title: Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes.
abstract: The 434 repressor binds more tightly to OR1 than it does to OR3. The repressor makes several specific contacts with the symmetrically arrayed outer four base-pairs of the 14 base-pair site, and no specific contacts to the central six base-pairs. The sequence of the outer base-pairs of OR1 and OR3 differs only by an A-->G substitution at position 4 in one half-site of OR3, while that of central bases is very different. As expected from sequence analysis of wild-type operators, the data show repressor prefers an A.T base-pair at position 4. The magnitude of this preference depends on operator sequence context and solution conditions. Position 4 changes in the context of OR1 have a greater effect on operator affinity for 434 repressor than do similar changes in OR3. Although OR1 and OR3 display different affinities for 434 repressor, their repressor-operator complexes are similarly insensitive to changes in salt concentration and temperature. By contrast, complexes formed between repressor and position 4 mutant OR1, bearing an A.T-->G.C change, and OR3, which bears a G.C-->A.T change, are affected greatly, and to similar extents, by changes in ionic strength and temperature. Nuclease protection experiments show that 434 repressor protects the DNA phosphate backbone of wild-type operators from cleavage more efficiently than those of mutant operators. These data show that the biochemical and structural properties of a repressor-operator complex, while affected by position 4 base sequence, are independent of the identity of this base. The ability of repressor to recognize the base at position 4 depends on the sequence context at operator positions 5 to 7. Apparently there is an interplay between the bases at operator positions 4 to 7 which has a global effect on the structure of the repressor-operator complex.
authors.affiliation: Department of Biological Sciences, State University of New York at Buffalo 14260.
authors.forename: A C
authors.initials: AC
authors.lastname: Bell
authors.forename: G B
authors.initials: GB
authors.lastname: Koudelka
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002151:Calorimetry; D003090:Coliphages / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D004279:DNA, Viral / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D008969:Molecular Sequence Data; D009994:Osmolar Concentration; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism*; D015183:Restriction Mapping; D013329:Structure-Activity Relationship
chemical_list: D004269:DNA, Bacterial; D004279:DNA, Viral; D012097:Repressor Proteins