1
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Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated protein kinase C regulation. eLife 2024; 13:e92884. [PMID: 38687676 PMCID: PMC11060717 DOI: 10.7554/elife.92884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of full-length Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a conformation in which it uses the WW and PPIase domains to engage two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, respectively. Hydrophobic motif is a non-canonical Pin1-interacting element. The structural information combined with the results of extensive binding studies and experiments in cultured cells suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Karuna Dixit
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Yuan Yang
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Mark I McDermott
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Hasan Tanvir Imam
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
| | - Vytas A Bankaitis
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
| | - Tatyana I Igumenova
- Department of Biochemistry & Biophysics, Texas A&M UniversityCollege StationUnited States
- Department of Cell Biology & Genetics, Texas A&M UniversityCollege StationUnited States
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2
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Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol 2024; 12:1343938. [PMID: 38745861 PMCID: PMC11091292 DOI: 10.3389/fcell.2024.1343938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024] Open
Abstract
This review examines the complex role of Pin1 in the development and treatment of cancer. Pin1 is the only peptidyl-prolyl isomerase (PPIase) that can recognize and isomerize phosphorylated Ser/Thr-Pro peptide bonds. Pin1 catalyzes a structural change in phosphorylated Ser/Thr-Pro motifs that can modulate protein function and thereby impact cell cycle regulation and tumorigenesis. The molecular mechanisms by which Pin1 contributes to oncogenesis are reviewed, including Pin1 overexpression and its correlation with poor cancer prognosis, and the contribution of Pin1 to aggressive tumor phenotypes involved in therapeutic resistance is discussed, with an emphasis on cancer stem cells, the epithelial-to-mesenchymal transition (EMT), and immunosuppression. The therapeutic potential of Pin1 inhibition in cancer is discussed, along with the promise and the difficulties in identifying potent, drug-like, small-molecule Pin1 inhibitors. The available evidence supports the efficacy of targeting Pin1 as a novel cancer therapeutic by analyzing the role of Pin1 in a complex network of cancer-driving pathways and illustrating the potential of synergistic drug combinations with Pin1 inhibitors for treating aggressive and drug-resistant tumors.
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Affiliation(s)
- Robert Stewart
- Department of Biochemistry, Western University, London, ON, Canada
| | - Shaunik Sharma
- Department of Biochemistry, Western University, London, ON, Canada
| | - Timothy Wu
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sho Okuda
- Department of Biochemistry, Western University, London, ON, Canada
| | - George Xie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brian Shilton
- Department of Biochemistry, Western University, London, ON, Canada
| | - Kun Ping Lu
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
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3
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Bai Y, Yuan Z, Yuan S, He Z. Recent advances of Pin1 inhibitors as potential anticancer agents. Bioorg Chem 2024; 144:107171. [PMID: 38325131 DOI: 10.1016/j.bioorg.2024.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Pin1 (proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1), as a member of PPIase family, catalyzes cis-trans isomerization of pThr/Ser-Pro amide bonds of its substrate proteins, further regulating cell proliferation, division, apoptosis, and transformation. Pin1 is overexpressed in various cancers and is positively correlated with tumor initiation and progression. Pin1 inhibition can effectively reduce tumor growth and cancer stem cell expansion, block metastatic spread, and restore chemosensitivity, suggesting that targeting Pin1 may be an effective strategy for cancer treatment. Considering the promising therapeutic effects of Pin1 inhibitors on cancers, we herein are intended to comprehensively summarize the reported Pin1 inhibitors, mainly highlighting their structures, biological functions and binding modes, in hope of providing a reference for the future drug discovery.
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Affiliation(s)
- Yiru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Ziqiao Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China.
| | - Zhangxu He
- Pharmacy College, Henan University of Chinese Medicine, 450046 Zhengzhou, China.
