Energy scaffolds for non-HMG proteins able
to assume the shape of the HMG-1 box
In these proteins, strong pairwise interaction energies
(< -1 kcal/mol) are observed for all 11 of the
critical HMG-1 box residues involved in
maintaining the three-dimensional structure of the domain.
Homology model building
experiments indicate that these
proteins all give a statistically significant match of
sequence to structure despite not containing the
HMG-1 box signature.
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.
DNA adenine methylase from bacteriophage T2
(Miner & Hattman, 1988)
Translational activator GCN1 from Saccharomyces cerevisiae
(Marton et al., 1993)
Transcriptional activator RINA from bacteriophage phi-11
(Ye & Lee, 1993)
Anticodon nuclease from Escherichia coli
(Levitz et al., 1990)
Protein gp2 from bacteriophage LP7
(Petri & Schmieger, 1990)
CHL1 protein from Saccharomyces cerevisiae, similar to yeast RAD3
(Gerring et al., 1990)
DNA-directed RNA polymerase from Schizosaccharomyces pombe
(Hirano et al., 1989)