GO:0003755 peptidyl-prolyl cis-trans isomerase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0003755 describes the catalytic activity that interconverts the cis and trans conformations of peptide bonds preceding proline residues.
• Peptidyl-prolyl cis-trans isomerases (PPIases) are classified into cyclophilins, FK506-binding proteins (FKBPs), and parvulins, with distinct inhibitor sensitivities.
• PPIase activity is essential for protein folding, immune regulation, and cell signaling, and is implicated in cancer, neurodegeneration, and host-pathogen interactions [1,7].
• Pin1, a parvulin-family PPIase, is a key regulator of cell cycle and aging, and is linked to Alzheimer disease and multiple cancers.
• PPIase activity can be measured on the cell surface and correlates with extracellular matrix development.
• CRISPR-based knockout, point mutation, knock-in, and overexpression models enable precise dissection of PPIase gene function in disease and development [5,8].
Description
Peptidyl-prolyl cis-trans isomerase (PPIase) activity, encoded by the Gene Ontology term GO:0003755, is a fundamental enzymatic function that catalyzes the rotation of the peptide bond preceding proline between its cis and trans conformations. This isomerization is often the rate-limiting step in protein folding, and PPIases are therefore critical for maintaining proteostasis and regulating protein function in all living organisms. The importance of this activity extends beyond basic protein folding: PPIases participate in immune responses, cell cycle control, and signal transduction, and their dysfunction is associated with cancer, neurodegeneration, and infectious diseases [1,7]. Researchers study PPIases to understand how conformational switches in proline-containing proteins drive physiological and pathological processes, and to develop therapeutic inhibitors [3,8]. The availability of CRISPR-based genetic models has further accelerated functional studies of PPIase genes in human cells and animal models.
peptidyl-prolyl cis-trans isomerase activity At A Glance
| GO ID | GO:0003755 |
|---|---|
| GO term | peptidyl-prolyl cis-trans isomerase activity |
| Ontology | molecular_function |
| Synonym | cyclophilin activity; rotamase activity; PPIase activity; immunophilin; parvulin |
| Major function | Catalysis of the cis-trans isomerization of peptidyl-proline bonds |
| Definition | Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0) |
| Related families | Cyclophilins, FK506-binding proteins (FKBPs), parvulins |
| Inhibitors | Cyclosporin A (cyclophilins), FK506 (FKBPs), juglone (parvulins) |
| Subcellular location | Cytosol, nucleus, endoplasmic reticulum, mitochondria, cell surface |
What Is GO:0003755?
GO:0003755 peptidyl-prolyl cis-trans isomerase activity is defined as the catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0). In other words, it is the enzyme activity that accelerates the interconversion between the cis and trans isomers of the peptide bond that immediately precedes a proline residue in a polypeptide chain. This activity is also known as rotamase, cyclophilin, FK506-sensitive PPIase, parvulin, and immunophilin activity, reflecting the different protein families that possess it.
Why Is peptidyl-prolyl cis-trans isomerase activity Important in Cell Biology?
PPIase activity is essential for protein folding and function, and its dysregulation is linked to a wide range of human diseases, including cancer, Alzheimer disease, and infectious diseases [1,7]. Because proline isomerization is a slow step that can control protein activity, PPIases act as molecular switches in signaling pathways, making them attractive drug targets [3,8]. Understanding GO:0003755 is therefore critical for researchers in structural biology, chemical biology, and translational medicine.
• PPIases catalyze a rate-limiting step in protein folding, influencing proteostasis.
• Cyclophilins and FKBPs are targets of immunosuppressive drugs, linking PPIase activity to immune regulation.
• Pin1 (a parvulin) regulates cell cycle and is implicated in cancer and Alzheimer disease.
• PPIase activity on the cell surface correlates with extracellular matrix development.
• PPIases are involved in host-pathogen interactions and are potential antimicrobial targets.
• Small-molecule inhibitors of PPIases are being developed for cancer and other diseases [3,8].
• PPIase activity can be measured using isomer-specific substrates and proteomics.
• CRISPR screens can identify PPIase genes essential for cell fitness and drug response.
What Happens During peptidyl-prolyl cis-trans isomerase activity?
Substrate recognition and binding
In simple terms: The enzyme grabs a protein that has a proline residue and holds it in place.
PPIases recognize their substrates through a hydrophobic binding pocket that accommodates the proline ring and adjacent residues. Different families (cyclophilins, FKBPs, parvulins) have distinct substrate specificities, often determined by phosphorylation of residues near the proline.
