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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.
Publication : Physical review letters

Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Physical review letters - 24 Feb 2009

Koehl P, Orland H, Delarue M

Link to Pubmed [PMID] – 19257790

Link to HAL – Click here

Link to DOI – 10.1103/PhysRevLett.102.087801

Phys. Rev. Lett. 2009 Feb;102(8):087801

We present an extension to the Poisson-Boltzmann model in which the solvent is modeled as an assembly of self-orienting dipoles of variable densities. Interactions between these dipoles are included implicitly using a Yukawa potential field. This model leads to a set of equations whose solutions give the dipole densities; we use the latter to study the organization of water around biomolecules. The computed water density profiles resemble those derived from molecular dynamics simulations. We also derive an excess free energy that discriminates correct from incorrect conformations of proteins.