An electronic effect on protein structure

Abstract

The well-known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N-formyl group (H(i-1)-C'(i-1)=O(i-1)), in which H(i-1) presents less steric hindrance than does O(i-1), likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n --> pi* interaction between the oxygen of the peptide bond (O(i-1)), and the subsequent carbonyl carbon in the polypeptide chain (C'(i)) also contributes to this preference. The O(i-1) and C'(i) distance and O(i-1).C'(i)=O(i) angle are especially favorable for such an n --> pi* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure.

Figure 1.

n → π* Interaction between O_i−1 and C′_i. (A) Structure of the trans isomer of N-formyl-l-proline methyl ester (1) in its C^γ-exo conformation. The C′_i−1–H and C′_i−1 =O_i−1 bond lengths are from the structure of crystalline dimethyl formamide (Borrmann et al. 2000). (B) Depiction of the n and π* natural bond orbitals of the trans isomer of N-acetyl-l-proline methyl ester (2) in its C^γ-exo conformation. The O_i−1· · · C′_i distance is δ_BD = 2.87 Å and the O_i−1· · · C′_i=O_i angle is τ_BD = 99.35° (DeRider et al. 2002). (C) Bürgi–Dunitz trajectory for the attack of a nucleophile on a carbonyl group to displace a leaving group (LG; Bürgi et al. 1973, 1974a,b; Bürgi and Dunitz 1983; Eliel and Wilen 1994). (D) Major and minor resonance forms of amide 1 (Pauling 1960) and a very minor structure that arises from the hyperconjugative delocalization of an n → π* interaction.

Figure 2.

¹H NMR spectrum of N-formyl-l-proline methyl ester (1) in dioxane-d₈ at 25°C. Values of K_trans/cis were determined from integration of the indicated resonances.

Figure 3.

Implications of the n → π* interaction between O_i−1 and C′_i. (A) Ramachandran plot (Ramachandran and Sasisekharan 1968; Richardson 1981) showing the two “n → π*” regions of the trans isomer of AcGlyNH₂. In these regions, the O_i−1· · · C′_i distance is δ_BD ≤ 3.2 Å and the O_i−1· · · C′_i=O_i angle is 99° ≤ τ_BD ≤ 119°. The white dot indicates the φ and ψ angles for an ideal polyproline II helix (B). (B) Energy-minimized structure of AcGly₃NH₂ in the conformation of a polyproline II helix with φ = −75° and ψ = +145°. The structure is depicted as a ball-and-stick (left) or space-filling (right) model. The O_i−1· · · C′_i distance (δ_BD = 3.2 Å) and O_i−1· · · C′_i=O_i angle (τ_BD = 103°) is indicated in the ball-and-stick model.

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