Catalysis of cis-trans isomerization
In simple terms: The enzyme twists the peptide bond so it can flip between two shapes.
The catalytic mechanism involves distortion of the peptide bond and stabilization of the twisted transition state, lowering the energy barrier for rotation around the prolyl peptide bond. This allows the substrate to switch between cis and trans conformations, which can alter protein structure and function.
Release and downstream effects
In simple terms: Once the shape is changed, the protein is released and can do its job.
After isomerization, the substrate is released and may fold into its active conformation or interact with partners. This can affect signaling, transcription, and cell cycle progression. For example, Pin1-catalyzed isomerization of phospho-Thr-Pro motifs can regulate protein stability and activity.
Regulation by inhibitors and post-translational modifications
In simple terms: Other molecules can block or modify the enzyme to control its activity.
PPIase activity is regulated by endogenous inhibitors, phosphorylation, and redox state. Immunosuppressive drugs such as cyclosporin A and FK506 inhibit cyclophilins and FKBPs, respectively. Juglone inhibits parvulins, providing a tool to study Pin1 function.
Key Genes Involved in GO:0003755 peptidyl-prolyl cis-trans isomerase activity
The following genes encode proteins with peptidyl-prolyl cis-trans isomerase activity or are directly involved in its regulation.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PPIA | Cyclophilin A, cytosolic PPIase | Target of cyclosporin A; involved in inflammation and cancer |
| PPIB | Cyclophilin B, ER PPIase | Required for collagen folding; mutations cause osteogenesis imperfecta |
| PPIC | Cyclophilin C, PPIase | Expressed in fibroblasts; role in extracellular matrix |
| PPID | Cyclophilin D, mitochondrial PPIase | Regulates mitochondrial permeability transition |
| PPIE | Cyclophilin E, nuclear PPIase | Involved in pre-mRNA splicing |
| PPIF | Cyclophilin F, mitochondrial PPIase | Modulates apoptosis and necrosis |
| PPIG | Cyclophilin G, nuclear PPIase | Component of spliceosome |
| PPIH | Cyclophilin H, nuclear PPIase | Part of U4/U6 snRNP |
| PPIL1 | Cyclophilin-like PPIase | Component of spliceosome; mutations cause microcephaly |
| FKBP1A | FKBP12, PPIase | Target of FK506 and rapamycin; regulates mTOR |
| FKBP5 | FKBP51, PPIase | Regulates glucocorticoid receptor; implicated in depression |
| PIN1 | Parvulin PPIase | Regulates cell cycle; linked to cancer and Alzheimer disease |
| PIN4 | Parvulin PPIase | Role in pre-rRNA processing |
| NIMA | Never in mitosis A kinase | Interacts with Pin1; target in hepatocellular carcinoma |
| CYP1 | Cyclophilin in pathogens | Host-pathogen interactions |
| MIP | Macrophage infectivity potentiator | Bacterial PPIase virulence factor |
| SlyD | FKBP-type PPIase in E. coli | Model for PPIase structure-function |
How Is peptidyl-prolyl cis-trans isomerase activity Regulated?
PPIase activity is regulated at multiple levels. Transcriptionally, expression of cyclophilins and FKBPs is induced by stress, growth factors, and immune signals. Post-translationally, phosphorylation of PPIases such as Pin1 can modulate substrate specificity and catalytic activity. Endogenous inhibitors and redox modifications also control PPIase function. In addition, the mTOR pathway regulates FKBP12 and its interactions, linking PPIase activity to cell growth.
peptidyl-prolyl cis-trans isomerase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PIN1 | Cancer, Alzheimer disease | Knockout and point-mutation cell lines; mouse models |
| PPIA | Inflammation, cancer | Overexpression and knockout in cancer cell lines |
| PPIB | Osteogenesis imperfecta | Patient-derived fibroblasts; knock-in mouse models |
| FKBP5 | Depression, stress response | Knockout mice; neuronal cell lines |
| MIP | Legionella infection | Bacterial knockout; host cell infection models |
Cancer
PPIases are frequently overexpressed in cancers and contribute to tumor progression. Pin1 is overexpressed in many cancers and regulates oncogenes and tumor suppressors. NIMA-interacting 1 (Pin1) has been proposed as a therapeutic target in hepatocellular carcinoma. Cyclophilin A promotes cancer cell proliferation and metastasis.
