Arginine ionizing groups

Some amino acids have additional ionizable groups in their side-chains. These may be acidic or potentially acidic (aspartic acid, glutamic acid, tyrosine, cysteine), or basic (lysine, arginine, histidine). We use the term potentially acidic to describe the phenol and thiol groups of tyrosine and cysteine respectively under physiological conditions, these groups are unlikely to be ionized. It is relatively easy to calculate the amount of ionization at a particular pH, and to justify that latter statement. 

When the R group contains another ionizable group, the amino acid will have more than two dissociation constants. The carboxylic acid gronps of aspartic acid and glutamic acid, the amine of lysine, and the guanidino group of arginine will all... 

Titration curve of /3-lactoglobulin. At very low values of pH (<2) all ionizable groups are protonated. At a pH of about 7.2 (indicated by horizontal bar) 51 groups (mostly the glutamic and aspartic amino acids and some of the histidines) have lost their protons. At pH 12 most of the remaining ionizable groups (mostly lysine and arginine amino acids and some histidines) have lost their protons as well. 

Equation (7.62) applies to any species having two ionizing groups. If there are more, as with certain other amino acids or the proteins, the situation is usually not much more complicated, since two ionizations commonly dominate the situation. Consider, for example, the case of arginine, for which the ionizations are... 

The interactions of the amino acid derivatives with a modified C18 column and micellar mobile phases of the anionic SDS are mainly of hydrophobic and electrostatic nature. The basic structure of the amino acid isoindoles is the same. Consequently, in the absence of electrostatic interactions, the hydrophobic character of the Rj substituent should be responsible of the retention. The nitrogen atom in the isoindole heterocycle is nonprotonated at pH 3, and thus, electrostatic interactions can only exist with ionizable groups giving a positive charge to R in the molecule. This occurs with arginine and histidine, which have amino groups that do not react with OPA. 

Similar calculations as above for the basic side-chain groups of arginine pK 12.48) and lysine pK 10.52), and the acidic side-chains of aspartic acid (pATa 3.65) and glutamic acid (pAfa 4.25) show essentially complete ionization at pH 7.0. However, for cysteine (pATa of the thiol group 10.29) and for tyrosine (pAfa of the phenol group 10.06) there will be negligible ionization at pH 7.0. 

We have shown the cysteine thiol group as uncharged. The pAfa for this group in cysteine is about 10.3, and application of the Henderson-Hasselbach equation (see Section 4.9) indicates there will be negligible ionization at pH 7. Nevertheless, under the influence of a suitable basic group, e.g. arginine pATa 12.5, ionization to thiolate may be possible. In such an environment, thiolate may act as the nucleophile in the mechanism. 

An additional point should be noted from table 3.3. Whereas the amino acid side chains (R groups) that are normally charged at physiological pH are restricted to five amino acids (aspartic acid, glutamic acid, lysine, arginine, and sometimes histidine), a number of potentially ionizable R groups are part of other amino acids. These include cysteine, serine, threonine, and tyrosine. The ionization reac-... 

The carboxyl group occupies a prominent place in protein structure and function and is commonly taken to be ionized as a carboxylate, particularly when paired in a salt bridge with a Whereas this may be the case in a protein environment, it is not obvious that a —COOH group will donate its proton to a base to form an ion pair in the gas phase. For example, SCF calculations with a polarized 6-31G basis set indicate that neither methy-lamine nor an arginine model is able to extract a proton from acetic acid so as to form an ion pair. On the other hand, there is some indication that correlation might stabilize the ion pair for formic acid -f methylamine. ... 

Seven of the 20 amino acids have readily ionizable side chains. These 7 amino acids are able to donate or accept protons to facilitate reactions as well as to form ionic bonds. Table 3.1 gives equilibria and typical pi( values for ionization of the side chains of tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids in proteins. Two other groups in proteins—the terminal a-amino group and the terminal a- carboxyl group—can be ionized, and typical pi( ... 

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