Question

1. The following amino acid sequence is observed in an alpha-helical segment of a polypeptide:

L D E N I K R N A Q L V E Q Q I R

What pattern, if any, seems to characterize this sequence? Explain why this pattern might be occurring in terms of the 3D structure of the protein.

2. Indicate the probable location of the following amino acid residues in a native globular protein.

a) Asp

b) Phe

c) Met

d) Asn

e) Leu

f) Arg

Answer 1

The amino acids are a mixture of hydrophobic and hydrophilic types. The hydrophilic ones remain on the outside while the hydrophobic ones remain inside. Generally the negativity charged residues like aspartate glutamate stabilize the alpha helices than positively charged residues. There are no glycine proline present because they are helix breakers. Glycine has a very small backbone and proline has no free NH₂ groups. Leucine and phenylalanine being hydrophobic amino acids remain on the inside hydrophobic core while the others being polar remain on the outside and can interact with the polar solvents.