Neurodegeneration
Pin1 is implicated in Alzheimer disease, where it regulates tau phosphorylation and amyloid precursor protein processing. Dysregulation of Pin1 leads to tau hyperphosphorylation and neurofibrillary tangle formation.
Infectious diseases
Pathogen PPIases, such as MIP in Legionella and cyclophilins in parasites, are virulence factors that modulate host immune responses. Targeting these PPIases is a potential antimicrobial strategy.
Genetic disorders
Mutations in PPIB cause osteogenesis imperfecta, and mutations in PPIL1 are associated with microcephaly, highlighting the importance of PPIases in development.
From peptidyl-prolyl cis-trans isomerase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the effect of PPIase gene knockout on cell viability? | CRISPR knockout in cancer cell lines |
| How does a point mutation in the catalytic site affect isomerase activity? | CRISPR point mutation (e.g., Pin1 active-site mutant) |
| Does a disease-associated mutation alter protein function? | Knock-in of mutant allele in isogenic cell lines |
| Where does the PPIase localize in cells? | Tagged knock-in with fluorescent protein |
| What happens when PPIase is overexpressed? | CRISPR activation or cDNA overexpression |
| Which genes are essential in PPIase-dependent pathways? | Genome-wide CRISPR library screening |
How to Study the peptidyl-prolyl cis-trans isomerase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| PPIase activity assay | Catalytic rate of cis-trans isomerization | Enzyme kinetics and inhibitor testing |
| Cell surface PPIase assay | Extracellular PPIase activity | ECM development studies |
| Co-immunoprecipitation | Protein-protein interactions | Identifying PPIase substrates |
| Phospho-peptide pull-down | Binding to phosphorylated motifs | Pin1 substrate discovery |
| CRISPR knockout screen | Gene essentiality and fitness | Identifying PPIase dependencies |
| RNA-seq | Transcriptional changes | PPIase-regulated gene expression |
| Proteomics | Protein abundance and modifications | Global effects of PPIase inhibition |
| Structural biology (X-ray/NMR) | 3D structure of PPIase-substrate complexes | Mechanistic studies |
Enzymatic assays for PPIase activity
PPIase activity is typically measured using chromogenic or fluorogenic substrates that contain a proline residue, such as N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide, in a coupled assay with chymotrypsin. This allows kinetic characterization of purified enzymes or cell lysates.
Cell surface PPIase activity
PPIase activity can be detected on the cell surface using specific substrates, and this activity correlates with extracellular matrix development. This method is useful for studying secreted or membrane-associated PPIases.
Proteomics and interactomics
Affinity purification coupled with mass spectrometry can identify PPIase substrates and interacting proteins. For example, Pin1 interactors have been mapped using phospho-peptide pull-downs.
CRISPR screening and functional genomics
Genome-wide CRISPR knockout screens can identify PPIase genes required for cell growth or drug sensitivity. These screens provide unbiased insights into PPIase function in health and disease.
How CRISPR Can Be Used to Study GO:0003755 peptidyl-prolyl cis-trans isomerase activity
Knockout
CRISPR knockout of PPIase genes (e.g., PPIA, PIN1) in cell lines can reveal their roles in proliferation, apoptosis, and stress responses. Knockout models are essential for validating drug targets and understanding loss-of-function phenotypes.
Point Mutation
Introducing point mutations in the catalytic domain of PPIases (e.g., Pin1 C113A) using CRISPR can dissect the contribution of isomerase activity versus other functions. Such models are valuable for separating catalytic and non-catalytic roles.
Knock-in
Knock-in of disease-associated mutations (e.g., PPIB mutations in osteogenesis imperfecta) into isogenic cell lines allows study of mutation-specific effects on protein folding and function. Tagged knock-in (e.g., GFP) enables localization and interaction studies.
Overexpression
CRISPR activation (CRISPRa) or cDNA overexpression can model PPIase upregulation observed in cancers. Overexpression models help identify downstream signaling changes and test inhibitors.
How EDITGENE Supports peptidyl-prolyl cis-trans isomerase activity Research
Researchers studying peptidyl-prolyl cis-trans isomerase activity-related genes often need to determine whether a candidate gene is causally involved in a specific phenotype, such as cancer cell growth, protein folding, or drug response. EDITGENE provides a comprehensive suite of CRISPR-based services to generate precisely engineered cell models, enabling rigorous functional validation of PPIase genes and their variants.
