Proline C−H Bonds as Loci for Proline Assembly via C−H/O Interactions

Abstract

Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized CÀ H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. CÀ H/O interactions, between proline CÀ H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular CÀ H/O interactions in the crystallographic state, with H•••O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of CÀ H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular CÀ H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular CÀ H/O interactions at proline CÀ H bonds, suggesting that CÀ H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized CÀ H bonds, proline residues are uniquely positioned as sites for binding and recognition via CÀ H/O interactions.

4,4-Difluoroproline as a Unique 19F NMR Probe of Proline Conformation

“…Interestingly, the difluoroproline carbonyl exhibited a close C–H/O interaction ,− with chloroform (H···O distance 2.25 Å) (Figure b), as well as a C–H/O interaction (2.60 Å) between one ProHβ and the carbamate carbonyl (Figure d). These observations are consistent with our recent report that C–H/O interactions are a general mode for structure stabilization and molecular assembly at proline residues …”

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

“…C-H/O interactions are inherently favorable at the polarized C-H bonds of proline. 17 We observed that C-H/O interactions can stabilize all type VI β-turn subtypes.…”

“…In order to examine Ser– Pro structures via small-molecule X-ray crystallography, we synthesized dipeptides with the unnatural proline derivative (2 S ,4 S )-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)] (Scheme 1). 17,29,30 This amino acid promotes crystallization via the aryl iodide. The aryl iodide has also been employed for further amino acid modification via Suzuki or Sonogashira cross-coupling reactions, which can be conducted on peptides in water.…”

“…Pro exhibited an exo ring pucker, consistent with the relatively modest endo/exo ring pucker preference of aryloxy groups. 17,30…”

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