) is an enzyme
found in both prokaryotes
that interconverts the cis
and trans isomers
of peptide bonds
with the amino acid proline
. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain
bonded to its secondary amine
nitrogen. Most amino acids
have a strong energetic preference for the trans
peptide bond conformation due to steric
hindrance, but proline's unusual structure stabilizes the cis
form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity include cyclophilin
, and parvulin
, although larger proteins can also contain prolyl isomerase domains
The process of cis-trans
isomerization is often the rate-limiting step
in the process of protein folding
. Prolyl isomerases therefore function as protein folding chaperones
peptide bonds before proline residues are often located at the first residue of certain types of tight turns
in the protein backbone. Proteins that contain structural cis
-prolines in the native state
include ribonuclease A
, ribonuclease T1
, beta lactamase
, and some interleukins
Prolyl isomerase folding can be autocatalytic and therefore the speed of folding depends on reactant concentration. Parvulin and human cytosolic FKBP are thought to catalyze their own folding processes.
Evidence for proline isomerization
Methods for identifying the presence of a rate-limiting proline isomerization process in a protein folding event include:
- Activation energies consistent with proline isomerization, which typically has an activation of about 20 kcal/mol.
- Two-state folding kinetics indicative of both fast-folding and slow-folding populations in the unfolded or denatured state.
- "Double-jump" assays in which proline-containing proteins are unfolded and refolded, and the population of non-native proline conformations are studied as a function of the extent of folding.
- Acceleration of the in vitro folding rate by the addition of a prolyl isomerase.
- Acceleration of the in vitro folding rate in mutant protein variants with one or more proline residues replaced by another amino acid.
It is important to note that not every proline peptide bond is critical to the structure or function of a protein, and not every such bond has a significant influence on folding kinetics, especially trans bonds. Furthermore, some prolyl isomerases have a degree of sequence specificity and therefore may not catalyze the isomerization of prolines in certain sequence contexts.
Assays for prolyl isomerase activity
Prolyl isomerase activity was first discovered using a chymotrypsin
-based assay. The proteolytic
enzyme chymotrypsin has a very high substrate specificity for the four-residue peptide Ala
only when the proline peptide bond is in the trans
state. Adding chymotrypsin to a solution containing a reporter peptide with this sequence results in the rapid cleavage of about 90% of the peptides, while those peptides with cis
proline bonds - about 10% in aqueous
solution - are cleaved at a rate limited by uncatalyzed proline isomerization. The addition of a potential prolyl isomerase will accelerate this latter reaction phase if it has true prolyl isomerase activity.
- Balbach J, Schmid FX. (2000). Proline isomerizarion and its catalysis in protein folding. In Mechanisms of Protein Folding 2nd ed. Editor RH Pain. Oxford University Press.
- Fischer G, Bang H, Mech C. (1984). Nachweis einer Ensymkatalase für die cis-trans-Isomerisierung der Peptidbindung in prolinhaltigen Peptiden. Biomed Bioim Acta 43(10):1101-11. (Determination of enzyme catalysis for the cis-trans isomerization of peptide binding in proline-containing peptides.)