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MCB124_PROBLEM_SET3B - 3 This protein binds...

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MCB 124 Protein Stability Enoch Baldwin PROBLEM SET IIIB page 1 Electrostatics Question: An enzyme binds peptide substrates. This protein has a carboxylate residue, Glu238. The pKa of this residue in the absence of substrate by NMR is 6.5. The pKa in the unfolded form is 4.8. a) How does the ionization of this residue contribute to protein stability? ______favorably OR ______unfavorably. b) If the pH dependence of folding was only determined by this residue, what would happen to the protein Tm at pH 7 compared to pH 4.0 ? c) Why? d). If this residue were mutated to a Gln residue, what would you estimate the change in protein stability to be, in kcal/mol at pH 7.8?
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Unformatted text preview: 3. This protein binds lysine-containing peptides. The pKa of Glu238 is decreased to 3.5 if the protein is saturated with substrate. a) Why does the pKa change in this way? b) What would happen to the T m of the enzyme in the presence of substrate? c) Why ? d) Compare ± H f of the free enzyme and enzyme-peptide complex? e) Why the difference? f) What is the electrostatic contribution to binding free energy of the substrate? (Hint, think LINKAGE!) g) If ALL of the binding energy was electrostatic, what would the stability difference be, quantitatively , between bound and free forms of the enzyme at pH 7.8? h) Where is Glu238 located and what does it do?...
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