Helix Wheel Question Biochemistry 1. The helical wheel diagram is a representati

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Helix Wheel Question Biochemistry

1. The helical wheel diagram is a representation of an alpha helix oriented as if you were looking up from the bottom of the helix. Based upon your knowledge of amino acid side chains, the helical wheel model above, and a 3D model. Indicate below the amino acids on the half of the helix that would face the INSIDE of a globular protein. The answer will include a total of 8 amino acids.

Ser1

Glu2

Ile3

Trp4

Tyr5

Ser6

Ser7

Val8

His9

Leu10

Asn11

Lys12

Thr13

Ala14

Phe15

Gln16

2. Are there any amino acids that look out of place on the indicated side? If so, what are they and how might hey be accommodated on the inside of the globular protein?

3. The alpha helix is part of a signing protein that is regulated by post-translation modifications (or PTMs). Kinase proteins are enzymes that phosphorylate a specific substrate. In this case, a kinase phosphorylates all exposed serine, threonine, tyrosine residues on our protein. Which amino acids would you expect to find this PTM on the helix above?

S1

E2

I3

W4

Y5

S6

S7

V8

H9

L10

N11

K12

T13

A14

F15

Q16

4. When these PTMs occur in the alpha helix shown above, the helix denatures into flexible loop and causes the protein to stop propagating its cellular signal. Explain briefly chemically why this happens.

Explanation / Answer

1. The amino acids which would face inside the globular protein are those which have hydrophobic side chains. The amino acids included will be Trp4, Ile3, Phe15, Leu10, Tyr5, Val8, Ala14.

2. Yes, there are two amino acids which are hydrophobic i.e. need to be inside but are indicated as hydrophillic in helical wheel (placed in circle shape). These are Val8 and Ala14. These two have aliphatic side chains can have hydrophobic interactions inside the globular protein.

3. Phosphorylation will occur on all the serine and threonine i.e on S1, S6, S7, T13 but not on tyrosine i.e. Y5 because as per helix wheel it is considered hydrophobic (placed in diamond shape) and hence has to be inside. So, it will not be exposed and hence will not undergo PTM.

4. When PTMs occur in above alpha helix, the denaturation occurs because phosphorylation of hydroxyl group of Serine and threonine residues prevent those hydrogen bonds which were formed between the hydroxyl of these residues and polar groups of other amino acids. The denaturing of this helix causes the modification in the structure of whole of the protein and hence affects its function.

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