Electrostatic
potentials and solvation energies in YASARA
YASARA provides various ways to visualize
electrostatic potentials
(ESPs) and calculate solvation energies. They are based on two very
different approaches:
The Particle
Mesh Ewald approach (PME) uses the reciprocal space part of
Ewald summation to obtain the smoothed electrostatic potential in vacuo, without singularities and
short-range noise[1]. The left column of figure 1 shows
the
resulting long-ranged PME potentials around the enzyme SOD (superoxide
dismutase), where an electropositive channel (shown in blue) leads to
the
active site to help capture the superoxide anions.
The Poisson-Boltzmann
approach (PBS) uses a customized version of the APBS program[2]
to solve the Poisson-Boltzmann equation, yielding the electrostatic
potential with implicit solvent and counter ions. Compared to PME, the
PBS potential shows more short-range details (right column in figure 1).
Each of the two electrostatic potential types can be visualized in a
number of different ways:
The styles Density
and Points (first two rows in
figure 1) visualize the ESP at each point on a grid, using either
transparent or opaque dots.
The Contour style
consists of two surfaces, first a
contour of the regions with a certain negative potential
(red), and second a contour of the
regions with a certain positive potential (blue).
The Surface style
is the most common one, it simply colors a surface of the protein
as a function of the ESP at each surface point. Van der Waals,
molecular or
solvent accessible surfaces can be chosen.
Finally, solvation energies can be calculated in three different ways:
A very fast empirical approximation (fraction of a
second).
A fast PME-based boundary element approach (one
second).
A slow PBS-based calculation with APBS[2] (many
seconds).
R E F E R E N C E S
[1] Fast empirical pKa prediction by Ewald summation
Krieger E, Nielsen JE, Spronk CA, Vriend G (2006) J.Mol.Graph.Model.25,481-486
[2] Electrostatics of nanosystems: application to microtubules and
the ribosome
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Proc.Natl.Acad.Sci.USA98, 10037-10041
Figure 1: The electrostatic
potential around superoxide dismutase, visualized using various
calculation methods and graphics styles.
Figure 2: Screen recording of
YASARA's interactive electrostatics tutorial. A higher quality version
can be watched at
YouTube, click on 'Watch in high quality' below the video. Since
YASARA creates these animations in real-time using
OpenGL, simply download the corresponding macro (GNU GPL licensed) from
the YASARA movie page to watch it in highest
resolution with up to 60 frames per second.