Peptidylprolyl Isomerase

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Introduction

Peptidyl prolyl isomerase (PPI) is ubiquitous in prokaryotic and eukaryotic cells. They are primaryly responsible for catalyzing the cis-trans isomerization of peptide bond N-terminal to proline residues in the polypeptide chain. Based on drug specificity, PPI can be divided into three different categories: cyclosporin A (CsA) binding cyclophilin; FK506 binding protein (FKBP); and Parvulin-like PPI, these three types of PPI are also different in structure. Cyclophilin is characterized by the presence of a hydrophobic pocket formed by an eight-stranded β-barrel that binds to CsA. FKBPs are composed of an amphipathic five-stranded β-sheet, with a single, short α-helix in the middle of the structure. Members of the parvulin family consist of half a β-barrel, and its four antiparallel strands are surrounded by four α-helices. At present, eukaryotic parvulin-like PPI has been proven to be essential for cell cycle progression, and there is reliable evidence linking parvulin-like PPI with certain aspects of gene regulation. In both cases, they appear to work in concert with protein kinases to control the activity or stability of key regulatory components.

Figure 1. Peptidyl-prolyl isomerisation. Cis/trans isomerisation of the peptide bond (arrow) preceding proline (in red) in the tri-peptide pSer-Pro-Ala (Shaw, P.E. 2002)

Roles for PPIs in transcription and gene silencing

The first data linking PPI function to transcriptional control are those involving cyclophilins in the regulation of cMyb protein. The intramolecular interaction between the N-terminal DNA-binding domain and the C-terminal regulatory domain of cMyb inhibits its DNA binding. In vitro studies of this inhibitory effect indicate that it requires the cyclophilin Cyp-40 and is involved in PPI activity, because the inhibitory effect can be blocked by CsA. FKBP has also been found to be involved in transcription events, and the association of interferon regulatory factor 4 (IRF-4) with FKBP52 can block DNA binding in a manner that depends on the activity of PPI. The yeast genetic screen involved in pre-mRNA processing indicates parvulin-like PPI in gene expression. The expression of Ess1 rescued two temperature-sensitive mutants defective in 3'end formation. It was found that these two mutants had conservative residue substitutions in the PPI domain of Ess1, which reduced the catalytic activity of the protein. There is little evidence that Pin1 is directly involved in the transcription process of vertebrate cells. In fact, in a study involving in vitro transcription and in vivo assay, the only evidence that Pin1 is involved in inhibition of pre-initiation complex formation by Juglone, a naphthoquinone with dubious specificity for parvulin-like PPIs.

Pin1 is also regulated by WW domain phosphorylation

Pin1 itself is a protein kinase substrate. The phosphorylation of Ser16 in the WW domain appears to be regulated in a cell cycle-dependent manner, so cells in G2/M contain unphosphorylated Pin1. Since phosphorylated Pin1 or Pin1 mutants with Ser16 replaced by glutamate cannot bind to mitotic phosphoproteins, it is speculated that phosphorylation can limit the effects of Pin1 to nuclear proteins phosphorylated later in the cell cycle. Pin1 kinase and phosphatase have not been clearly identified. The conformation of the polypeptide backbone can determine the initial phosphorylation rate of the Ser-Pro motif. For example, ERK2 shows a clear preference for the cis form of the Ser-Pro peptide bond in short peptide substrates in vitro. This finding reveals that in a protein with multiple Ser-Pro/Thr-Pro motifs (such as Cdc25), the initial phosphorylation event may trigger a series of alternating phosphorylation-isomerization steps, each of which reveals a further target for modification, to prescribe the overall conformational change.

In addition, the peptidyl-prolyl bond conformation may also affect the specificity of other proteins, including other WW domain proteins or protein phosphatases such as PP2A interacting with p Ser-Pro/ p Thr-Pro motifs, thereby affecting the half-lives of target phosphoproteins.

Figure 2. Two-step tag and twist mechanism involving a protein kinase and PPI (Shaw, P.E. 2002)