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4
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Foor SD, Brangulis K, Shakya AK, Rana VS, Bista S, Kitsou C, Ronzetti M, Alreja AB, Linden SB, Altieri AS, Baljinnyam B, Akopjana I, Nelson DC, Simeonov A, Herzberg O, Caimano MJ, Pal U. A unique borrelial protein facilitates microbial immune evasion. mBio 2023; 14:e0213523. [PMID: 37830812 PMCID: PMC10653885 DOI: 10.1128/mbio.02135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Lyme disease is a major tick-borne infection caused by a bacterial pathogen called Borrelia burgdorferi, which is transmitted by ticks and affects hundreds of thousands of people every year. These bacterial pathogens are distinct from other genera of microbes because of their distinct features and ability to transmit a multi-system infection to a range of vertebrates, including humans. Progress in understanding the infection biology of Lyme disease, and thus advancements towards its prevention, are hindered by an incomplete understanding of the microbiology of B. burgdorferi, partly due to the occurrence of many unique borrelial proteins that are structurally unrelated to proteins of known functions yet are indispensable for pathogen survival. We herein report the use of diverse technologies to examine the structure and function of a unique B. burgdorferi protein, annotated as BB0238-an essential virulence determinant. We show that the protein is structurally organized into two distinct domains, is involved in multiplex protein-protein interactions, and facilitates tick-to-mouse pathogen transmission by aiding microbial evasion of early host cellular immunity. We believe that our findings will further enrich our understanding of the microbiology of B. burgdorferi, potentially impacting the future development of novel prevention strategies against a widespread tick-transmitted infection.
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Affiliation(s)
- Shelby D. Foor
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Kalvis Brangulis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Human Physiology and Biochemistry, Riga Stradins University, Riga, Latvia
| | - Anil K. Shakya
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Vipin S. Rana
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Sandhya Bista
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Chrysoula Kitsou
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Michael Ronzetti
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Adit B. Alreja
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Sara B. Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Amanda S. Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Inara Akopjana
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Daniel C. Nelson
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Melissa J. Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
- Virginia-Maryland College of Veterinary Medicine, College Park, Maryland, USA
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5
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Chen XR, Dixit K, Yang Y, McDermott MI, Imam HT, Bankaitis VA, Igumenova TI. A novel bivalent interaction mode underlies a non-catalytic mechanism for Pin1-mediated Protein Kinase C regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558341. [PMID: 37781616 PMCID: PMC10541119 DOI: 10.1101/2023.09.18.558341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Regulated hydrolysis of the phosphoinositide phosphatidylinositol(4,5)-bis-phosphate to diacylglycerol and inositol-1,4,5-P3 defines a major eukaryotic pathway for translation of extracellular cues to intracellular signaling circuits. Members of the lipid-activated protein kinase C isoenzyme family (PKCs) play central roles in this signaling circuit. One of the regulatory mechanisms employed to downregulate stimulated PKC activity is via a proteasome-dependent degradation pathway that is potentiated by peptidyl-prolyl isomerase Pin1. Here, we show that contrary to prevailing models, Pin1 does not regulate conventional PKC isoforms α and βII via a canonical cis-trans isomerization of the peptidyl-prolyl bond. Rather, Pin1 acts as a PKC binding partner that controls PKC activity via sequestration of the C-terminal tail of the kinase. The high-resolution structure of Pin1 complexed to the C-terminal tail of PKCβII reveals that a novel bivalent interaction mode underlies the non-catalytic mode of Pin1 action. Specifically, Pin1 adopts a compact conformation in which it engages two conserved phosphorylated PKC motifs, the turn motif and hydrophobic motif, the latter being a non-canonical Pin1-interacting element. The structural information, combined with the results of extensive binding studies and in vivo experiments suggest that non-catalytic mechanisms represent unappreciated modes of Pin1-mediated regulation of AGC kinases and other key enzymes/substrates.
