EK FL 1: pKa and Protein Stability

[mcatjelly]

"Which of the following residues if replaced with a neutral leucine residue would cause the protein to become the most stable?

a) D12
b) D48
c) E6
d) E47

Explanation: The passage states that the change in pKa closely reflects the change in G between the unfolded and unfolded protein states. Therefore, the residue with the largest change in pKa in the positive direction will destabilize the protein the most."

Graph is attached. I got this question correct just based on "one of these things is not like the others" reasoning, but I'm not sure why it's correct. Is is because the higher pKa = weaker acid = stronger conjugate base upon deprotonation?

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[carpediem22]

The graph is showing change in pKa between the unfolded (i.e. free amino acids) and folded protein states of the residues. We know that change in pKa between folded and unfolded mimics change in G between folded and unfolded. Since the change in pKa of E6 is positive (pKa folded - pkA unfolded = + number), this means that G must be higher in the folded state of the protein than the unfolded state of the protein (G folded - G unfolded = + number). G is a measure of stability, with lower G equating to greater stability. Thus, higher pKa in folded state --> higher G in folded state --> less stable protein . Replacing this residue with the hydrophobic, neutral lysine would therefore stabilize the protein because of the hydrophobic effect.

Hope that helps. The reasons why change in pKa of the amino acid mimics change in G/contribution to protein stability is beyond the scope of the question. I too got confused by this question so I did some extra journal reading, and it seems as though the pKa increases in folded proteins for certain acidic residues (depending on where they are) because when the -COOH group is buried within the hydrophobic core, dissociating into ionic form is less favorable because there are fewer (+) charges to stabilize the -COO anion. Hence why pKa increases. At least this is my understanding of what I read, could be wrong!

 

[mcatjelly]

Brilliant, thank you so much!!

 

[drechie]

did anyone understand the very first question of the phys/chem. about mass ratio and current of a phosphate buffered solution