The pKa values associated with charged aminoacid side chains

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.

Solution

The pKa value associated with charge amino acid side chains within proteins are highly influenced by their local environments. In this table given four charge amino acide- lysine, histidine,2 glutamic acid, all four amino acid are located near active site of protein. All charge is given At pH 7 there is two amino acid (lysine or histidine) is basic positive charge and lysine have long side chain, so pKa value of lysine side chain is must be high

Because of terminal NH3-group at long side chin of lysine is positive charged and pKa value of side chain is near 10.9(10.79) at ph 7, and Lys142 located near the active side, and reactive carboxyl-terminal make the bound with other local endowmental protein through side chain of charge amino acid, so that table showing 50% charge on Lys142, remaining charge group are associated with local environment amino acid

Second basic amino acid is also have very less positive charge at side chain of histidine, His195 because of aromatic ring structure and the isoelectric point of His is near 7, and His195 located nearly active site of functional protein local environment amino acid alter the pKa value of his195 by interacting with side chain of histidine and the pKa value of side chain histidine is pKa=6.03 that’s why in table it’s showing very less 10% free charge group percentage at ph 7,

Glutamic acid are negatively charge acidic amino acid and pKa value of Glu is 4.25 at pH 7, but in table showing two different charge on Glu, it’s happening because of reactive amino acid in local environment, first Glu259 have only 15% charge, the reason is this Glu259 may located near the active side and side chine of Glu259 interacted with other protein side chine of reactive amino acid in local environment, so there are very less free charge on Glu259, that’s way it’s showing 15% charge on Glu259,

Another Glu392 are showing 95% free charge, because this amino acid located away from the active side of protein due to difference in amino acid number(glu392) and side chain of Glu392 not interactive with other amino acid side chain in local environmental protein, that’s way Glu392 showing 95% free charge, and pKa value also differ from the Glu259 and pKa value more than 4.25 because of free charge group

Chemical characteristics of the local environment amino acid residues, and this residues are may be polar or non-polar, if they are polar and have hydroxyl group on side chain than they may act on our amino acid residue, and change pKa value of charge amino acid, and

They may interact with our protein through carboxyl ©- terminal or may NH3 amino terminal to change in pKa value, according to table lys142,glu259glu392,his195 is highly influence by local environment, that’s way fluctuation in % of charged.