Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments

Abstract

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.

Investigating diproline segments in proteins: Occurrences, conformation and classification

“…55 The first example occurs unexpectedly in the trans-cis category in the protein (Histone-Lysine N-methyltransferase, PDB ID: 2F69 A) with proline occurring at positions 341 and 342 of the amino acid sequence. Proline at position 342 has been inserted by molecular modeling methods and hence the cis peptide bond may be an outcome of this procedure.…”

Synthesis of Cyclic Peptides and Peptidomimetics by Metathesis Reactions

“…α-Helix-nucleating scaffolds are rather difficult to design; however, protein helices often contain proline residues especially in the N-cap region, e.g., at the N-terminus of the protein sequence. The Pro-Pro dipeptide segment forms a partial helical structure by two intramolecular hydrogen bonds [71] and might be used to nucleate helical folding [72,73]. Based on Kemp's Pro-Pro derivative designed to function as an α-helix-inducing N-cap motif [74,75], the groups of Kühne and Schmalz [41] designed a tricyclic diproline scaffold 48 for efficient α-helix induction in a linear peptide, as shown in Scheme 10.…”

Conformationally Constrained Peptides from CD2 To Modulate Protein–Protein Interactions between CD2 and CD58

“…The amide resonances of the peptide were spread over a range of 1.3 ppm, suggesting the well-defined structure of the peptide in solution 35 . The NOESY and ROESY spectra of peptide 6 showed sequential connectivities between C α H (i)-NH (i+1) residues as well as long-range connectivities, which are indicative of a β-strand type of structure of the peptide 40 . NOE connectivities in the NH-CαH and NH-NH region, a schematic diagram indicating the long-range NOE connectivities between NH-CαH and NH-NH are shown in Figure 6A–C.…”