Poisson Boltzmann

Marmur [12] has presented a guide to the appropriate choice of approximate solution to the Poisson-Boltzmann equation (Eq. V-5) for planar surfaces in an asymmetrical electrolyte. The solution to the Poisson-Boltzmann equation around a spherical charged particle is very important to colloid science. Explicit solutions cannot be obtained but there are extensive tabulations, known as the LOW tables [13]. For small values of o, an approximate equation is [9, 14]... 

Vlachy V 1999 Ionic effects beyond Poisson-Boltzmann theory Ann. Rev. Phys. Chem. 50 145... 

More sophisticated approaches to describe double layer interactions have been developed more recently. Using cell models, the full Poisson-Boltzmann equation can be solved for ordered stmctures. The approach by Alexander et al shows how the effective colloidal particle charge saturates when the bare particle charge is increased [4o]. Using integral equation methods, the behaviour of the primitive model has been studied, in which all the interactions between the colloidal macro-ions and the small ions are addressed (see, for instance, [44, 45]). 

A number of issues need to be addressed before this method will become a routine tool applicable to problems as the conformational equilibrium of protein kinase. E.g. the accuracy of the force field, especially the combination of Poisson-Boltzmann forces and molecular mechanics force field, remains to be assessed. The energy surface for the opening of the two kinase domains in Pig. 2 indicates that intramolecular noncovalent energies are overestimated compared to the interaction with solvent. 

Elamrani et al. 1996] Elamrani, S., Berry, M.B., Phillips Jr., G.N., McCammon, J.A. Study of Global Motions in Proteins by Weighted Masses Molecular Dynamics Adenylate Kinase as a Test Case. Proteins 25 (1996) 79-88 [Elcock et al. 1997] Elcock, A.H., Potter, M.J., McCammon, J.A. Application of Poisson-Boltzmann Solvation Forces to Macromolecular Simulations. In Computer Simulation of Biomoleeular Systems, Vol. 3, A.J. Wilkinson et al. eds., ESCOM Science Publishers B.V., Leiden... 

Prediction of pKaS of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System... 

Fig. 1. Explanation of the principles of the finite-difference method for solution of the Poisson-Boltzmann equation...

Tanford, C., Kirkwood, J. G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79 (1957) 5333-5339. 6. Garrett, A. J. M., Poladian, L. Refined derivation, exact solutions, and singular limits of the Poisson-Boltzmann equation. Ann. Phys. 188 (1988) 386-435. Sharp, K. A., Honig, B. Electrostatic interactions in macromolecules. Theory and applications. Ann. Rev. Biophys. Chem. 19 (1990) 301-332. 

Sharp, K. A., Honig, B. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94 (1990) 7684-7692. Zhou, H.-X. Macromolecular electrostatic energy within the nonlinear Poisson-Boltzmann equation. J. Chem. Phys. 100 (1994) 3152-3162. 

Davis, M. E., McCammon, J. A. Solving the finite difference linearized Poisson-Boltzmann equation A comparison of relaxation and conjugate gradients methods.. J. Comp. Chem. 10 (1989) 386-394. 

Another way of calculating the electrostatic component of solvation uses the Poisson-Boltzmann equations [22, 23]. This formalism, which is also frequently applied to biological macromolecules, treats the solvent as a high-dielectric continuum, whereas the solute is considered as an array of point charges in a constant, low-dielectric medium. Changes of the potential within a medium with the dielectric constant e can be related to the charge density p according to the Poisson equation (Eq. (41)). 

If there are ions in the solution, they will try to change their location according to the electrostatic potential in the system. Their distribution can be described according to Boltzmarm. Including these effects and applying some mathematics leads to the final linearized Poisson-Boltzmann equation (Eq. (43)). 

Methods Based upon the Poisson-Boltzmann Equation... 

The final class of methods that we shall consider for calculating the electrostatic compone of the solvation free energy are based upon the Poisson or the Poisson-Boltzmann equatior Ihese methods have been particularly useful for investigating the electrostatic properties biological macromolecules such as proteins and DNA. The solute is treated as a body of co stant low dielectric (usually between 2 and 4), and the solvent is modelled as a continuum high dielectric. The Poisson equation relates the variation in the potential (f> within a mediu of uniform dielectric constant e to the charge density p ... 

The linearised Poisson-Boltzmann equation is obtained by taking only the first term in the expansion, giving ... 

How can Equation (11.79) be solved Before computers were available only simple ihapes could be considered. For example, proteins were modelled as spheres or ellipses Tanford-Kirkwood theory) DNA as a uniformly charged cylinder and membranes as planes (Gouy-Chapman theory). With computers, numerical approaches can be used to solve the Poisson-Boltzmann equation. A variety of numerical methods can be employed, including finite element and boundary element methods, but we will restrict our discussion to the finite difference method first introduced for proteins by Warwicker and Watson [Warwicker and Watson 1982]. Several groups have implemented this method here we concentrate on the work of Honig s group, whose DelPhi program has been widely used. 

Fig. 11.28 Focusing can improve the accuracy of finite difference Poisson-Boltzmann calculations.

Applications of Finite Difference Poisson-Boltzmann Calculations... 

The Poisson-Boltzmann equation is a modification of the Poisson equation. It has an additional term describing the solvent charge separation and can also be viewed mathematically as a generalization of Debye-Huckel theory. 

The continuum treatment of electrostatics can also model salt effects by generalizing the Poisson equation (12) to the Poisson-Boltzmann equation. The finite difference approach to solving Eq. (12) extends naturally to treating the Poisson-Boltzmann equation [21], and the boundary element method can be extended as well [19]. 

SASA), a concept introduced by Lee and Richards [9], and the electrostatic free energy contribution on the basis of the Poisson-Boltzmann (PB) equation of macroscopic electrostatics, an idea that goes back to Born [10], Debye and Htickel [11], Kirkwood [12], and Onsager [13]. The combination of these two approximations forms the SASA/PB implicit solvent model. In the next section we analyze the microscopic significance of the nonpolar and electrostatic free energy contributions and describe the SASA/PB implicit solvent model. 

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