Intrinsic Folding Motifs versus Solvent Effects: Secondary Structures of the Gly-DPro-Ala Tripeptide

Abstract

Folding motifs of the secondary structures of peptides are governed by a delicate balance between amino acid sequence, conformational preferences of the residues, and solvent effects. Herein, we examine the conformational behavior of a capped tripeptide Boc-Gly-DPro-Ala-NHBn-OMe (GDPA), a minimal model system relevant to collagen-related sequence motifs. A combined experimental and computational approach involving gas phase laser spectroscopy, DFT calculations, solution phase NMR, circular dichroism spectroscopy, and single-crystal X-ray diffraction was employed to probe its structure in the isolated and condensed phases. Gas phase infrared spectroscopy supported by quantum chemical calculations reveals that the isolated GDPA molecule adopts a C5 structure, a representative of an extended β-strand, combined with a double γ-turn backbone. In contrast, both solution phase spectroscopy and the crystal structure show that GDPA forms a compact folded loop stabilized by a β-turn located at the DPro-Ala segment and defined by a C10 hydrogen bond. The results demonstrate that the intrinsic folding preference of the peptide observed in the gas phase differs from the structure stabilized in condensed phases, highlighting the role of solvent and intermolecular interactions in modulating peptide secondary structure. These findings provide molecular-level insight into how sequence context and environmental effects together govern folding motifs in short Gly-Pro containing peptides.