Contact EDITGENE today to design your custom CRISPR model for peptidyl-prolyl cis-trans isomerase activity research.
Frequently Asked Questions About peptidyl-prolyl cis-trans isomerase activity
What is peptidyl-prolyl cis-trans isomerase activity?
It is the enzymatic activity that catalyzes the interconversion between cis and trans conformations of peptide bonds preceding proline residues, as defined by GO:0003755.
What genes are involved in peptidyl-prolyl cis-trans isomerase activity?
Genes include PPIA, PPIB, PPIC, PPID, PPIE, PPIF, PPIG, PPIH, PPIL1, FKBP1A, FKBP5, PIN1, and PIN4, among others [3,4,7].
What diseases are associated with PPIase activity?
PPIases are linked to cancer, Alzheimer disease, infectious diseases, and genetic disorders such as osteogenesis imperfecta [1,4,7].
How is PPIase activity measured?
It is commonly measured using chromogenic substrates like N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in a coupled assay with chymotrypsin.
What is the role of Pin1 in disease?
Pin1 regulates cell cycle and is implicated in cancer and Alzheimer disease through isomerization of phosphorylated Ser/Thr-Pro motifs.
Can PPIases be targeted by drugs?
Yes, cyclophilin inhibitors (e.g., cyclosporin A) and FKBP inhibitors (e.g., FK506) are used clinically, and non-immunosuppressive inhibitors are in development.
What are the different families of PPIases?
The three main families are cyclophilins, FK506-binding proteins (FKBPs), and parvulins, each with distinct inhibitor sensitivities.
How does CRISPR help study PPIase genes?
CRISPR knockout, point mutation, knock-in, and overexpression models allow precise functional dissection of PPIase genes in disease and development [5,8].
Is PPIase activity found on the cell surface?
Yes, cell surface PPIase activity has been detected and correlates with extracellular matrix development.
What is the difference between PPIase and rotamase?
Rotamase is a synonym for peptidyl-prolyl cis-trans isomerase activity, referring to the same catalytic function.
Conclusion
Peptidyl-prolyl cis-trans isomerase activity (GO:0003755) is a critical enzymatic function that controls protein folding and signaling through proline isomerization. Its involvement in cancer, neurodegeneration, and infectious diseases makes it a prime target for therapeutic development [1,7]. Advances in CRISPR-based models and screening technologies are accelerating our understanding of PPIase biology and enabling the discovery of novel inhibitors [3,5,8]. Continued research into this activity will likely yield new insights into disease mechanisms and therapeutic strategies.
References
- 1. Steinert M. 2022. Editorial: Peptidyl-prolyl cis/trans isomerases (PPIases) in host-pathogen interactions.. Front Cell Infect Microbiol 12:1097771 PMID: 36569202
- 2. Lin W et al.. 2019. Peptidyl prolyl cis/trans isomerase activity on the cell surface correlates with extracellular matrix development.. Commun Biol 2:58 PMID: 30775459
- 3. Schiene-Fischer C et al.. 2022. Non-Immunosuppressive Cyclophilin Inhibitors.. Angew Chem Int Ed Engl 61(39):e202201597 PMID: 35290695
- 4. Schiene-Fischer C. 2015. Multidomain Peptidyl Prolyl cis/trans Isomerases.. Biochim Biophys Acta 1850(10):2005-16 PMID: 25445709
- 5. Kim G et al.. 2015. Peptidyl-Prolyl cis/trans Isomerase NIMA-Interacting 1 as a Therapeutic Target in Hepatocellular Carcinoma.. Biol Pharm Bull 38(7):975-9 PMID: 26133706
- 6. Anto NP et al.. 2023. The Peptidyl-Prolyl cis-trans isomerase, Pin1, associates with Protein Kinase C θ via a critical Phospho-Thr-Pro motif in the V3 regulatory domain.. Front Immunol 14:1126464 PMID: 36969236
- 7. Lee TH et al.. 2011. Peptidyl-prolyl cis-trans isomerase Pin1 in ageing, cancer and Alzheimer disease.. Expert Rev Mol Med 13:e21 PMID: 21682951
- 8. da Costa KS et al.. 2020. Targeting Peptidyl-prolyl Cis-trans Isomerase NIMA-interacting 1: A Structure-based Virtual Screening Approach to Find Novel Inhibitors.. Curr Comput Aided Drug Des 16(5):605-617 PMID: 31654518
