Calculating the theoretical net charge

[researcher87]

I was given this peptide:

GAKKIYPRVSACMIHGGAVIAIDMDGTDA

I then amidated the C-terminal, and i need to figure out how to calculate the theoretical net charge of the amidated peptide.
Can anyone help me please!
I have a feeling it is something to do with the isoelectric point but I'm not sure.
Thanks

 

[chemisttree]

Since you have capped the carboxyl terminus (the amine terminus remains), this question is asking you to determine the charges of the side groups of the peptide. Write down all of the peptides that have ionizable side groups and their pKa's. Determine which ones will be protonated and deprotonated at the pH (which is not given by you in your OP). Ignore ion pairs and count the excess negative or excess positive charges. Don't ignore the amine terminus' pKa (as ammonium ion).

 

[Blueshift5]

Calculating the theoretical net charge of a peptide involves determining the number of positively charged amino acids (such as lysine and arginine) and negatively charged amino acids (such as aspartic acid and glutamic acid) in the sequence and taking into account any modifications, such as amidation of the C-terminal.

To calculate the theoretical net charge of the amidated peptide, you will need to first identify the positively and negatively charged amino acids in the sequence. In this case, the positively charged amino acids are lysine (K) and arginine (R), while the negatively charged amino acids are aspartic acid (D) and glutamic acid (E). You can assign a charge of +1 to lysine and arginine, and -1 to aspartic acid and glutamic acid.

Next, you will need to take into account the amidation of the C-terminal. Amidation involves replacing the carboxyl group (-COOH) with an amide group (-CONH2), resulting in a neutral charge. Therefore, the C-terminal will no longer contribute to the net charge of the peptide.

To calculate the theoretical net charge, you can add up the charges of all the amino acids in the sequence, taking into account the amidation of the C-terminal. In this case, the sequence contains 3 lysine, 1 arginine, 2 aspartic acid, and 1 glutamic acid. Therefore, the net charge would be (+3) + (+1) + (-2) + (-1) = +1.

Alternatively, you can also use a tool such as the online isoelectric point calculator to determine the theoretical net charge of your peptide. This tool takes into account the pKa values of each amino acid and can also consider modifications such as amidation.

In summary, to calculate the theoretical net charge of an amidated peptide, you will need to identify the positively and negatively charged amino acids in the sequence and take into account any modifications. This can be done manually or with the help of online tools. I hope this helps!