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bioRxiv · 10.1101/2024.03.14.585129

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

Oven, H. C.·Yap, G. P. A.·Zondlo, N. J.
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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 exhibited cis-proline and a type VIa2 {beta}-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 {beta} conformation in the other, each with Pro in the {delta} 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{gamma} 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 {beta}-turn. 53% of Ser- trans-Pro sequences exhibited main-chain C=Oi***H-Ni+3 or C=Oi***H-Ni+4 hydrogen bonds, with Ser as the i residue and Pro as the i+1 residue. These structures were overwhelmingly either type I {beta}-turns or N-terminal capping motifs on -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 {beta} conformation, with the Ser O{gamma} capable of engaging in a hydrogen bond with the amide N-H of the i+2 (type I {beta}-turn or 3 -helix; Ser{chi} 1 t) or i+3 (-helix; Ser{chi} 1 g+) residue. Non-proline cis amide bonds can also be stabilized by C-H/O interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/585129v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1b84fdorg.highwire.dtl.DTLVardef@b81090org.highwire.dtl.DTLVardef@47636forg.highwire.dtl.DTLVardef@d12a4d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Table of ContentsC_FLOATNO C_FIG

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Oven, H. C., Yap, G. P. A., Zondlo, N. J.. 2024-03-16. Helical Twists and beta-Turns in Structures at Serine-Proline Sequences: Stabilization of cis-Proline and type VI beta-turns via C-H/O interactions. https://doi.org/10.1101/2024.03.14.585129

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