Biochem 101: Structural and Physical Biochemistry

DESIRED RESPONSES

Figs. 1 and 2 illustrate that H-bonding between the backbone carbonyl oxygens and amide hydrogens and van der Waals interactions between the side chains are important stabilizing forces in the folded peptide. In fact, the primary structure of the peptide was designed to promote van der Waals interactions between side chains in the folded peptide [1]. Similar to other bond-forming processes, the formation of these interactions will be exothermic. Thus, in proceeding from the unfolded to the folded state, these interactions result in a negative contribution to the total enthalpy change. (Many students were satisfied to end the discussion here. It was helpful to point out that the data in Table I indicates that the enthalpy of folding for the peptide is positive (endothermic) and remind them that the process is occurring in water.) However, these factors alone cannot account for the total enthalpy change upon folding. Solvation of the unfolded peptide involves: 1) hydrogen bonding between water and the backbone carbonyls and amides and 2) extensive H-bond networks of water in the form of clathrate structures around the hydrophobic side chains. In proceeding from the unfolded to the folded state, these interactions will be disrupted, resulting in a positive contribution to the total enthalpy change. The overall enthalpy change is small and positive, indicating the latter contributions are slightly dominant, which is often the case when folding is driven by the hydrophobic effect [1].

As with Question 1, the obvious answers will come directly from the figures, while the effect of solvent will be less obvious but no less important. The folding process leads to a more ordered state for the peptide and is expected to result in a negative contribution to entropy. This increased order includes the side chains, which are expected to lose some freedom of movement when stacked together above the β-sheet. (Students were tempted to stop the discussion after these more obvious conclusions. Point out, however, that in this case their prediction of the overall entropy change as negative does not agree with the decidedly positive entropy change determined experimentally. If students have trouble reconciling the discrepancy, remind them again that this process is occurring in water.) In the unfolded peptide, water forms clathrate structures around nonpolar amino acid chains. The clathrate is a highly ordered solvent structure. Sequestering of the nonpolar amino acids in the folded peptide disrupts the clathrate structure, leading to less ordered solvent and a positive contribution to the total entropy term. This is the basis for the hydrophobic effect and, from the data (seeTable I), is the primary driving force for peptide folding in this system [1].

As the concentration of methanol increases, the enthalpy and entropy become more negative. So the folding process is increasingly driven by enthalpy and less by entropy effects. Methanol is less polar than water and can effectively interact with nonpolar side chains through van der Waals interactions. In other words, the addition of methanol prevents clathrate formation. Now the major contribution to the total entropy is from the conformational entropy of the folded peptide chain that, as pointed out in Question 2, is negative [1]. Enthalpy becomes increasingly negative because the extensive H-bond networks in the clathrate are replaced by weaker van der Waals interactions between methanol and the nonpolar side chains in the unfolded peptide. Because the formation of H-bonds (negative) in the folded peptide is no longer balanced by the disruption of clathrate H-bonds (positive) in the unfolded state, the net enthalpy term is exothermic (negative). Furthermore, nonpolar solvents have lower ionic strength than pure water and are not effective at shielding the partial negative and positive charges on the backbone carbonyls and amides in the unfolded peptide. Therefore, as methanol concentration increases, and the ionic strength of the solvent decreases, electrostatic interactions between backbone carbonyls and amides (formation of H-bonds) become more favorable [1].

ΔGfolding in water = 0.35 kJ/mol. ΔGfolding in 50% methanol = –35 kJ/mol. The free energy for the process at constant pressure can be calculated from the relationship, ΔG = ΔHTΔS at 298 K. According to Maynard et al., the peptide is 50% folded in water, and the calculated ΔG for folding in water is consistent with that claim [1]. ΔG of folding in 50% methanol is –35 kJ/mol, and thus the peptide is more stable in methanol.

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