Evidence of an Unusual N–H···N Hydrogen Bond in Proteins

Abstract

Many residues within proteins adopt conformations that appear to be stabilized by interactions between an amide N–H and the amide N of the previous residue. To explore whether these interactions constitute hydrogen bonds, we characterized the IR stretching frequencies of deuterated variants of proline and the corresponding carbamate, as well as the four proline residues of an Src homology 3 domain protein. The CδD2 stretching frequencies are shifted to lower energies due to hyperconjugation with N i electron density, and engaging this density via protonation or the formation of the N i+1–H···N i interaction ablates this hyperconjugation and thus induces an otherwise difficult to explain blue shift in the C–D absorptions. Along with density functional theory calculations, the data reveal that the N i+1–H···N i interactions constitute H-bonds and suggest that they may play an important and previously underappreciated role in protein folding, structure, and function.

4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions

“…The crystal structure exhibited an endo proline ring pucker, a cis Boc-proline bond, and main chain torsion angles ϕ , ψ that were ideal for β-turn formation ( ϕ , ψ = −77°, +1°, near the ideal values for the i +2 residue of type I (−90°, 0°), type II′ (−80°, 0°), or type VIa1 (−90°, 0°) β-turns). 12 This conformation was also observed in the crystal structure of Ac-hyp-OMe (CSD: EMITEA; ϕ , ψ = −84°, +18°). 13 β-turns are central components of protein structure, 12a, b, 14 and are also common recognition motifs in protein-protein interactions, 15 suggesting the use of this amino acid (and other 4 S -substituted prolines) in the stabilization of β-turn motifs in peptides and proteins and in molecular recognition.…”

“…12 This conformation was also observed in the crystal structure of Ac-hyp-OMe (CSD: EMITEA; ϕ , ψ = −84°, +18°). 13 β-turns are central components of protein structure, 12a, b, 14 and are also common recognition motifs in protein-protein interactions, 15 suggesting the use of this amino acid (and other 4 S -substituted prolines) in the stabilization of β-turn motifs in peptides and proteins and in molecular recognition. 16 …”

“…7a, b, 21 These data, including the compact ϕ ~ −60°, suggest the application of 4 R -iodophenyl hydroxyproline in contexts where a more compact proline conformation (α R or PPII) is preferred, including at the i +1 position of type I, type II, or type VIa1 β-turns. 12a, b, 14, 22 Indeed, Raines and coworkers observed that related 4 R -hydroxyproline derivatives (-OH, -OMe, -OAc) can alternatively adopt α R or PPII conformations, with both conformations exhibiting favorable n→π* interactions. 22 These data also emphasize the conformational control possible with the judicious use of appropriate 4 R - and 4 S -substituted prolines, with each stereoisomer exhibiting divergent presentation of its functional group and distinct conformational preferences, suitable for structurally orthogonal applications (Figure 7).…”

“…One derivative exhibited a combination of ϕ and ψ ideal for the i +2 residue of different β-turns ( ϕ , ψ ~ −80°, 0°). 12a, b β-Turn stabilization has been the subject of extensive work in protein design, medicinal chemistry, and biomaterials. 12a, b, 14–16, 32 This amino acid thus suggests the ability both to stabilize a β-turn and to employ this location as a site for functionalization for target optimization.…”

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations

“…This behavior is the reverse of the Bohlmann effect, 54–57 where a “negative” hyperconjugation transfers electron density from a lone pair orbital to an optimally positioned C–H σ * orbital. This decreases the C–H bond order and substantially downshifts the C–H stretching frequencies.…”