Protein-DNA Interaction from NMR and Monte Carlo Docking

Abstract

An essential step in the regulation of gene expression is the binding of a regulatory protein to a specific DNA sequence in the promotor region of the gene. The understanding of protein-DNA recognition is, therefore, a major theme in structural biology. Much progress has been made since the early ’80s when the first structures of bacterial DNA-binding proteins and protein-DNA complexes were solved by X-ray crystallography (for reviews see Steitz (1990), Pabo and Sauer (1992) and Travers (1993)). NMR started to contribute around 1985 with the structure elucidation of the lac repressor headpiece (Kaptein et al., 1985) and a low resolution structure of the headpiece-operator complex (Boelens et al., 1987). These first prokaryotic DNA-binding proteins all contained the helix-turn-helix motif as the DNA-binding subdomain. However, subsequently a large number of other structural motifs has been characterized including zinc-fingers, leucine zippers, helix-loop-helix proteins and β-sheet DNA binding proteins.