Editing Peptide bond (section)

==Cis/trans isomers of the peptide group==

Significant delocalisation of the [[lone pair]] of electrons on the nitrogen atom gives the group a [[Amide#Structure and bonding|partial double-bond]] character. The partial double bond renders the amide group [[Plane (geometry)|planar]], occurring in either the [[Cis-trans isomerism|cis]] or [[trans isomer]]s. In the unfolded state of proteins, the peptide groups are free to isomerize and adopt both isomers; however, in the folded state, only a single isomer is adopted at each position (with rare exceptions). The trans form is preferred overwhelmingly in most peptide bonds (roughly 1000:1 ratio in trans:cis populations).  However, X-Pro peptide groups tend to have a roughly 30:1 ratio, presumably because the symmetry between the C<sup>α</sup> and C<sup>δ</sup> atoms of [[proline]] makes the cis and trans isomers nearly equal in energy, as shown in the figure below.
[[Image:Cis trans isomerization kinetics X Pro peptide bonds.png|thumb|center|alt=Diagram of the isomerization of an X-Pro peptide bond. The diagram shows the cis isomer on the left, the transition states in the center, and the trans isomer on the right, with bidirectional arrows between each pair of states.|Isomerization of an X-Pro peptide bond. Cis and trans isomers are at far left and far right, respectively, separated by the transition states.|500x500px]]
The [[dihedral angle]] associated with the peptide group (defined by the four atoms C<sup>α</sup>–C'–N–C<sup>α</sup>) is denoted <math>\omega</math>; <math>\omega = 0^\circ</math> for the cis isomer ([[synperiplanar]] conformation), and <math>\omega = 180^\circ</math> for the trans isomer ([[antiperiplanar]] conformation). Amide groups can isomerize about the C'–N bond between the cis and trans forms, albeit slowly (<math>\tau \sim 20</math>&nbsp;seconds at room temperature). The [[transition state]]s <math>\omega = \pm 90^\circ</math> require that the partial double bond be broken, so that the activation energy is roughly 80&nbsp;kJ/mol (20&nbsp;kcal/mol). However, the [[activation energy]] can be lowered (and the isomerization [[catalysis|catalyzed]]) by changes that favor the single-bonded form, such as placing the peptide group in a hydrophobic environment or donating a hydrogen bond to the nitrogen atom of an X-Pro peptide group. Both of these mechanisms for lowering the activation energy have been observed in ''peptidyl prolyl isomerases'' (PPIases), which are naturally occurring enzymes that catalyze the cis-trans isomerization of X-Pro peptide bonds.

Conformational [[protein folding]] is usually much faster (typically 10–100&nbsp;ms) than cis-trans isomerization (10–100&nbsp;s). A nonnative isomer of some peptide groups can disrupt the conformational folding significantly, either slowing it or preventing it from even occurring until the native isomer is reached. However, not all peptide groups have the same effect on folding; nonnative isomers of other peptide groups may not affect folding at all.