Helical Twists and ß-Turns in Structures at Serine–Proline Sequences: Stabilization of cis-Proline and type VI ß-turns via C–H/O interactions

Structures at serine-proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2 S ,4 S )-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)]. The crystal structure of Boc-Ser-hyp(4-I-Ph)-OMe had two molecules in the unit cell. One molecule exhibited cis -proline and a type VIa2 β-turn (BcisD). The cis -proline conformation was stabilized by a C–H/O interaction between Pro C–H and the Ser side-chain oxygen. NMR data were consistent with stabilization of cis -proline by a C–H/O interaction in solution. The other crystallographically observed molecule had trans -Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac-Ser-hyp(4-I-Ph)-OMe, with Ser adopting PPII in one and the β conformation in the other, each with Pro in the δ conformation and trans -Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser–Pro versus Ala-Pro sequences were compared to identify bases for Ser stabilization of local structures. C–H/O interactions between the Ser side-chain O and Pro C–H were observed in 45% of structures with Ser- cis -Pro in the PDB, with nearly all Ser- cis -Pro structures adopting a type VI β-turn. 53% of Ser- trans -Pro sequences exhibited main-chain C=O •••H–N or C=O •••H–N hydrogen bonds, with Ser as the i residue and Pro as the i +1 residue. These structures were overwhelmingly either type I β-turns or N-terminal capping motifs on α-helices or a 3 -helices. These results indicate that Ser-Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or β conformation, with the Ser O capable of engaging in a hydrogen bond with the amide N–H of the i +2 (type I β-turn or 3 -helix; Ser χ t ) or i +3 (α-helix; Ser χ g ) residue. Non-proline cis amide bonds can also be stabilized by C–H/O interactions.