Peptide linkage trans

FIGURE 5.2 The peptide bond is shown in its usnal trans conformation of carbonyl O and amide H. The atoms are the oi-carbons of two adjacent amino acids joined in peptide linkage. The dimensions and angles are the average valnes observed by crystallographic analysis of amino acids and small peptides. The peptide bond is the light gray bond between C and N. (Adapted from Ramachandran, G. A., ct ai, 1974. Biochimica Biophysica Acta 359 298-302.)... 

One precaution should be kept in mind for n -methyl amino acids. N-methylatlon of the peptide linkage results in the energy of the usual trans amide becoming comparable to that of the cis ( ). The trans to cis transformation at a point in the peptide backbone results in a significMt conformational change. This possibility must be considered in interpreting results based on incorporation of N -methyl amino acids. 

While the trans peptide linkage shown in Fig. 2-4 is usual, the following cis peptide linkage, which is 8 kj/mol less stable than the trans linkage, also occurs in proteins quite often. The nitrogen atom is usually but not always from proline.81 84... 

The a helix is an important component of integral membrane proteins. These are proteins that traverse the hydrophobic plasma and organelle membranes (see Chapter 9) and perform important biologic functions. The portion of the protein that is embedded in the membrane is a-helical because the a helix provides for a maximum number of hydrogen bonds, which serve to reduce the hydrophilic nature of peptide linkages. The side chains of such trans-membrane a helices are also hydrophobic, even though under normal circumstances, such amino acids would prefer to form other secondary structures. 

It was a surprise to discover that all of the cyclo-philins and FK506-binding proteins are peptidyl prolyl cis-trans isomerases or rotamases. They all catalyze the following simple and reversible reaction of a prolyl peptide linkage ... 

Proteins are linear condensation products of various a-L-amino acids (a.a.) that differ in molecular weight, charge, and nonpolar character (Table 7.1), bound by trans-peptide linkages. They differ in number and distribution of various a.a. residues in the molecule. The chemical properties, size of the side chain, and sequence of the a.a. affect the conformation of the molecule, i.e., the secondary structure containing helical regions, [3-plcalcd sheets, and [3-tunis the tertiary structure or the spatial arrangement of the chain and the quaternary structure — the assembly of several polypeptide chains. 

Three-bond Couplings (Table 16). As with possibility "of"lIsing J c"foT" nformational analysis has been particularly attractive. However, values are small and no pronounced dihedral angle dependence has yet been adduced experimentally, although several have been calcualted (41) J] ( (ci3) is predicted to be only slightly greater than J Q(trans) in a peptide linkage. 

A careful stereochemical analysis has led to the conclusion that for all of the different aminoacyl groups to be able to react in the same way at the peptidyltransferase site and to all generate trans amide linkages, the torsion angles < ) and q/ of the resulting peptide must be approximately those of an a helix.388 Thus, the peptide emerging from the ribosome exit tunnel may be largely helical. 

Figure 25-12 Ball-and-stick model of a peptide unit showing the coplanarity of the CNCC atoms of the amide linkage, here in the trans configuration, and the possibility of rotation about the C-C and N-C bonds.

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