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Peptide sequencing help!! his-pro-trp-asp-lys ?
I have to draw [his-pro-trp-asp-lys] pentapeptide at ph of 1-- in its predominant form... I am having problems drawing the proline link because it has to connect to the N of the previous peptide bond... I am also having problems determining the charges of the amino and carboxyl ends... I think that because the solution is acidic (ph1) that the amino terminus attached to (his) will be charged (Nh3+) and the carboxyl terminus will NOT be deprotinated and will be COOH instead of COOH- ...
also: do you have to consider charges other than the terminal ends?
Re: Peptide sequencing help!! his-pro-trp-asp-lys ?
1) His [(+2 charge) Alpha amino as well as side chain imidazole is protonated at pH 1 while alpha COOH don't exist in because of the peptide bonds with Pro ]
2) Pro [ (0 Charge) Both NH and COOH groups in proline don't exist in because of the peptide bonds with His and Trp].
3)Trp [(0 Charge) Both NH2 and COOH groups in Trp don't exist in because of the peptide bonds with Pro and Asp]
4) Asp [ ( 0 Charge ) Both NH2 and COOH groups in Asp don't exist in because of the peptide bonds with Trp and Lys]
5) Lys [ ( +1 Charge) alpha NH2 agroups in Lys don't exist in because of the peptide bonds with Asp , While alpha COOH is free but it having charge 0 at pH 1 While NH2 of side chain of lysine is protonated and exit +1 charge at pH 1]
So Net charge on Peptide NH2 -his-pro-trp-asp-lys-COOH is
His(+2) + Pro(0) + Trp (0) + Asp (0) + Lys (+1) = +3
|hisprotrpasplys , peptide , sequencing|
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