Download Zinc Finger Folding Activity

Zinc Finger Folding Activity
Based on amino acids 4-31 of 1zaa.pdb
Parts List
- Toober segment – 28 amino acids long (approx 72 cm)
- Sidechains
2 Cys
2 His
1 Phe
1 Arg
1 Leu
- 7 metal clips
- Zinc Atom
- Zinc Finger Folding Map
- 1 Blue end cap (for designating the amino terminus)
- 1 Red end cap (for designating the carboxy terminus)
Introduction
A C2H2 zinc finger is a 28 amino acid protein motif composed of a short alpha helix and a two-stranded
beta sheet. The structure of the zinc finger is stabilized by a zinc atom that binds 2 cysteine and 2
histidine sidechains, and by hydrophobic amino acid sidechains that are buried on the inside of the
folded motif. Zinc finger proteins function as regulators of gene expression. They bind to the
negatively-charged backbone of DNA through a positively-charged arginine amino acid sidechain
located at the beginning of the short alpha helix.
The construction of a physical model of the 3D structure of a zinc finger serves as a good example of
how Toobers can be used to model protein structures.
This kit is based on 1ZAA.pdb and represents amino acids 4-31.
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Getting Started: Laying out the primary sequence
1. Lay out the protein folding map and position the toober below it.
2. Align the toober with the
protein folding map and draw
a line for each amino acid.
3. Number and place the
seven clips on the toober
according to the protein
folding map.
4. Add the blue and red
end caps.
Folding the Protein
1. Bend the first 13 amino acids into a β-sheet (amino acids 4-16). You can create a β-sheet by
bending the toober at every amino acid (approximately every 2 cm).
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2. Next, create an α-helix with amino acids 19-31 (the last 13 amino acids of the protein). Do this by
wrapping the toober segment around an alpha helix bending jig (wooden dowel or your finger) and
then stretch it out so that so that there are approximately 3.6 amino acids per turn of the helix.
Wrap the toober around the jig.
Slide the toober off the jig.
Stretch the toober.
Is your helix right-handed or left-handed?
Alpha-helices are right-handed. Make sure that your model
has a right-handed helix. To do this, imagine that your alpha
helix is a spiral staircase. If you can climb that staircase with
your right hand on the outside railing (the toober), then you
have a right-handed helix.
3. Now, bend the beta pleated strand in half at the 7th
amino acid (Glu10).
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4. Next bend the toober
segment at the “turn” (between
the 17th and 18th amino acids)
so that it resembles the picture
shown to the right.
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5. Finally, using the zinc finger folding map included within this activity, decipher which amino acids
have sidechains represented and attach the sidechains to the clips at their correct amino acid
locations. There are two cysteines (positions 7 and 9), two histidines (positions 25 and 29), one
phenylalanine (position 16), one arginine (position 18) and one leucine (position 22). Then position
the zinc atom in the middle so that it is coordinated by the two histidines and two cysteines.
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