Lorenz M. Mayr

Prolyl Isomerases: Role in Protein Folding

Publisher Summary This chapter discusses the function of prolyl isomerases in protein folding. The importance of prolyl isomerization reactions as slow, rate-limiting steps of folding, and their interdependence with other events in protein folding are described. Some experimental data on the catalysis by prolyl isomerases of various slow in vitro protein folding reactions are reviewed. The enzymatic functions of prolyl isomerases in vitro are fairly well characterized. They catalyze cis-trans isomerizations of Xaa-Pro bonds in small peptides and some proline-limited steps in the slow folding of several proteins. The characterization of the molecular nature of rate-limiting steps is a major aim in the elucidation of the folding mechanism of proteins. Folding reactions that involve prolyl isomerization are identified by measuring their kinetic properties and by comparing them with the properties of prolyl isomerization in short peptides. The chapter also explores the results that possibly suggest a role for prolyl isomerases in cellular folding and a close inter-relationship with disulfide bond formation. The efficiencies of various prolyl isomerases as catalysts of the slow-folding reactions of different proteins under varying folding conditions are tabulated.

Non-prolyl cis-trans peptide bond isomerization as a rate-determining step in protein unfolding and refolding

In wild-type ribonuclease T1 the peptide bond between Tyr38 and Pro39 is in the cis conformation. When Pro39 is replaced by an alanine this cis conformation is retained, and a non-prolyl cis Tyr38-Ala39 peptide bond is generated. We employed a stopped-flow double-mixing technique to investigate the kinetics of the cis-->trans isomerization of this peptide bond in the unfolding and the trans-->cis isomerization in the refolding of Pro39Ala-ribonuclease T1. In 6.0 M GdmCl (pH 1.6) and 25 degrees C the protein unfolds rapidly with a time constant of 20 ms, followed by Tyr38-Ala39 cis-->trans isomerization. This reaction shows a time constant of 730 ms and is about 60-fold faster than the isomerization of the Tyr38-Pro39 bond in the wild-type protein. Unfolded molecules with the Tyr38-Ala39 bond still in the native-like cis conformation accumulate transiently for a short time after unfolding is initiated, and they can refold very rapidly to the native state with a time constant of 290 ms (in 1.0 M GdmCl, pH 4.6, 25 degrees C). After more than three seconds of unfolding virtually all protein molecules contain an incorrect trans Tyr38-Ala39 bond and refolding is decelerated approximately 1000-fold, because Tyr38-Ala39 trans-->cis re-isomerization is very slow and, with its time constant of 480 s, determines the overall rate of refolding. Due to the coupling of the cis-trans equilibrium with protein folding it was possible to measure the kinetic parameters of the isomerization of a non-prolyl peptide bond in a protein. Previously this could not be accomplished, because the trans isomer is strongly preferred for unsubstituted peptide bonds in oligopeptides under virtually all conditions. Our data indicate that the kinetics of Tyr38-Pro39 and of Tyr38-Ala39 isomerization differ predominantly in the rate of the cis-->trans, rather than of the trans-->cis reaction. The rate of the trans-->cis reaction is, however, measured during refolding and may be influenced by the formation of ordered protein structure.