A NEGATIVE ELECTROSTATIC DETERMINANT MEDIATES THE ASSOCIATION BETWEENTHE ESCHERICHIA-COLI TRP REPRESSOR AND ITS OPERATOR DNA

The electrostatic potential surfaces were characterized for trp repres sor models that bind to DNA with sequence specificity, without specifi city, and not at all. Comparisons among the surfaces were used to isol ate protein surface features likely to be important in DNA binding. Mo dels that differ in protein conformation and tryptophan-analogue bindi ng consistently showed positive potential associated with the protein surfaces that interact with the DNA major groove. However, negative po tential is associated with the trp repressor surface that contacts the DNA minor groove. This negative potential is significantly neutralize d in the protein conformation that is bound to DNA. Positive potential is also associated with the tryptophan binding-site surface, a conseq uence of the tryptophanor tryptophan analogue-induced allosteric chang e. This protein region is complementary to the strongest negative pote ntial associated with the DNA phosphate backbone and is also present i n the isolated protein structure from the protein-DNA complex. The eff ects of charge-change mutation, pH dependence, and salt dependence on the electrostatic potential surfaces were also examined with regard to their effects on protein-DNA binding constants. A consistent model is formed that defines a role for long-range electrostatics early in the protein-DNA association process and complements previous structural, molecular association, and mutagenesis studies.