Chemistry Reference
In-Depth Information
Fig. 9.5
Characterization of the largest cavities of bovine recoverin surface and identification of
residues involved in their formation
Binding sites of proteins are usually associated to structural cavities and/or pock-
ets situated on protein surface and it becomes important not only to identify but also
to characterize these cavities. The scientific literature is abundant in computational
tools allowing characterization of cavities and pockets situated at protein surface.
One of these tools is Computed Atlas of Surface Topography of proteins (CASTp)
that can be used to study surface features and functional regions of proteins (Dun-
das et al.
2006
). It provides an online resource (http://sts.bioengr.uic.edu/castp/) for
locating and characterizing concave surface regions (pockets located on protein sur-
faces and voids buried in the interior) on three-dimensional structures of proteins
and allows the measurement of the area and volume of pocket or void and identi-
fication of all residues and even atoms participating in their formation. For bovine
recoverin, CASTp tool identifies 23 cavities, the measured areas and volumes for the
largest cavities being presented in Table
9.3
. The largest cavity identified by CASTp
involves the residues TRP31, PHE35, GLU38, CIS39, ILE44, GLU48, THR51,
