Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function

Abstract

Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.

Figure 1.

Examples of (A) α-helices, (B) β-sheets (C) helix dimers, and (D) irregular loops at protein-protein interaction interfaces. PDB codes: (A) 1BXL (Bcl-xL/Bak); (B) 1F3U (Rap30/Rap74); (C) 3CL3 (vFLIP/IKKγ); (D) 1NPO (Bovine neurophysin II/oxytocin)

Figure 2.

Interfacial α-helices may use one, two or all three faces to recognize partner proteins. Examples of each molecular recognition category are depicted. (PDB entries 1xl3, 1xiu, and 1or7).

Figure 3.

Stabilized helices and non-natural helix mimetics.

Figure 4.

Peptide stapling techniques for -helix stabilization with i to i+3, i+4, i+7 and i+11 linkers. Linkers that include disulfide, thioether, lactam, triazole and olefin bonds have been included into peptides.

Figure 5.. Three Classes of β-Sheet/β-hairpin Peptide Mimics for Molecular Recognition.

(A) Molecules in the top left have planar functional groups that position backbone amide hydrogen bond donors and acceptors in a β-strand arrangement. This β-strand mimic templates folding of a second segment of the peptide into another β-strand for molecular recognition. (B) Molecules on the right have either non-covalent or covalent side chain interactions between β-strands on one face to reinforce β-sheet hydrogen bonding, leaving a single face free for molecular recognition. (C) Molecules on the bottom left have functional groups that stabilize β-sheet formation independent of any amino acid side chains. This approach allows both β-sheet faces to participate in molecular recognition. A model β-hairpin structure is shown in the center.

Figure 6.

(A) Antiparallel and Parallel helix dimers. (B) Helical wheel representation of a parallel helix dimer. Positions a and d comprise the hydrophobic core and are represented by yellow spheres. The polar positions of the helical wheel are represented by blue spheres.

Figure 7.

(a) Helical wheel diagram of parallel dimer CHD-4 with the bis-triazole linkage. (b) CD spectra of parallel and antiparallel CHD dimers in 50 mM aqueous KF, pH 7.4. (c, d) Overlay of the 20 lowest conformations derived from parallel dimer NMR analysis and the lowest energy structure.

Figure 8.. Stabilizing Non-Regular Conformations for Molecular Recognition.

Peptide macrocyclization via lactam, thioether, and disulfide bonds stabilize non-regular peptide conformations in many natural product and synthetic peptides. Lactam bridges can be derived from the N- and C-termini, the N- or C-terminus and one side chain, or two side chains (e.g., Lys and Glu). Thioether bridges are formed from Cys residues, including linkage to an N-terminal acetyl group or electrophilic crosslinkers. Disulfide bonds are observed strictly between Cys residues. Other crosslinking chemistries include triazole, lactone, alkyne, biaryl, and unusual side chain crosslinks discovered in natural products.