Chemistry Reference
In-Depth Information
Fig. 9.7
Illustration of global (entire protein—
a
) and local (the biggest cavity—
b
) surface fractal
dimension calculation for bovine recoverin
by Craciun et al. (
2009
). These studies revealed strong correlations between the sur-
face fractal dimension and the macromolecule size (Goetze and Brickman
1992
), the
molecular and cellular function of proteins (Stawiski et al.
2000
; Pitulice et al.
2008a
)
and their catalytic activity (Stawiski et al.
2002
). Also, such studies emphasized that
surface roughness does not depend on the composition of protein in secondary struc-
ture elements (Pitulice at al.
2008b
) but it strongly depends on the properties of the
protein environment such as pH, electrolyte concentration and temperature (Vreeker
et al.
1992
; Petit and Bowie
1999
) being always higher for proteins in solution than
for proteins in crystal (Craciun et al.
2012
). Moreover, there are published papers
illustrating that protein surfaces reveal both global and local surface fractal dimen-
sions, usually cavities and pockets presenting a higher roughness than the global
surface (Avnir and Farin
1990
; Pettit and Bowie
1999
; Ciorsac et al.
2011
; Isvoran
et al.
2013
). This finding is important because it is known that the rate of substrate
trapping by the active sites is largest when the protein surface has a dimension close
to 2.2 (Aon et al.
2000
). Also, the presence of hydrophobic cavities at the protein
surface with a complex shape, expressed by a higher surface fractal dimension, has
been shown to be an important property related to the ability of proteins to bind
alpha-helical peptides (Isvoran et al.
2013
).
Figure
9.7
illustrate the determination of the surface fractal dimension for bovine
recoverin, both at global (a) and local (b) levels. The contact surface for the entire
protein is computed using GETAREA server and the contact surface for the big-
gest identified cavity is computed using CASTp web-server respectively. For these
calculations, distinct values for the probe-sphere radii are used, from 1.4 to 3.0 Å.
Every computed contact surface is plotted against the probe sphere radius in double
logarithmical scale and the surface fractal dimensions are extracted from the slopes
of the lines: Dsg
0.09. These
values are in good agreement with other published data (Craciun et al.
2009
).
It seems that the distribution pattern of atoms on the protein surface is fractal
and has determinant contribution to the biological function. Moreover, the surface
fractal dimension seems to be a quantitative parameter that can be used to describe
the complexity of the shape of protein surface.
=
2.21
±
0.03 for the global surface and Dsl
=
2.40
±
