The pKa values associated with charged amino-acid side chains within proteins ar

Question

The pKa values associated with charged amino-acid side chains within proteins are highly influenced by their local environments. The table to the right shows the percent ionized form for four residues (amino acid and position given) within a fictitious protein at pH 7. From these data, calculate the 'actual' pKa associated with the side chain functional groups for each of the four amino-acids given. If the pKa of a given residue's side chain varies significantly from the value associated with a "free amino acid' (see your text's pKa table), describe the "chemical' characteristics the local environment for that residue that likely induce the change in pKa value.

Explanation / Answer

For the amino acids we woud use Hendersen-Hasselbalck equation,

pH = pKa + log(base/acid)

For,

lys142,

charged species is NH3+ side chain

% charged = 50%

at pH = 7

7 = pKa + log(50/50)

pKa of side chain = 7.0

For,

his195,

charged species is NH+ in the ring

% charged = 10%

at pH = 7

7 = pKa + log(90/10)

pKa of side chain = 6.046

For,

glu259,

charged species is -COO- side chain

% charged = 15%

at pH = 7

7 = pKa + log(15/85)

pKa of side chain = 7.75

For,

glu392,

charged species is -COO- side chain

% charged = 95%

at pH = 7

7 = pKa + log(95/5)

pKa of side chain = 5.721

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