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6
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Chen XR, Igumenova TI. Regulation of eukaryotic protein kinases by Pin1, a peptidyl-prolyl isomerase. Adv Biol Regul 2023; 87:100938. [PMID: 36496344 PMCID: PMC9992314 DOI: 10.1016/j.jbior.2022.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The peptidyl-prolyl isomerase Pin1 cooperates with proline-directed kinases and phosphatases to regulate multiple oncogenic pathways. Pin1 specifically recognizes phosphorylated Ser/Thr-Pro motifs in proteins and catalyzes their cis-trans isomerization. The Pin1-catalyzed conformational changes determine the stability, activity, and subcellular localization of numerous protein substrates. We conducted a survey of eukaryotic protein kinases that are regulated by Pin1 and whose Pin1 binding sites have been identified. Our analyses reveal that Pin1 target sites in kinases do not fall exclusively within the intrinsically disordered regions of these enzymes. Rather, they fall into three groups based on their location: (i) within the catalytic kinase domain, (ii) in the C-terminal kinase region, and (iii) in regulatory domains. Some of the kinases downregulated by Pin1 activity are tumor-suppressing, and all kinases upregulated by Pin1 activity are functionally pro-oncogenic. These findings further reinforce the rationale for developing Pin1-specific inhibitors as attractive pharmaceuticals for cancer therapy.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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7
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Lee YM, Teoh DEJ, Yeung K, Liou YC. The kingdom of the prolyl-isomerase Pin1: The structural and functional convergence and divergence of Pin1. Front Cell Dev Biol 2022; 10:956071. [PMID: 36111342 PMCID: PMC9468764 DOI: 10.3389/fcell.2022.956071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
More than 20 years since its discovery, our understanding of Pin1 function in various diseases continues to improve. Pin1 plays a crucial role in pathogenesis and has been implicated in metabolic disorders, cardiovascular diseases, inflammatory diseases, viral infection, cancer and neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease. In particular, the role of Pin1 in neurodegenerative diseases and cancer has been extensively studied. Our understanding of Pin1 in cancer also led to the development of cancer therapeutic drugs targeting Pin1, with some currently in clinical trial phases. However, identifying a Pin1-specific drug with good cancer therapeutic effect remains elusive, thus leading to the continued efforts in Pin1 research. The importance of Pin1 is highlighted by the presence of Pin1 orthologs across various species: from vertebrates to invertebrates and Kingdom Animalia to Plantae. Among these Pin1 orthologs, their sequence and structural similarity demonstrate the presence of conservation. Moreover, their similar functionality between species further highlights the conservancy of Pin1. As researchers continue to unlock the mysteries of Pin1 in various diseases, using different Pin1 models might shed light on how to better target Pin1 for disease therapeutics. This review aims to highlight the various Pin1 orthologs in numerous species and their divergent functional roles. We will examine their sequence and structural similarities and discuss their functional similarities and uniqueness to demonstrate the interconnectivity of Pin1 orthologs in multiple diseases.
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8
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Born A, Soetbeer J, Henen MA, Breitgoff F, Polyhach Y, Jeschke G, Vögeli B. Ligand-specific conformational change drives interdomain allostery in Pin1. Nat Commun 2022; 13:4546. [PMID: 35927276 PMCID: PMC9352728 DOI: 10.1038/s41467-022-32340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.
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Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Morkos A Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.,Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.
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9
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Mori T, Saito S. Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase. J Phys Chem B 2022; 126:5185-5193. [PMID: 35795989 DOI: 10.1021/acs.jpcb.2c02095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins are intrinsically dynamic and change conformations over a wide range of time scales. While the conformational dynamics have been realized to be important for protein functions, e.g., in activity-stability trade-offs, how they play a role during enzyme catalysis has been of debate over decades. By studying Pin1 peptidyl-prolyl isomerase using extensive molecular dynamics simulations, here we discuss how the slow intrinsic dynamics of Pin1 observed in the NMR relaxation dispersion experiment occur and couple to isomerization reactions in molecular detail. In particular, we analyze the angular correlation functions of the backbone N-H bonds and find that slow conformational transitions occur at about the 310 helix in the apo state. These events at the helical region further affect the residues at about the ligand binding site. Unfolding of this helix leads to a tight hydrogen bond between the helical region and the ligand binding loop, thus forming a stable coiled structure. The helical and coiled structures are found to be characteristic of the Pin1-ligand complex with the ligand in the trans and cis states, respectively. These results indicate that the changes in the slow dynamics of Pin1 by the isomerization reaction occur via the shift in populations of the helical and coiled states, where the balance is dependent on the ligand isomerization states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan.,Department of Interdisciplinary Engineering Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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10
