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Un Modèle de Solvatation Semi-Implicite pour la Simulation des Macromolécules Biologiques

Abstract : In the cell of the living organisms, the solvent (water) plays an important part in the stabilization of the tridimensional structures of biological macromolecules and in their interactions. Theoretical methods like molecular modeling simulations can complete the partial informations on biomolecules hydration provided by experimental methods. We have developed a new semi-implicit solvation model to represent solvent in molecular modeling of biological macromolecules. Our model considers the solvent as microscopic particles with dielectric properties based on macroscopic electrostatic equations. The resulting solvent is a fluid composed, at electrostatic equilibrium, by non polar Lennard-Jones particles, polarizable by the electric field created by the solute. This model can describe the molecular details of solvent and can also easily calculate the electrostatic solvation free energy of the system. It is also numerically very efficient compared with explicit models. We have implemented our model in a molecular dynamics code, parameterized it in a simple way and applied it to the dynamics of several peptides, proteins and nucleic acids (DNA and transfer RNA). The trajectories of these dynamics are stable over one or two nanoseconds, and their structural properties are in very good agreement with experimental results, and with simulations using explicit methods. Our model allows also to find the preferential hydration sites of the molecules identified by experimental or theoretical studies, in spite of the absence of hydrogen bonds in our solvent. Moreover, correlations between the electrostatic solvation free energies calculated with our method and those from the Poisson-Boltzmann resolution methods are quite good, and thus provide very encouraging results.
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https://tel.archives-ouvertes.fr/tel-00010619
Contributor : Nathalie Basdevant <>
Submitted on : Thursday, October 13, 2005 - 5:21:42 PM
Last modification on : Wednesday, April 17, 2019 - 1:43:26 AM
Long-term archiving on: : Friday, September 14, 2012 - 3:05:36 PM

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  • HAL Id : tel-00010619, version 1

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Nathalie Basdevant. Un Modèle de Solvatation Semi-Implicite pour la Simulation des Macromolécules Biologiques. Biophysique [physics.bio-ph]. Université d'Evry-Val d'Essonne, 2003. Français. ⟨tel-00010619⟩

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