Biochemistry and Molecular Biology Education
Synthetic peptides are valuable models for studying intramolecular (protein folding) as well as intermolecular (protein-protein recognition) interactions. These peptide models have the advantage of being smaller than proteins and thus are more amenable to study by techniques such as nuclear magnetic resonance spectroscopy. One of the most common secondary structural motifs in proteins is the β-hairpin. The characteristic structural element of a β-hairpin is the sharp turn (i.e. hairpin turns) that leads to the formation of an anti-parallel β-sheet. Various interactions, such as hydrogen bonding, van der Waals interactions, solvent structure, and the hydrophobic effect, contribute to the stability of this type of structural element. Recent studies have examined the key structural factors that govern the thermodynamic stability of synthetic peptides containing β-hairpin motifs. In separate studies, the structure and stability of a 16-residue  and 24-residue peptide  were examined. Some results from these studies are presented in Figs. 1 and 2 and Table I. This problem focuses on the smaller 16-residue peptide. After analyzing the data, answer Questions 1–4 regarding the various interactions that affect the thermodynamic stability of the β-hairpin.
FIGURE 1. Structure of the 16-residue and 24-residue β-hairpin. a, cartoon of the β-hairpin backbone illustrating the position of H-bonds between C=O…H-N groups of the backbone. b, structure of the 24-residue hairpin based on nuclear magnetic resonance data. The 16-residue peptide that was synthesized is shown within the dotted box. Highlighted are some nonpolar amino acids that are oriented above the β-sheet in the peptides [1, 2].
FIGURE 2. Possible mechanism for the folding of a β-hairpin. The left side shows the open unfolded conformation; the right side shows the folded β-sheet structure .
- Based on Figs. 1 and 2, what interactions play a role in the folding of a β-hairpin? How might these interactions contribute to ΔH for the folding process?
- Based on Figs. 1 and 2, what factors contribute to ΔS for the folding process? Predict the overall ΔS of folding of a β-hairpin peptide in water. Does your prediction agree with the experimentally measured ΔS for the peptide folding in water as shown in Table I?
- Rationalize the change in ΔH and ΔS for the folding of the peptide in water versus aqueous (20 and 50%) methanol.
- Calculate the overall free energy change for the folding of this peptide in water versus 50% methanol. Is the folded peptide more or less stable in 50% methanol?
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