Biology Reference
In-Depth Information
Fig. 1.
Comparative structure model of the yeast Sec61 complex modeled on the
structure of the
M. jannaschii
SecYEβ translocon.
90
The model, shown as a ribbon
representation in stereo, allowed designing a deletion mutant of the plug domain
(residues 52-74, displayed as a space-filling contour) for studying the functional role
of the plug domain
in vivo
.
83
atomic structures that optimally fit the experimental data. As these can-
not be measured directly, they have to be obtained using experimental
methods such as heavy-atom isomorphous replacement, anomalous
scattering, or molecular replacement.
2,69,70,91
The latter approach gen-
erally requires a good-quality atomic structure of a related protein that
is then rotated and translated into the new crystal system until there is
a good match with the experimental data. The first application of a
model built with SWISS-MODEL in molecular replacement was per-
formed by Karpusas
et al
.
92
to obtain a 2 Å resolution X-ray structure
of the human CD40 ligand (PDB entry 1aly). The authors used our
published murine homology model
14
(PDB entry 1cda) to build a
human model of CD40L, and then applied the latter “model of a
model” to the molecular replacement approach. A more recent example
can be seen in Hou
et al
.
93
