Nucleic Acids Research, 1995, Vol. 23, No. 6 1019-1029
© 1995
COMPUTATIONAL BIOLOGY |
Homology model building of the HMG-1 box structural domain
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Building 38A, Room 8N-805, Bethesda, MD 20894, USA
*To whom correspondence should be addressed
Received October 31, 1994. Revised February 1, 1995. Accepted February 1, 1995.
Nucleoproteins belonging to the HMG-1/-2 family possess homologous domains 
75 amino acids in length. These domains, termed HMG-1 boxes, are highly structured, compact, and mediate the interaction between HMG-1 box-containing proteins and DNA in a variety of biological contexts. Homology model building experiments on HMG-1 box sequences ‘threaded’ through the 1H-NMR structure of an HMG-1 box from rat indicate that the domain does not have rigid sequence requirements for its formation. Energy calculations indicate that the structure of all HMG-1 box domains is stabilized primarily through hydrophobic interactions. We have found structural relationships in the absence of statistically significant sequence similarity, identifying several candidate proteins which could possibly assume the same three-dimensional conformation as the rat HMG-1 box motif. The threading technique provides a method by which significant structural similarities in a diverse protein family can be efficiently detected, and the ‘structural alignment’ derivedby this method provides a rational basis through which phylogenetic relationships and the precise sites of interaction between HMG-1 box proteins and DNA can be deduced.
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