Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions.
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.
Koehl
Patrice
P
Department of Computer Science and Genome Center, University of California, Davis, Davis, California 95616, USA.
Orland
Henri
H
Delarue
Marc
M
D008956:Models, Chemical; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
D011506:Proteins; D014867:Water