Chemistry Reference
In-Depth Information
Fig. 9.4
Illustration of 3D-SURFER tool utilization to characterize and compare the bovine
recoverin surface
(Fig.
9.4
, red—first largest cavity, green—second largest cavity, blue—third largest
cavity), protrusions and flat regions that may represent potential ligand binding sites
of bovine recoverin. The characteristics of identified geometric features are also
provided, including areas and volumes for these regions and the list of the residues
forming the three largest groups (Fig.
9.5
). A large number of these residues are
known to be functionally important, see further. This tool also allows comparison
of surface of considered protein to all protein structures in the PDB and retrieves
PDB structures that have similar surface shapes giving the opportunity to identify
functionally related proteins that, due to distant evolutionary relationship, cannot be
emphasized otherwise.
For bovine recoverin, the result of using 3D-SURFER for identification of similar
surfaces in PDB is presented in Table
9.2
. The comparison is based on the Euclidean
distance between the descriptor vectors representing the proteins (Li et al.
2008
). We
have considered the default value of 25 for selection of the number of entries to be
listed and we also performed structural alignment of considered structures expressed
by root-mean-square distance (RMSD) between equivalent atom pairs (Carugo and
Eisenhaber
1997
). Identical structures have zero value for the RMSD and it increases
for dissimilar structures. Results display also includes the CATH codes (Orengo et al.
1997
) that reflect the structural topology of proteins. The result illustrated in Table
9.2
indicates 1OMV, chain A (Ames et al.
2002
) as a structural file of a protein having
high surface similarity with bovine recover-in. 1OMV is the structural file of E85Q
mutant of bovine recoverin, so it is expected the two files share high structural and
surface similarity and this infor-mation is not relevant for biological interpretation.
It is not the case of 3FXV that is the structural file of the ligand binding domain
(residues 248-475) of NR1H4 (nuclear receptor subfamily 1, group H, member 4)
protein (Feng et al.
2009
) that also shares structural and surface similarity to bovine
recoverin and this information could be meaningful.
