Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically

Abstract

Results of systematic base-substitution experiments suggest that the lambda repressor dimer, made of identical subunits, recognizes the "pseudo(2-fold)symmetric" operator sequence asymmetrically. Base substitutions within the consensus half of the operator affect binding more than base substitutions within the nonconsensus half of the operator. Furthermore, changing the nonconsensus base pairs to the consensus base pairs does not increase, but decreases, binding. Evidently, the two subunits of the lambda repressor dimer bind to the two halves of the operator differently. This is consistent with the recently determined crystal structure of the complex, which shows that the relative positioning of the amino acids to the DNA bases are slightly different in the two halves of the operator. The sequence-specific interactions indicated by the systematic base-substitution experiments correlate well with the locations of the specific contacts found in the complex. Thus, the amino acids of lambda repressor, mainly of alpha 3-helix and the N-terminus arm, seem to directly read-out the DNA sequence by forming specific hydrogen bonds and hydrophobic contacts to the DNA bases. The observed asymmetric recognition suggests that no recognition code governs amino acids and DNA bases in protein-DNA interactions.