Backbone and Side Chain Dynamics of lac Repressor Headpiece (1−56) and Its Complex with DNA

• Published in: Biochemistry (Easton) 1997-01, Vol.36 (1), p.249-254
• Main Authors: Slijper, M, Boelens, R, Davis, A. L, Konings, R. N. H, van der Marel, G. A, van Boom, J. H, Kaptein, R
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; DNA - metabolism; DNA Primers; DNA-Binding Proteins - chemistry; Escherichia coli; Escherichia coli - chemistry; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins; Gene Expression - genetics; Helix-Turn-Helix Motifs - genetics; Lac Repressors; Magnetic Resonance Spectroscopy; Models, Molecular; Polymerase Chain Reaction; Protein Conformation; Protein Structure, Secondary; Repressor Proteins - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi961670d

The dynamics of the backbone and (some of) the side chains of lac headpiece (1−56; lac HP56) have been studied for the free protein and for its complex with lac half-operator DNA by 15N T 1 and T 1 ρ relaxation measurements combined with [1H−15N] NOE experiments. For the structurally well-defined part of the free lac HP56 (i.e., residues 3−49) a rigid backbone was found for residues in the three α-helices and for the turn of the helix−turn−helix motif. The loop between helices II and III of lac headpiece, which was characterized by slight disorder in the structure calculations, shows increased mobility. The detected side chains are very mobile. These data are in full agreement with the rms deviations in the structural data of free lac HP56. When lac HP56 is complexed with DNA, several changes in mobility take place. The most remarkable change was found for the loop region between helices II and III:  residue His-29 within this loop interacts with Thy-3 of the operator DNA. As a result this mobile loop adapts itself to the DNA and becomes more rigid. Moreover, most DNA-contacting side chains show a significant decrease in flexibility, although these side chains do not become as rigid as the backbone. These results suggest that the mobility of the regions within lac HP56 important for complexation, i.e., the loop and the DNA-contacting side chains, is essential for a good fit onto the counterparts of the target DNA.