Prolyl isomerases isomerization

As indicated above, the barrier to prolyl cis—trans isomerization is the resonance stabilization energy that is possessed by the C-N imide bond. The task of a prolyl isomerase is, therefore, to develop an enzymatic-chemical strategy that will result in the lowering of this barrier. When one reflects on the strategies that might be used by an enzyme, one realizes that there are two general mechanisms catalysis by distortion and nucleophilic catalysis (see Scheme V). 

Finally, several investigators have examined the reaction of these prolyl isomerases toward substrates of general structure Suc-Ala-Xaa-Pro-Phe-pNA. In a 1989 paper, Fischer investigated CyP-catalyzed isomerization for Xaa = Ala, Gly, Ser, and Val and found values oikJK of 6.6, 2.1, 5.4, and 8.8 sec", respectively. He interpreted these results in... 

The catalytic strategy that an enzyme develops over evolutionary time is dictated by the chemistry of the reaction being catalyzed. The prolyl isomerases that have been studied to date are able to simply stabilize the nonenzymatic transition state without formation of covalent intermediates. Based on a value of lO" sec for CyP (Harrison and Stein, 1992 Kofron et ai, 1991) and a of sec" for the cis-to-trans isomerization of Suc-Ala-Ala-cis-Pro-Phe-pNA, we calculate an acceleration factor, of 10 , which corresponds to a transition state... 

Most of the small proteins that were used initially as substrates to test the function of prolyl isomerases contained disulfide bonds, which were left intact during unfolding and refolding. These proteins were used because their unfolding is reversible under a wide variety of conditions and because good evidence existed for a number of them that prolyl isomerizations were involved as rate-limiting steps in their slow-folding reactions. A protein chain without disulfides should be a better model... 

Clearly, the action of prolyl isomerases is not restricted to the slow folding of polypeptide chains with intact disulfides, but they also accelerate the oxidative folding of reduced proteins, which resemble more closely the nascent polypeptide chains as they occur in the endoplasmic reticulum. The simultaneous presence of PPI markedly enhances the efficiency of PDI as a catalyst of disulfide bond formation. Both enzymes act according to their specificity and catalyze the isomerization of prolyl peptide bonds and the formation of disulfide bonds, respectively, in the folding protein chains. It remains to be demonstrated that a similar concerted action of the two enzymes can take place in the course of de novo synthesis and folding of proteins in the cell. 

All amino acids except Gly are susceptible to isomerization or racemization. Enzymes such as peptidyl prolyl isomerases exist solely to isomerize specific amino acids. The cyclic imide pathway of degradation for both Asn and Asp can result in a racemic mixture of... 

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