Calculation of Net Charge of a protein at a given pH
(Using the HendersonHasselbalch equation)
pH = pK
a
+ log [A

]
[HA]
Solve for D (pK = 4.5) at a pH 4.9
4.9 =4.5 + log [A]/[HA]
10
4.94.5
=log [A

]/[HA]
10
0.4
= [A

]/[HA]
2.512=[A

]/[HA]
remember that this a ratio over 1. The easiest way to calculate this is use “parts”
of the total solution :
[A

] has 2.512 “parts”
[HA] has 1 “part”
The total “parts” is 3.512
Calculate the concentration of the charged elements as a percentage of the total
:
average charged (A

) = 2.512/3.512 = 0.71
Remember that your base equation is going to look a little different:
pH=pKa + log [B]/[BH
+
]
Solve in the same way, finding “parts’ for [BH
+
]
To calculate pI
To calculate the net charge of a protein at a given pH
1. List ionizable residues
2. Make assumptions: If pKa ≤ 2 units away from pH, charge can be
assigned (as 1, 0, 1) without calculation.
3.
Use HH equation to calculate % ionization (Remember difference
between H
+
acceptor and donator)
4.
Multiply charge (z
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 Fall '08
 ANDREWFISHER
 Physical chemistry, pH, Pk, Charge, Average Charge

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