Double-Stranded DNA

3D Structure l Cro Protein Binding to DNA

CPK Color Scheme C O N P S

You can see the l Cro homodimer binding to its recognition site in a piece of double-stranded DNA. The l Cro protein is a part of a toggle switch that is discussed in chapters about genomic circuits.

Reset and spin structure.

Zoom in to see where the DNA and proteins interact.

Look at the Cro side chain in spacefill mode and the DNA in CPK colors. You can also see the H-bonds between the base pairs of DNA. (You might want to compare this with the yeast Gal4 Jmol tutorial.)

In this view, one of the monomers has been converted to cartoon display with the secondary structures highlighted by red for alpha helices (there are no b sheets in this protein). The other Cro monomer is colored so that each amino acid is a different color. The DNA is color coded by strand.

Add in the side chains of the cartoon structure to see from where the DNA-binding side chains originate.

Does each protein bind to one or two of the DNA strands? Do you think each monomer binds to the same sequence or different sequences?

Genomics

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