Zinc fingers are small proteins that wrap around Zn2+ ions in order to maintain their structures.
These proteins then recognize and wrap around specific DNA sequences, and are involved in
regulating DNA transcription. In the structure below (PDB ID 3znf), the protein backbone is
depicted as “cartoon,” with alpha helices shown as ribbons and strands without secondary
structure shown as thin lines. Most of the amino acid side chains are not shown, but the ones
that ligate the zinc ion (grey sphere) are rendered as ball and stick.
1) The cysteine residues are shown in their anionic, deprotonated form. What does this tell
you about how Zn2+ changes the pKa of the Cys side chains
2.Proteins in this family are among those targeted by lead poisoning in infants and children.
What do you think happens to the protein in the presence of Pb2+, and how do you think
this could this lead to developmental issues in children
3.The human genome contains 30 types of zinc finger proteins. These are easy to identify in
the genome because they have portions that are homologous to one another. Are these
different zinc finger proteins orthologs or paralogs?
4.An alignment of zinc finger protein primary sequences shows a strictly conserved (i.e.,
totally invariant) sequence motif. What amino acids do you think must be encoded within
the strictly conserved motif? Why?
5jThe primary structure for the Zn finger protein above is:
RPYHCSYCNFSFKTKGNLTKHMKSKAHSKK. How many amino acids in this sequence are
nonpolar, polar, acidic, and basic, respectively? The phosphodiester backbone of DNA, as we
will see, is highly negatively charged. In light of that, does the composition of the sequence
make sense? Why?