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Selles B, Dhalleine T, Boutilliat A, Rouhier N, Couturier J. A Redox-Sensitive Cysteine Is Required for PIN1At Function. FRONTIERS IN PLANT SCIENCE 2021; 12:735423. [PMID: 34975936 PMCID: PMC8716364 DOI: 10.3389/fpls.2021.735423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Parvulins are ubiquitous peptidyl-prolyl isomerases (PPIases) required for protein folding and regulation. Among parvulin members, Arabidopsis PIN1At, human PIN1, and yeast ESS1 share a conserved cysteine residue but differ by the presence of an N-terminal WW domain, absent in PIN1At. In this study, we have explored whether the cysteine residue of Arabidopsis PIN1At is involved in catalysis and subject to oxidative modifications. From the functional complementation of yeast ess1 mutant, we concluded that the cysteine at position 69 is mandatory for PIN1At function in vivo, unless being replaced by an Asp which is found in a few parvulin members. This result correlates with a decrease of the in vitro PPIase activity of non-functional PIN1At cysteinic variants. A decrease of PIN1At activity was observed upon H2O2 treatment. The in vitro oxidation of cysteine 69, which has an acidic pKa value of 4.9, leads to the formation of covalent dimers that are reduced by thioredoxins, or to sulfinic or sulfonic acid forms at higher H2O2 excess. These investigations highlight the importance of the sole cysteine residue of PIN1At for activity. The reversible formation of an intermolecular disulfide bond might constitute a protective or regulatory mechanism under oxidizing conditions.
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Affiliation(s)
| | | | | | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, Nancy, France
- Institut Universitaire de France, Paris, France
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11
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Born A, Soetbeer J, Breitgoff F, Henen MA, Sgourakis N, Polyhach Y, Nichols PJ, Strotz D, Jeschke G, Vögeli B. Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance. J Am Chem Soc 2021; 143:16055-16067. [PMID: 34579531 DOI: 10.1021/jacs.1c06289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States.,Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nikolaos Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Dean Strotz
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
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12
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Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021; 4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Accurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the "CTD code" that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing. Saccharomyces cerevisiae Ess1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26 of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4-5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.
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Affiliation(s)
- Kevin E. W. Namitz
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.29857.310000 0001 2097 4281Present Address: Department of Chemistry, Pennsylvania State University, University Park, PA USA
| | - Tongyin Zheng
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Ashley J. Canning
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Nilda L. Alicea-Velazquez
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.247980.00000 0001 2184 3689Present Address: Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT USA
| | - Carlos A. Castañeda
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Michael S. Cosgrove
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Steven D. Hanes
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
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13
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Identification of a potent and selective covalent Pin1 inhibitor. Nat Chem Biol 2020; 16:979-987. [PMID: 32483379 PMCID: PMC7442691 DOI: 10.1038/s41589-020-0550-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 04/15/2020] [Indexed: 12/16/2022]
Abstract
Peptidyl-prolyl cis/trans isomerase NIMA-interacting 1 (Pin1) is commonly overexpressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC). While Pin1 is dispensable for viability in mice, it is required for activated Ras to induce tumorigenesis, suggesting a role for Pin1 inhibitors in Ras-driven tumors, such as PDAC. We report the development of rationally designed peptide inhibitors that covalently target Cys113, a highly conserved cysteine located in the Pin1 active site. The inhibitors were iteratively optimized for potency, selectivity, and cell permeability to give BJP-06–005-3, a versatile tool compound with which to probe Pin1 biology and interrogate its role in cancer. In parallel to inhibitor development, we employed genetic and chemical-genetic strategies to assess the consequences of Pin1 loss in human PDAC cell lines. We demonstrate that Pin1 cooperates with mutant KRAS to promote transformation in PDAC, and that Pin1 inhibition impairs cell viability over time in PDAC cell lines.
