in large proteins only 15% of the amino acid side chains are buried( i.e inacces
ID: 23432 • Letter: I
Question
in large proteins only 15% of the amino acid side chains are buried( i.e inaccessible to solvant) tweleve proteins were studied and the proportions of each amino aicd that was buried within the protein was noted see table
amino acid side chain proportion buried
I 0.60
V0.54
C0.50
F 0.50
L 0.45
M0.40
A0.38
G0.36
W 0.27
T 0.23
S 0.22
E 0.18
P 0.18
H 0.17
D 0.15
Y 0.15
N 0.12
Q 0.07
K 0.03
R 0.01
examine the top sevan amino acids on the list what class of the amino acid is most commonly buried?
are there any amino aicds in the top seven on the list that do not fit your expectations ( ie do not belong to this class) expalin
Explanation / Answer
Of the top 7, all are neutrally charged and no polar except for Cysteine. Cysteine has a neutrally changed slightly polar side chain. I guess that Cysteine would be the one that didn't belong because it is slightly polar, but we need to remember that it can participate in disulfide binding with other cysteines in the peptide chain, so maybe that is why a higher amount of cysteine is buried than we might expect. Alternatively, I might think about phenylalanine as the one that doesn't belong with the others. It has a phenyl group in its side chain (meaning that it is large). So it seems like it might be a little big to be buried.
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