Peptide bonds, cis/trans

Fig. 9.1 Reaction profile for peptide bond cis-trans isomerization. The kinetic constants for the trans to cis (k, J and cis to trans (kM>) isomerization are dependent on the Gibbs free energy of activation (AG ). The ground state energy difference AG° (G°as - C°mm) determines the population of the cis and trans isomers in the equilibrium state.

Enzymes Catalyzing Peptide Bond Cis-Trans Isomerizations... 

In most organisms, including humans, multiple members of each subtype of peptide bond cis-trans isomerases are expressed that differ in their molecular masses, domain composition, intracellular localization, and substrate specificity. Only a few investigations exist about the cooperation of the extra modules with the catalytic core. 

To form catalytically productive enzyme/substrate complexes, many peptide bond cis-trans isomerases essentially require the location of the reactive bond of the substrate in the context of secondary binding sites or a specific spatial organization of the polypeptide chain thus creating features of stereo- and regiospecifi-city [19,20]. As in the case of many endoproteases, PPIases can utilize an extended array of catalytic subsites to enhance catalytic efficiency and substrate specificity. These properties precondition peptide bond cis-trans isomerases toward a complex reaction pattern. Consequently, biochemical investigations have led to the elucidation of three distinct molecular mechanisms that might be operative either in isolation or collectively in the cellular action of both prototypical and multidomain peptide bond cis-trans isomerases ... 

Mechanistic pathways 1 and 2 involving isomerization catalysis and holding of unfolded polypeptide chains can be discussed in relation to all subfamilies of peptide bond cis-trans isomerases. In contrast, only members of the two families of cydophilins and FKBP, were found to play a role in presenting physiological ligands to further cellular constituents. 

In conclusion, among all known enzymes, peptide bond cis-trans isomerases exhibit a unique reaction profile with the potential of targeting a large number of rather similar reactive sites in a polypeptide chain, and a low degree of chemical differences that separates the reactant and product state of the enzyme reaction. 

There is evidence that the trigger factor and the hsp70 chaperone DnaK, a PPIase and a secondary amide peptide bond cis-trans isomerase (APIase) respectively, contribute to the formation of native proteins by apparently overlapping functions with the trigger factor as the primary interaction partner of the emerging polypeptide chain [122-124]. Consequently, synthetic lethality was observed... 

Secondary Amide Peptide Bond Cis-Trans Isomerases I 213... 

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]. 

Despite the amount of data and the simplicity of the chemical reaction catalyzed, the molecular basis of the catalytic mechanism of PPIases and APIases is still only poorly understood [155]. The considerable degree of amino acid sequence dissimilarity between the subgroups of peptide bond cis-trans isomerases also raises the challenging question of the mechanistic relatedness among the enzymes. At present there is a lack of detailed mechanistic investigations on APIases and multidomain PPIases. Thus, prototypic PPIases of all three families serve as the bases for unraveling catalytic pathways. One or more potential transition-state structures for enzyme-catalyzed prolyl isomerizations, alone or in combination, are consistent with the acceleration of the spontaneous rate of prolyl isomerization (Fig. 10.4). 

The design of selective and potent inhibitors of PPIases is of interest and numerous molecules have been designed or selected from chemical libraries with a view to curing these major diseases. The study of Pinl, which is clearly distinct from other members of the PPIase family on the basis of structure, binding site, catalytic mechanism, and biological implications, has opened up new perspectives in the biological chemistry of PPIases. The recent discoveries of the secondary amide peptide bond cis-trans isomerase (APIase) DnaK [209] and of a novel class of FK506 and cyclosporine-sensitive PPIase [210] are also major advances in this field. 

Beyond protein folding, the discovery of peptidyl prolyl isomerases (PPIases) and related proteins has opened the way to novel concepts in biology the notion of chaperone-assisted receptor binding is an emerging field of research which sheds light on receptor function and protein-protein interactions. The recent discovery of a secondary amide peptide bond cis-trans isomerase (APIase) heralds new advances in this field. 

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