Mercedes Benz model of neutral amino-acid side chains
| Autor: | Olivier Collet, Jean-Paul Becker |
|---|---|
| Rok vydání: | 2006 |
| Předmět: |
chemistry.chemical_classification
Physics::Biological Physics Quantitative Biology::Biomolecules Hydrogen bond Thermodynamics Condensed Matter Physics Biochemistry Gibbs free energy Amino acid Solvent symbols.namesake Solvation shell chemistry Computational chemistry symbols Side chain Molecule Polar Physics::Chemical Physics Physical and Theoretical Chemistry |
| Zdroj: | Journal of Molecular Structure: THEOCHEM. 774:23-28 |
| ISSN: | 0166-1280 |
| Popis: | We present a 2-d coarse-grain model of polar and non-polar amino-acid side chains, and investigate their thermodynamic and structural properties in solution. The molecules interact via a Lennard-Jones potential and a local treatment of the hydrogen bond energy. Such a form allows very fast highly converged calculations. Estimates of the Gibbs free energy of hydration (GFEH) of the solutes show good qualitative agreement with experiments. We find moreover that contributions to the GFEH are linked to the perturbations of the solvent hydration shell structure. For large hydrophobic solutes, unfavorable GFEH results mainly from an increase of the water–water energy contribution, while for hydrophilic solutes the increase in solvent energy is compensated by the solute–solvent energy. The model appears therefore to capture the main features of non-charged amino-acids hydration. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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