The Peptide Unit

The very ability of a protein to exist as a complex three-dimensional structure depends upon the properties of the amide linkages between the amino acid units. Many of these properties follow from the fact that an amide can be viewed as a resonance hybrid of the following structures. Because of the partial doublebond character, the C–N bond is shorter than that of a normal single bond and the C=O bond is lengthened.



The observed lengths in nanometers determined by X-ray diffraction measurements are given. The partial double-bond character of the C–N bond has important consequences. The peptide unit is nearly planar as is indicated by the dashed parallelogram.
However, the bonds around the nitrogen retain some pyramidal. Even more important is the fact that there is flexibility. As a result, the torsion angle ω may vary over a range of ± 15° or even more from that in the planar state. The resonance stabilization of the amide linkage is thought to be about 85 kJ/mol. Rotation around the C–N bond through 90° would be expected to require about this much energy. This fact immediately suggests a way in which proteins may sometimes be able to store energy—by having one or more peptide units twisted out of complete planarity.

Dimensions of the peptide linkage. Interatomic distances in nm, including the hydrogen bond length to an adjacent peptide linkage, are indicated. The atoms enclosed by the dotted lines all lie approximately in a plane. However, as indicated in the lower drawing, the nitrogen atom tends to retain some pyramidal character.

An important effect of the resonance of the amide linkage is that the oxygen atom acquires some negative charge and the NH group some positive charge. Some of the positive charge is usually depicted as residing on the nitrogen, but some is found on the hydrogen atom. The latter can be pictured as arising from a contribution of a fourth resonance form that contains no bond to hydrogen.



Nevertheless, this picture is inadequate. Various evidence indicates that the nitrogen actually carries a net negative charge.
The positive and negative ends of the dipoles in the amide group tend to associate to form strong hydrogen bonds. These hydrogen bonds together with the connecting amide linkages can form chains that may run for considerable distances through proteins. The tendency for cooperativity in hydrogen bond formation may impart unusual stability to these chains. As with individual amide linkages, these chains of hydrogen-bonded amides can also be thought of as resonance hybrids:



The two structures pictured are extreme forms, the true structure being something in between. In the lower form, rotation about the C–N bond would be permitted but then the charge separation present in the upper structure would no longer exist. Thus, the hydrogen bonds would be weakened. We can conclude that if an amide linkage in such a chain becomes twisted, the hydrogen bonds that it forms will be weakened. If there is cooperativity, the hydrogen bonds will all be strongest when there is good planarity in all of the amides in the chain.
Amides have very weak basic properties and protonation is possible either on the oxygen (A) or on the nitrogen (B).


The pKa values for such protonation are usually less than zero, but it is possible that a correctly placed acidic group in a protein could protonate either oxygen or nitrogen transiently during the action of a protein. Protonation on oxygen would strengthen hydrogen bonds from the nitrogen whereas protonation on nitrogen would weaken hydrogen bonds to oxygen and might permit rotation. The amide group has a permanent dipole moment of 3.63 debyes oriented as follows:



Here the arrow points toward the positive end of the dipole.