The Problem
A proteins net charge depends on the number of
charged amino acids it contains and the pH of its
environment.
The isoelectric point is the pH at which the net
charge is zero.
Each amino acid has a different dissociation
constant, KD.
The amino acids that can be ionized at
physiological pHs are: aspartate (D),
glutamate (E), lysine (K), arginine (R), and
histidine (H).
Also, the N and C termini can be ionized.
The important point is: most of these amino
acids are not fully ionized or fully unionized at
physiological pHs.
It is your job to calculate the proportion of
each amino acid that is ionized at a given pH.
Once this is done, calculating the net charge is
straightforward.
Multiply the proportion by the number of that
amino acid, taking into account the differences
between acidic (-COOH) and basic (-NH2) types.
Amino Acids Contributing to Charge
Charged amino acids come in two forms:
Acidic amino acids (and the C-terminal) are in the COOH form (uncharged)
at low pH and in the COO- form (-1 charge) at high pHs.
These include aspartic acid (D) and glutamic acid (E)
Basic amino acids (and the N-terminal) are in the NH3+ form (+1 charge)
at low pH and in the NH2 form (uncharged) at high pH.
These include lysine (K), arginine (R) and histidine (H).
All other amino acids do not affect charge under physiological conditions.
Dissociation Constant
The association and dissociation of the H+ with the amino acid
is governed by its dissociation constant, KD.
Dissociation constant is the ratio of the concentration of the
dissociated forms to the concentration of the combined form.
Each amino acid has a separate dissociation constant.
The equation below uses [R-] to indicate the concentration of the
amino acid when the H+ is dissociated from it.
The pK value is analogous to pH.
pK = -log10KD
KD = 10-pK
[ H ][ R ]
KD
[ RH ]
Calculating the We rearrange to get:
[ H ][ R ]
[ RH ]
Proportion with H KD