Amide Cis-Trans Isomerization in Peptides and Proteins

Z/E isomerism is not limited to true double bonds and may be used when sp2 electrons of a heteroatom are conjugated with a 7r-system to form a planar pseudo double bond. In particular, in the case of amides, the cis isomer is called E. Although the general tendency now is to use the E/Z nomenclature in chemistry, despite their inaccuracy cis and trans are still utilized by biochemists because they give a more readily understandable description of molecular shape, in particular for amides in peptides and proteins. When the chains are connected through a motif containing more than three dihedral angles (i.e. carbamates), the syn-anti... 

Amide cis-trans isomerism is well documented [15-17], in particular for peptides and proteins since it plays a central role in the structure and biological activity of these molecules. This point will be detailed further in Chapter 9 and peptides will be only tackled here for the purposes of comparison with other chemically related motifs. 

The concept of cis-trans (Z-E) isomerism, originally used for the description of the relative geometry of olefins, has been extended to many other functions which feature a double bond character (pseudo double bonds), such as amides, as well as single bonds with a partial or complete limited rotation due to steric or stereoelec-tronic effects. Cis-trans isomerization (CTI) therefore exists in non-re-bonded or overcrowded molecules that switch from a given stable conformational state to another. This is the case of biaryl compounds which have been utilized in organic chemistry as the basis of molecular switches and rotors [1,2]. Nature has also exploited CTI of single bonds to increasing molecular diversity, in particular with the bulky thyroxin, a thyroid hormone, and the well-known disulfide bond which plays a critical role in the structure of peptides and in the conformation of proteins. 

Thrl67 bond in the cis Prol67Thr TEM-1 /J-lactamase variant is also characterized by a rate constant between 1 x 10-3 s-1 and 4 x 10 3 s-1 for the trans to cis interconversion [26]. Therefore the trans to cis isomerization can be rate-limiting in protein folding under native-like conditions, as was shown for a proline-free variant of the a-amylase inhibitor tendamistat [27]. This seems to be proven in the discovery of a novel protein dass, the secondary amide peptide cis/trans isomerases (APIases), which can accelerate interconversion of these peptide bonds conformers [28],... 

Whereas peptidyl prolyl cis-trans isomerases constitute a well-characterized enzyme class comprising well over 1000 members with small sequence variations in the proteins of different species, the discovery of secondary amide peptide bond cis-trans isomerases (APIases) had to await the development of suitable enzyme assays. Fortunately, spectral differences in the UV region between cis and trans isomers of dipeptides could be exploited to identify and quantify isomerization rate-enhancing factors in biological material [149]. 

Two structurally unrelated immunosuppressant drugs, cyclosporin A and FK506, have been shown to bind to separate proteins, which have in common the ability to catalyse the interconversion (8) of the cis and trans rotamers of peptidyl-proline bonds of peptide substrates. A profound change in the conformation, and hence the shape and binding properties of the protein, may result. The mechanism of this isomerization appears, on the basis of recent work (Rosen et al., 1990 Van Duyne et al., 1993 Albers et al., 1990), to involve simple twisting about the amide bond, rather than such alternatives as conversion to a C-N single bond by addition of a nucleophile to C=0.y The proteins which catalyse the reaction may be... 

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