Question

1. Draw the peptide DCTEVKKR at a ph 7.4 in the trans configuration.

2. Consider the peptide from #1 for the questions below.  

Calculate the pI of the above peptide. (I recommend showing your work – you can attach it on a separate sheet of paper or insert pictures).

3. Based on it’s sequence of amino acids and the answer to (2) above, suggest a possible function for the peptide.

4.What interactions would contribute most to tertiary structure? Explain your choice.

5.If a neutral mutation occurred, what do you think the peptide might be changed to? Explain your choice. (Multiple correct answers are possible).

Answer 1

Ans. #1. The –NH₂ group at N-terminal and basic residue (K, R) predominantly occurs as –NH₃⁺ at pH 7.4.

# The –COOH group of C-terminal and acidic residue (E, D) predominantly occurs as –COO^- bearing 1.0 unit negative charge.

# The side chain of remaining residues remains neutral.

#2. Calculating the pH from given net charge or for determining the pI can NOT be done with ease. The only affordable method is to use “Hit & Trial Method” – calculate the net charge on different pH to get the specified charge. Excel calculations. A sample calculation for charge calculation is shown at the bottom of the page.

Result: pI of the given peptide (DCTEVKKR) = 9.96

#3. The peptide has five ionizable side groups (D, E, K, K, R), all of which are in ionizable state at physiological pH. The –COO^- groups of acidic residues may act as proton acceptor. The –NH₃⁺ groups of basic residues may act as proton acceptor. By doing so, the peptide may facilitate acid-base catalysis. Moreover, the ionic groups of peptide may also stabilize the intermediate (say, forming ES complex) through ionic interactions. The O-atoms of –COO^- group on acid residues and N, and N-linked H-atoms of basic residues may also form hydrogen bond with the substrate to optimize substrate binding at the active site.

#4. Hydrogen bonds and ionic interactions exhibited by the acidic and basic residues of the peptide may contribute the stabilization of the tertiary structure (interaction between two or more peptide chains).