Planar peptide group

FIGURE 4-2 The planar peptide group, (a) Each peptide bond has some double-bond character due to resonance and cannot rotate. 

Fig. 4b. Structure of polyglycine II (from Crick and Rich, 1955). A projection of the structure with the screw axis vertical. The chain on the right is nearer the reader than that on the left. The planar peptide groups are edge-on at the bottom of the figure with hydrogen bonds from these groups virtually perpendicular to the plane of the paper.

A new phenomenon is introduced with the cyclic hexapeptides in that the same compound can assume a number of different conformations. For example, each unit cell in the crystal of cyclic hexaglycine contains four different conformers of the molecule (Karle and Karle, 1963). Each conformer has all-trans planar peptide groups, but only one conformer contains intramolecular hydrogen bonds, a pair of parallel 4 1 bonds (Fig. 9). Two of the conformers contain a center of symmetry coincident with centers in the crystal the conformer with the transannular hydrogen bonds also contains a center, although it is not required by the symmetry elements of the crystal and the fourth conformer is asymmetric. The centers of symmetry in the cyclo Gly)e molecules are possible since glycine residues do not contain asymmetric C atoms. 

The importance of oxyanion holes in enzymes was first discovered in chymot-rypsin by David Blow and co-workers and in subtihsin by Jo Kraut and co-workers [39]. In these enzymes, a tetrahedral intermediate is generated after nucleophilic attack of a deprotonated serine side chain on the peptide carbonyl group. It was recognized from the begirming that the geometry of the active site complexes was possibly better complementary to the tetrahedral intermediate than to the planar peptide substrate [40]. 

The nature of the covalent bonds in the polypeptide backbone places constraints on structure. The peptide bond has a partial doublebond character that keeps the entire six-atom peptide group in a rigid planar configuration. The N—C and Ca—C bonds can rotate to assume bond angles of (p and ip, respectively. 

The structures of fibrous proteins are determined by the amino acid sequence, by the principle of forming the maximum number of hydrogen bonds, and by the steric limitations of the polypeptide chain, in which the peptide grouping is in a planar conformation. 

In this structure, the peptide group is indicated by the dashed lines. Because the peptide group itself is rigid and planar, there is no rotation around the bond between the carbonyl carbon atom and the nitrogen atom (the C —N bond). However, free rotation is possible around the bond between the a carbon and the carbonyl carbon atom (the C —C bond) and about the bond between the nitrogen atom and the alanyl o-carbon atom the (N—Ca bond). Thus, for every peptide group in a protein, there are two rotatable bonds, the relative angles of which define a particular backbone conformation. 

This diagram shows the peptide groups represented as planar segments, with the a -carbon atom at the junctions of successive planes. 

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