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14
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Wang L, Zhou Y, Chen D, Lee TH. Peptidyl-Prolyl Cis/Trans Isomerase Pin1 and Alzheimer's Disease. Front Cell Dev Biol 2020; 8:355. [PMID: 32500074 PMCID: PMC7243138 DOI: 10.3389/fcell.2020.00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of dementia with cognitive decline. The neuropathology of AD is characterized by intracellular aggregation of neurofibrillary tangles consisting of hyperphosphorylated tau and extracellular deposition of senile plaques composed of beta-amyloid peptides derived from amyloid precursor protein (APP). The peptidyl-prolyl cis/trans isomerase Pin1 binds to phosphorylated serine or threonine residues preceding proline and regulates the biological functions of its substrates. Although Pin1 is tightly regulated under physiological conditions, Pin1 deregulation in the brain contributes to the development of neurodegenerative diseases, including AD. In this review, we discuss the expression and regulatory mechanisms of Pin1 in AD. We also focus on the molecular mechanisms by which Pin1 controls two major proteins, tau and APP, after phosphorylation and their signaling cascades. Moreover, the major impact of Pin1 deregulation on the progression of AD in animal models is discussed. This information will lead to a better understanding of Pin1 signaling pathways in the brain and may provide therapeutic options for the treatment of AD.
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Affiliation(s)
- Long Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ying Zhou
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Key Laboratory of Brain Aging and Neurodegenerative Diseases of Fujian Provincial Universities and Colleges, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Dongmei Chen
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Tae Ho Lee
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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15
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Mori T, Saito S. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase. J Chem Theory Comput 2020; 16:3396-3407. [PMID: 32268066 DOI: 10.1021/acs.jctc.9b01279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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16
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Chen D, Wang L, Lee TH. Post-translational Modifications of the Peptidyl-Prolyl Isomerase Pin1. Front Cell Dev Biol 2020; 8:129. [PMID: 32195254 PMCID: PMC7064559 DOI: 10.3389/fcell.2020.00129] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
The peptidyl-prolyl cis/trans isomerase (PPIase) Pin1 is a unique enzyme that only binds to Ser/Thr-Pro peptide motifs after phosphorylation and regulates the conformational changes of the bond. The Pin1-catalyzed isomerization upon phosphorylation can have profound effects on substrate biological functions, including their activity, stability, assembly, and subcellular localization, affecting its role in intracellular signaling, transcription, and cell cycle progression. The functions of Pin1 are regulated by post-translational modifications (PTMs) in many biological processes, which include phosphorylation, ubiquitination, SUMOylation and oxidation. Phosphorylation of different Pin1 sites regulates Pin1 enzymatic activity, binding ability, localization, and ubiquitination by different kinases under various cellular contexts. Moreover, SUMOylation and oxidation have been shown to downregulate Pin1 activity. Although Pin1 is tightly regulated under physiological conditions, deregulation of Pin1 PTMs contributes to the development of human diseases including cancer and Alzheimer's disease (AD). Therefore, manipulating the PTMs of Pin1 may be a promising therapeutic option for treating various human diseases. In this review, we focus on the molecular mechanisms of Pin1 regulation by PTMs and the major impact of Pin1 PTMs on the progression of cancer and AD.
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Affiliation(s)
- Dongmei Chen
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Long Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Tae Ho Lee
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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17
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Cheng CW, Tse E. Targeting PIN1 as a Therapeutic Approach for Hepatocellular Carcinoma. Front Cell Dev Biol 2020; 7:369. [PMID: 32010690 PMCID: PMC6974617 DOI: 10.3389/fcell.2019.00369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022] Open
Abstract
PIN1 is a peptidyl-prolyl cis/trans isomerase that specifically binds and catalyzes the cis/trans isomerization of the phosphorylated serine or threonine residue preceding a proline (pSer/Thr-Pro) motif of its interacting proteins. Through this phosphorylation-dependent prolyl isomerization, PIN1 is involved in the regulation of various important cellular processes including cell cycle progression, cell proliferation, apoptosis and microRNAs biogenesis; hence its dysregulation contributes to malignant transformation. PIN1 is highly expressed in hepatocellular carcinoma (HCC). By fine-tuning the functions of its interacting proteins such as cyclin D1, x-protein of hepatitis B virus and exportin 5, PIN1 plays an important role in hepatocarcinogenesis. Growing evidence supports that targeting PIN1 is a potential therapeutic approach for HCC by inhibiting cell proliferation, inducing cellular apoptosis, and restoring microRNAs biogenesis. Novel formulation of PIN1 inhibitors that increases in vivo bioavailability of PIN1 inhibitors represents a promising future direction for the therapeutic strategy of HCC treatment. In this review, the mechanisms underlying PIN1 over-expression in HCC are explored. Furthermore, we also discuss the roles of PIN1 in HCC tumorigenesis and metastasis through its interaction with various phosphoproteins. Finally, recent progress in the therapeutic options targeting PIN1 for HCC treatment is examined and summarized.
