Energy scaffolds for HMG-1 box proteins
Energy scaffolds generated for models of selected HMG-1 proteins are
shown below. These proteins, which contain all the elements of the
HMG-1 box signature,
have a well-packed domain that is held
together mostly by hydrophobic interactions. These interactions
involve most of the hydrophobic residues found in alpha-helices
1 and 2 within the HMG-1 box
(Weir et al., 1993).
The alpha-carbon backbone of the protein is depicted as a
curving "worm." Within the backbone, segments of the HMG-1 box
domain comprising the core folding motif are shown in blue, while
the intervening loop regions are shown in yellow.
Pairwise residue interaction energies between core residues
are indicated by the thickness and coloring of the connected
alpha-carbon positions on the protein backbone. Thick,
magenta-colored cylinders indicate the most favorable interactions.
Thick, cyan-colored cylinders indicate the least favorable
interactions. Intermediate colors and cylinder widths represent
interactions falling between these extremes.
Rat HMG-1 box 2
(Paonessa et al., 1987),
threaded through its own structure
(Weir et al., 1993)
Chicken HMG-2a box 2
(Oka et al., 1992)
Sea urchin HMG-1 box 2
(Niemeyer et al., 1993)
Human sex-determining factor SRY
(Denny et al., 1992)
Two proteins that had previously been reported as containing
HMG-1 boxes but that are not unambiguously identified as HMG-1/-2
homologues through database searches are shown below.
Both CCG1 and SIN1/SPT2 contain only some of the elements
of the
HMG-1 box signature.
Threading of the CCG1 sequence through the motif did not yield a
statistically significant fit of sequence to structure. In
contrast, threading of the SIN1/SPT2 sequence did yield
a statistically significant fit of sequence to structure. This
case provides an excellent example of how the threading technique
is able to identify a structural replationship between proteins
in the absence of sequence identity.
Human CCG1 (TAF-250)
(Sekiguchi et al., 1991)
Yeast SIN1/SPT2
(Kruger & Herskowitz, 1991)