and structured cytosolic domain. Both the transmembrane (TM) and cytosolic moieties contribute to the dimerization of the antiporter. The close contacts between the TM and the cytosolic domains provide a link between regulation and transport activity of the antiporter. © 2012 Elsevier Ltd.


Franco-Gonzalez J.F.,BIOPHYM | Cruz V.L.,BIOPHYM | Ramos J.,BIOPHYM | Martinez-Salazar J.,BIOPHYM
Journal of Molecular Modeling | Year: 2013

Human epidermal growth factor receptor 2 (ErbB2) is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called trastuzumab which interacts with the ErbB2 extracellular domain (ErbB2-ECD). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more effective anticancer therapies. In order to discuss the flexibility of the complex ErbB2-ECD/trastuzumab, we present, in this study, a multi-nanosecond molecular dynamics simulation (MD) together with an analysis of fluctuations, through a principal component analysis (PCA) of this system. Previous to this step and in order to validate the simulations, we have performed a detailed analysis of the variable antibody domain interactions with the extracellular domain IV of ErbB2. This structure has been statically elucidated by x-ray studies. Indeed, the simulation results are in excellent agreement with the available experimental information during the full trajectory. The PCA shows eigenvector fluctuations resulting in a hinge motion in which domain II and CH domains approach each other. This move is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the domain II and trastuzumab residues located in the CH domain. Finally, we discuss the flexibility of the MD/PCA model in relation with the static x-ray structure. A movement of the antibody toward the dimerization domain of the ErbB2 receptor is reported for the first time. This finding could have important consequences on the biological action of the monoclonal antibody. [Figure not available: see fulltext.] © 2012 Springer-Verlag Berlin Heidelberg.

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