Charge on Proteins

The charge on proteins arises from some of the amino acid side chains, as well as the carboxy- and amino-termini, some prosthetic groups and bound ions. This application is designed to calculate charge based only on the side chains and carboxy - and amino-termini.

The charge on amino acid side chains depends on the pH of the solution and the pKA of the side chains. It is also affected by the localized environment around a side chain. We assume the following pKA values for ionizable groups on the protein and that the side chains will have these pKA values regardless of their environment within the protein. We also assume that the separation is based on the total charge on the protein, not the mass-to-charge ratios. Therefore, a protein with a charge of +15 will bind more tightly to a cation exchange stationary phase (CM-Sephadex, for example) than a protein with a charge of +10, regardless of size.

Group pKA
Acids
Carboxy-terminus 3.1
Aspartate 4.4
Glutamate 4.4
Cysteine 8.5
Tyrosine 10.0
Bases
Amino-terminus 8.0
Lysine 10.0
Arginine 12.0
Histidine 6.5

The charge on these proteins can be calculated using the method described in Relationship of Charge to pH. In brief, when the pH is less than the pKA of a group, the protonated form of the group predominates. This leaves the acidic side chains with a charge approaching 0 and the basic side chains with a charge approaching a limiting value of +1. Conversely, when the pH is greater than the pKA of a group, the deprotonated form predominates, giving acidic side chains a charge approaching -1 and basic side chains a charge approaching 0.

The charge on the protein is the sum of the charges on the individual amino acid side chains. However, the charge on individual amino acid side chains can vary when they are near a group of non-polar or highly charged side chains. For example the normal pKA for glutamic acid is about 4.3. In lysozyme, two glutamic acid residues are in the active site. One is in a polar environment and has a normal pKA value. The other glutamate side chain is in a hydrophobic environment, where a negative charge is energetically unfavorable. Therefore the pKA value for this glutamate side chain increases, which then decreases the extent of the deprotonation of that side chain. This is very important in the mechanism of lysozyme, which requires that one of the side chains be charged (deprotonated) and the other be uncharged (protonated) at the same time.

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