Chemistry Reference
In-Depth Information
Fig. 9.3
Images of the electrostatic potential mapped on the molecular surface of the bovine re-
coverin (PDB code 1REC) obtained using PCE tool: view of two regions of protein from
−
2.0
kcal/mol/e (
red
)to
+
2.0 kcal/mol/e (
blue
)
and surface area, for bovine recoverin the surface area is 8609 Å
2
and the volume is
23,660 Å
3
.
Another possibility to analyze the electrostatic properties of the protein surface
is the electrostatic potential mapping on molecular surface using Protein Contin-
uum Electrostatics (PCE) tool (Miteva et al.
2005
). PCE server (
http://bioserv.rpbs.
jussieu.fr/cgi-bin/PCE-Pot)
allows calculation of electrostatic potential (PCE-pot)
and pKa values of titratable groups in proteins (PCE-pKa). When using PCE-pot
tool, electrostatic potentials are displayed on the molecular surface using a color-
code: blue regions are positively charged, red ones are nega-tively charged and white
regions are neutral. When using PCE-pKa tool, the pKint, pK1/2 and pH-dependent
protonation curves of all titratable groups, estimated isoelectric points (p)I and elec-
trostatic interaction energy in kcal/mole between titratable groups are provided. The
use of PCE-pot tool with default parameters for bovine recoverin is presented in
Fig.
9.3
. It illustrates the charge distribution on the bovine recoverin and we may
identify the balance of regions with negative charge in good correlation to known
data concerning other calcium binding proteins (Mouawad et al.
2009
).
Analysis and comparison of protein surfaces may be done using 3D-SURFER
computational tool (Li et al.
2008
). 3D-SURFER is a web-based tool (
http://dragon.
bio.purdue.edu/3d-surfer/)
used for protein surface comparison and analysis. It al-
lows a high throughput screening and visualization of a protein surface comparison
against all protein structures in the Protein Data Bank. The web interface renders
additional important information: animated protein rotations, protein structure clas-
sification codes, structure alignment calculations and identification of pocket regions
on a given structure (Li et al.
2008
). An example of using this tool in order to analyze
and compare the surface properties of bovine recoverin is presented in the Fig.
9.4
.
This picture also illustrates that this web-based tool allows identification, visual-
ization and characterization of local geometric features of surface such as cavities
