Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins.

Overview

The structures of the complexes between TATA-box binding proteins (TBPs) and DNA solved recently with X-ray crystallography identify both direct and indirect readout interactions. Examples of indirect readout mechanisms in these complexes are DNA bending and non-local electrostatic complementarity. An intriguing question arising from these structures is the role that a series of lysine residues may have in DNA binding. Thus, in the yeast complex, seven lysines are found to be close to the phosphate backbone, but they appear to form hydrogen bonds to the protein and not to be involved in any direct (or water-mediated) interactions with the DNA. The proposal based on the crystal structure, that these residues set up a delocalized electrostatic potential that stabilizes the complex with DNA, is evaluated here from calculations of the electrostatic potentials generated by the wild-type TBP and various lysine to leucine mutants. The results suggest a grouping of these mutants into three classes, based on their phenotypes and electrostatic profiles. As these groups are affected differently by specific measures taken to rescue DNA binding and transcription functions, the mechanistic inferences from the analysis can be probed experimentally in a manner that also reveals possible binding sites for transcription factors IIA and IIB to the TBP-DNA complex in the transcription preinitiation complex.