Cis peptide bonds

The peptide bond between two amino acids in proteins or peptides is formed when the carboxyl group of one amino acid and the amino group of the other amino acid react with each other under cleavage of water. Due to its partial double bond character the peptide bond is planar and there is a rotational barrier be-tween the trans (ω = 180°) and cis (ω = 0°) conformation^[90] (Fig. 4.14) of about

13–20 kcal/mol^[94–96] (for an overview on the nomenclature of the dihedral angles see Fig. 4.15).

(a) transpeptide bond (b) cispeptide bond

Figure 4.14: Trans andcis peptide bonds.

Figure 4.15: Torsion angles in a peptide bond;ϕ: ’C–N–Cα–C, ψ: N–Cα–C–N’, ω: Cα–C–N’–

C’_α; the prime before and after an atom name means that the corresponding atom is part of the preceding and succeeding residue relative to the discussed amino acid, respectively.

Due to steric repulsion of the two Cαcarbon atoms thecisconformation is energet-ically less favored. An energy difference betweencisandtrans of 0.5 kcal/mol[94, 96, 97]

was found for Xaa–Pro (i.e. any amino acid bonded to proline) peptide bonds and of 2.5–4 kcal/mol[94, 96, 97] for Xaa–nonPro bonds (Fig. 4.16). The reason for the lower energy difference in cis Xaa–Pro peptide bonds is that the C_δ atom in the proline also interacts with the C_α atom in the other amino acid. From the energy differences incis andtrans conformations it can be calculated that about 30 % of all Xaa–Pro and 1.5 % of all Xaa–nonPro peptide bonds should be incis conformation.

The values found (2.5–4 % and 0.03–0.05 %) are much smaller. One reason for this discrepancy could be that at low resolution it can easily happen that a cis confor-mation is overlooked and refined as a trans bond. This is also in accordance with the resolution dependence of the frequency of detected cis peptide bonds^{[97, 98]}.

(a) trans Xaa-Pro peptide bond (b) cis Xaa-Pro peptide bond

Figure 4.16: Trans andcis Xaa-Pro peptide bonds.

Cis peptide bonds occur very rarely, only about 0.3 % of all peptide bonds are cis and more than 80 % among them are Xaa–Pro cis bonds[94, 96–98]. This makes 0.003–0.005 % of all peptide bondscis Xaa–nonPro (amide) peptide bonds and 4.7–

6.5 % cis Xaa–Pro (imide) bonds. In A2 two of the 17 peptide bonds are in cis conformation, Asp2–Trp3 (ω = 14.419°) and Thr11–Gly12 (ω = 1.293°) (Table 4.3 and Fig. 4.17).

ω (°)

Ala1-Asp2 172.0

Asp2-Trp3 14.4

Trp3-Ala4 173.5

Ala4-Leu5 172.3

Leu5-Trp6 −178.1

Trp6-Glu7 176.6

Glu7-Cys8 −179.1

Cys8-Cys9 164.7

Cys9-Ala10 178.0

Ala10-Thr11 −172.1

Thr11-Gly12 1.3

Gly12-Ala13 169.2

Ala13-Leu14 −173.0

Leu14-Phe15 −178.1

Phe15-Ala16 174.7

Ala16-Cys17 178.1

Cys17-Cys18 −177.6/−168.9

Table 4.3: ^ωtorsion angles in labyrinthopeptin A2; the two values for theωangle between Cys17 and Cys18 result from the disorder in Cys18.

Figure 4.17: Cis peptide bonds between Asp2 and Trp3 and between Thr11 and Gly12 in labyrinthopeptin A2.

Jabs et al.^[98] found that cis peptide bonds in small rings occur more frequently than in acyclic systems. They searched the CSD (Cambridge Structural Database^[99]) and found 269 out of 527 (>50 %) peptide bonds in cyclic molecules to be in cis conformation, preferrably in small rings with not more than 12 atoms in the ring.

In small rings like the A and A’ rings in A2, which consist of 11 atoms each, the cis bond is formed for sterical reasons. If the peptide bonds Asp2–Trp3 and Thr11–

Gly12 in A2 were in trans conformation the carbonyl oxygen atoms or the amine hydrogen atoms would be directed towards the center of the ring which is not pos-sible for steric reasons. Jabs et al. also found all residues N-terminal and most residues C-terminal to thecis peptide bond to be in the B-region of the Ramachan-dran plot. In contrast to these findings, in A2 the N-terminal residue Trp3 is in the A-region whereas Gly12 lies in a special region as is expected for glycine, anyway.

The C-terminal residue Thr11 is also in the A-region whereas Asp2 indeed lies in the B-region. According to Jabset al.the majority of theψ1/ϕ2 angles lie in the region of (ψ1,ϕ2) = (+110.3°,−136.2°) and (ψ1,ϕ2) = (+158.3°,−102.0°). This corresponds to the angle pairs of (+80°,−150°) and (+150°,−80°), which have been calculated in a conformational study to be the only possible angles in a cis petide bond. In con-trast to these findings the (ψ1,ϕ2) angles in A2 have the values (−70.1°,−87.4°) for Asp2–Trp3 and (−41.2°,88.0°) for Thr11–Gly12 (see Table 4.4). In the Ramachan-dran plot the positions of the ϕand ψ angles for Asp2, Trp3, Thr11 and Gly12 are marked with a circle (see Fig.4.13).

Jabs et al. reported that none of their investigated structures showed a positive ϕangle at the C-terminus of thecis peptide bond. Both of the C-terminal ϕangles in A2 are negative, indeed (ϕ(Asp2) = −125.1°,ϕ(Thr11) = −61.8°; see Table 4.4).

ϕ ψ

Table 4.4: ϕandψtorsion angles in labyrinthopeptin A2; the two values for theϕandψangles between Cys17 and Cys18 result from the disorder in Cys18.

In cis peptide bonds the C_α–C–N’ as well as the C–N’–C’_α angles are found to be widened compared to non cis peptide bonds^[98]. The reason for this finding is a steric repulsion of the two neighboring Cα atoms. This holds true for A2 as the CA 2–C 2–N 3 and CA 11–C 11–N 12 angles are 121.3° and 126.2°, respectively.

Except for the C-terminal disordered residue Cys18 those angles are much larger than all the other C_α–C–N’ angles in A2. Also the angles between C 2–N 3–CA 3 (127.3°) and C 11–N 12–CA 12 (128.7°) are widened compared to the corresponding other angles in A2 (except for the respective angle between Cys17 and Cys18, again;

see Table4.5).

C_α–C–N’ C–N’–C_α’

Table 4.5: ^Cα–C–N’ and C–N’–C’_α angles in labyrinthopeptin A2; the respective angles for the amino acids involved in thecis peptide bonds (Asp2/Trp3 and Thr11/Gly12) are larger than the corresponding angles in trans peptide bonds; the two values for the angles between Cys17 and Cys18 result from the disorder in Cys18.