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Affiliation(s)
- Chi-Wai Cheng
- Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Eric Tse
- Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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18
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Born A, Henen MA, Vögeli B. Activity and Affinity of Pin1 Variants. MOLECULES (BASEL, SWITZERLAND) 2019; 25:molecules25010036. [PMID: 31861908 PMCID: PMC6983177 DOI: 10.3390/molecules25010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/07/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022]
Abstract
Pin1 is a peptidyl-prolyl isomerase responsible for isomerizing phosphorylated S/T-P motifs. Pin1 has two domains that each have a distinct ligand binding site, but only its PPIase domain has catalytic activity. Vast evidence supports interdomain allostery of Pin1, with binding of a ligand to its regulatory WW domain impacting activity in the PPIase domain. Many diverse studies have made mutations in Pin1 in order to elucidate interactions that are responsible for ligand binding, isomerase activity, and interdomain allostery. Here, we summarize these mutations and their impact on Pin1′s structure and function.
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Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO 80045, USA; (A.B.); (M.A.H.)
- Correspondence: ; Tel.: +1-303-724-1627
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19
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Ikura T, Yonezawa Y, Ito N. Mutational effects of Cys113 on structural dynamics of Pin1. Biophys Physicobiol 2019; 16:452-465. [PMID: 31984197 PMCID: PMC6976032 DOI: 10.2142/biophysico.16.0_452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/17/2019] [Indexed: 12/01/2022] Open
Abstract
Pin1 is a peptidyl-prolyl isomerase (PPIase) which catalyzes cis/trans isomerization of pS/pT-P bond. Its activity is related to various cellular functions including suppression of Alzheimer's disease. A cysteine residue C113 is known to be important for its PPIase activity; a mutation C113A reduced the activity by 130-fold. According to various nuclear magnetic resonance experiments for mutants of C113 and molecular dynamics (MD) simulation of wild-type Pin1, the protonation sate of Sγ of C113 regulates the hydrogen-bonding network of the dual-histidine motif (H59, H157) whose dynamics may affect substrate binding ability. However, it was still unclear why such local dynamic changes altered the PPIase activity of Pin1. In this study, we performed 500 ns of MD simulations of full-length wild-type Pin1 and C113A mutant in order to elucidate why the mutation C113A drastically reduced the PPIase activity of Pin1. The principal component analysis for both MD trajectories clearly elucidated that the mutation C113A suppressed the dynamics of Pin1 because it stabilized a hydrogen-bond between Nɛ of H59 and Oγ of S115. In the dynamics of wild-type protein, the phosphate binding loop (K63-S71) as well as the interdomain hinge showed the closed-open dynamics which correlated with the change of the hydrogen-bonding network of the dual-histidine motif. In contrast, in the dynamics of C113A mutant, the phosphate binding loop took only the closed conformation together with the interdomain hinge. Such closed-open dynamics must be essential for the PPIase activity of Pin1.
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Affiliation(s)
- Teikichi Ikura
- Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Nobutoshi Ito
- Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
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20
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Insight into the structural stability of wild-type and histidine mutants in Pin1 by experimental and computational methods. Sci Rep 2019; 9:8413. [PMID: 31182777 PMCID: PMC6557836 DOI: 10.1038/s41598-019-44926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/28/2019] [Indexed: 01/21/2023] Open
Abstract
Pin1, a polypeptide proline isomerase parvulin, plays a key role in Alzheimer’s disease (AD), common tumors and cancers. Two conservative histidine residues, His59 and His157, are important for maintaining the stability of the PPIase domain. Hence multiple spectral and computational techniques were performed to investigate the potential mechanism of two histidine residues. Thermal denaturation indicated that both residues His59 and His157 are not sensitive to the lower temperatures, while residue His59 is more sensitive to the higher temperatures than residue His157. Acidic denaturation suggested that influences of both residues His59 and His157 to acidic stability were the difference from Pin1-WT. ANS and RLS spectra hinted that there was no significant effect on hydrophobic change and aggregation by histidine mutations. The GndHCl-induced denaturation implied that residues His59 and His157 contributed the most to the chemical stability. MD simulations revealed that residues His59 and His157 mutations resulted in that the hydrogen bond network of the dual histidine motif was destroyed wholly. In summary, these histidine residues play an important role in maintaining the structural stability of the PPIase domain.
