DNA-Binding Proteins



The expression of proteins responsible for moment-to-moment chemical and structural tasks is critical to the functioning of living cells. This requires that the cell regulate the expression of new proteins. DNA-binding proteins play an important role in this process. These proteins interact with DNA by means of various structural motifs, and can stimulate or repress transcription of messenger RNA,depending on the properties and location of the DNA sequence to which they bind.

In this exercise we will explore four DNA-binding proteins. Each contains features that are highly conserved among many organisms.

The first DNA-binding protein is the TATA-binding protein (TBP). It binds a highly conserved sequence (TATAAAAG) in the promoter of eukaryotes and is essential for the assembly of the transcriptional apparatus.

The second protein is the E. coli lac repressor, which is representative of DNA-binding proteins that use the helix-turn-helix (HTH) motif to recognize DNA. The HTH motif is commonly used for transcriptional repression.

TATA-binding Protein
lac repressor

The third protein contains a motif called a leucine zipper. The leucine zipper generally appears as a dimer of a helices that form a coiled coil. The N-terminal end of the coiled coil is responsible for the dimerization, while the C-terminal end of the coil recognizes and binds DNA sequence-specifically.

The fourth protein is the Zif268 transcriptional regulator from the mouse. This DNA-binding protein uses the zinc finger motif to confer its DNA-binding properties. The zinc finger uses a tetrahedrally coordinated zinc cation that interacts ionically with the protein to facilitate an optimal fold for DNA interactions.

Leucine zipper
Zif 286 protein (zinc finger)

Learning objectives

  • Review the secondary and tertiary structures of DNA-binding proteins.
  • Recognize the general features of DNA-binging proteins and how the classes are different.
  • Understand how proteins and DNA interact in both sequence-specific and non-specific modes.