|
|
Several potential isosurfaces of an SOD enzyme.
The pictures below are various visualizations of an SOD molecule, and
the electrostatic potential fields generated by SOD in ionic solutions.
The potential fields were obtained with the help of the Debye-Huckle
continuum electrostatic model, which gives rise to the nonlinear
Poisson-Boltzmann equation.
X-Ray crystallography SOD data from the Brookhaven Protein Database was used
as model input, and the nonlinear Poisson-Boltzmann equation was solved
numerically, using a global inexact-Newton-multilevel method developed by
M. Holst in Applied Mathematics and CRPC at Caltech.
Linearized and nonlinear Poisson-Boltzmann models yield substantially
different electrostatic potential values near the binding sites, leading to
correspondingly different reaction rates predicted by Brownian dynamics
simulations.
This implies that the full nonlinear model is important for certain modeling
situations.
A parallel CC++ implementation of the global inexact-Newton-multilevel method
has recently been developed by M. Holst and John Garnett of the
Computational Biology Group at the Caltech Beckman Institute.
Additional collaborators on this project were Carl Kesselman of the
Beckman Institute and Dan Meiron in Applied Mathematics and
CRPC at Caltech.
Several of the plots below were produced by James Patton, also in the
Computational Biology Group at Caltech.
|
