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

Abstract

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 (2S,4S)-(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 exhibitedcis-proline and a type VIa2 β-turn (BcisD). Thecis-proline conformation was stabilized by a C–H/O interaction between Pro C–Hαand the Ser side-chain oxygen. NMR data were consistent with stabilization ofcis-proline by a C–H/O interaction in solution. The other crystallographically observed molecule hadtrans-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 andtrans-Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser–ProversusAla-Pro sequences were compared to identify bases for Ser stabilization of local structures. C–H/O interactions between the Ser side-chain Oγand Pro C–Hαwere 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=Oi•••H–Ni+3or C=Oi•••H–Ni+4hydrogen bonds, with Ser as theiresidue and Pro as thei+1 residue. These structures were overwhelmingly either type I β-turns or N-terminal capping motifs on α-helices or a 310-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 Oγcapable of engaging in a hydrogen bond with the amide N–H of thei+2 (type I β-turn or 3 -helix; Serχ1t) ori+3 (α-helix; Serχ1g+) residue. Non-prolinecisamide bonds can also be stabilized by C–H/O interactions.Abstract FigureGraphical Table of Contents