A COMPARATIVE-STUDY OF DYNAMIC STRUCTURES BETWEEN PHAGE 434-CRO AND REPRESSOR PROTEINS BY NORMAL-MODE ANALYSIS

Two DNA binding proteins, Cro and the amino-terminal domain of the rep ressor of bacteriophage 434 (434 Cro and 434 repressor) that regulate gene expression and contain a helix-turn-helix (HTH) motif responsible for their site-specific DNA recognition adopt very similar three-dime nsional structures when compared to each other. To reveal structural d ifferences between these two similar proteins, their dynamic structure s, as examined by normal mode analysis, are compared in this paper. Tw o kinds of structural data, one for the monomer and the other for a co mplex with DNA, for each protein, are used in the analyses. From a com parison between the monomers it is found that the interactions of Ala- 24 in 434 Cro or VaI-24 in 434 repressor, both located in the HTH moti f, with residues 44, 47, 48, and 51 located in the domain facing the m otif, and the interactions between residues 17, 18, 28, and 32, locate d in the PITH motif, cause significant differences in the correlative motions of these residues. From the comparison between the monomer and the complex with DNA for each protein, it was found that the first he lix in the HTH motif is distorted in the complex form. While the resid ues in the HTH motif in 434 Cro have relatively larger positive correl ation coefficients of motions with other residues within the HTH motif , such correlations are not large in the HTH motif of 434 repressor. I t is suggestive to their specificity because the 434 repressor is less specific than 434 Cro, Although a structural comparison of proteins h as been performed mainly from a static or geometrical point of view, t his study demonstrates that the comparison from a dynamic point of vie w, using the normal mode analysis, is useful and convenient to explore a difference that is difficult to find only from a geometrical point of view, especially for proteins very similar in structure. (C) 1996 W iley-Liss, Inc.