Mechanism of Enzymatic and Nonenzymatic Prolyl Cis-Trans Isomerization

Abstract

This chapter describes the mechanism of both enzymatic and non-enzymatic prolyl isomerization. Non-enzymatic prolyl isomerization and rotation about amide bonds are reviewed. Amide rotation is mechanistically related to prolyl isomerization and serves as a useful model for prolyl isomerization. A common mechanism for these reactions and a structure for the rate-limiting transition state are reviewed. The chapter also discusses on what is known of enzyme-catalyzed prolyl isomerization. The chemistry of non-enzymatic prolyl isomerizations and the mechanisms of the non-enzymatic catalysis of this reaction dictate the catalytic strategy that is used by prolyl isomerases. Finally, it leads to a mechanistic proposal for enzymatic prolyl isomerization. The catalytic strategy that an enzyme develops over the evolutionary time is dictated by the chemistry of the reaction being catalyzed. The prolyl isomerases are able to stabilize the non-enzymatic transition state without formation of covalent intermediates. Based on a k cat value of 10 4 sec -1 for CyP and a k uncut of 10 -2 sec -1 for the cis -to-trans isomerization of Suc-Ala-Ala- cis- Pro-Phe-pNA, an acceleration factor, k cat /k uncut of 10 6 , is calculated that corresponds to a transition state stabilization free energy of over 8 kcal/mol 3 . The energetic price to distort the Xaa-Pro bond out of planarity must ultimately be paid by favorable transition state interactions.