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
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 (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 α 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 γ and Pro C–H α
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
i•••H–N i
+3 or C=O i•••H–N
i +4 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 10-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 γ capable of engaging in a hydrogen bond with
the amide N–H of the i+2 (type I β-turn or 3
10-helix; Ser χ 1 t) or
i+3 (α-helix; Ser χ 1
g+) residue. Non-proline cis amide bonds
can also be stabilized by C–H/O interactions.