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21
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Rehic E, Hoenig D, Kamba BE, Goehring A, Hofmann E, Gasper R, Matena A, Bayer P. Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei. Biomolecules 2019; 9:biom9030093. [PMID: 30866577 PMCID: PMC6468809 DOI: 10.3390/biom9030093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
Trypanosoma brucei is a unicellular eukaryotic parasite, which causes the African sleeping sickness in humans. The recently discovered trypanosomal protein Parvulin 42 (TbPar42) plays a key role in parasite cell proliferation. Homologues of this two-domain protein are exclusively found in protozoa species. TbPar42 exhibits an N-terminal forkhead associated (FHA)-domain and a peptidyl-prolyl-cis/trans-isomerase (PPIase) domain, both connected by a linker. Using NMR and X-ray analysis as well as activity assays, we report on the structures of the single domains of TbPar42, discuss their intra-molecular interplay, and give some initial hints as to potential cellular functions of the protein.
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Affiliation(s)
- Edisa Rehic
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Dana Hoenig
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Bianca E Kamba
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Anna Goehring
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Raphael Gasper
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany.
| | - Anja Matena
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Peter Bayer
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
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22
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Mori T, Saito S. Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase. J Phys Chem Lett 2019; 10:474-480. [PMID: 30607953 DOI: 10.1021/acs.jpclett.8b03607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Conformational flexibility of protein is essential for enzyme catalysis. Yet, how protein's conformational rearrangements and dynamics contribute to catalysis remains highly controversial. To unravel protein's role in catalysis, it is inevitable to understand the static and dynamic mechanisms simultaneously. To this end, here the Pin1-catalyzed isomerization reaction is studied from the two perspectives. The static view indicates that the hydrogen bonds involving Pin1 rearrange in a tightly coupled manner with isomerization. In sharp contrast, the isomerization dynamics are found to be very rapid; protein's slow conformational rearrangements thus cannot occur simultaneously with isomerization, and the reaction proceeds in a nonequilibrium manner. The distinctive protein conformations necessary to stabilize the transition state are prepared a priori, i.e., as conformational excited states. The present result suggests that enzymatic reaction is not a simple thermal activation from equilibrium directly to the transition state, thus adding a novel perspective to Pauling's view.
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Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji , Okazaki , Aichi 444-8585 , Japan
- School of Physical Sciences , The Graduate University for Advanced Studies , Okazaki , Aichi 444-8585 , Japan
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23
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El Boustani M, De Stefano L, Caligiuri I, Mouawad N, Granchi C, Canzonieri V, Tuccinardi T, Giordano A, Rizzolio F. A Guide to PIN1 Function and Mutations Across Cancers. Front Pharmacol 2019; 9:1477. [PMID: 30723410 PMCID: PMC6349750 DOI: 10.3389/fphar.2018.01477] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
PIN1 is a member of a family of peptidylprolyl isomerases that bind phosphoproteins and catalyze the rapid cis-trans isomerization of proline peptidyl bonds, resulting in an alteration of protein structure, function, and stability. PIN1 is overexpressed in human cancers, suggesting it promotes tumorigenesis, but depending on the cellular context, it also acts as a tumor suppressor. Here, we review the role of PIN1 in cancer and the regulation of PIN1 expression, and catalog the single nucleotide polymorphisms, and mutations in PIN1 gene associated with cancer. In addition, we provide a 3D model of the protein to localize the mutated residues.
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Affiliation(s)
- Maguie El Boustani
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Doctoral School in Molecular Biomedicine, University of Trieste, Trieste, Italy
| | - Lucia De Stefano
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Doctoral School in Chemistry, University of Trieste, Trieste, Italy
| | - Isabella Caligiuri
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | - Nayla Mouawad
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | | | | | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Flavio Rizzolio
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy.,Department of Molecular Science and Nanosystems, Ca' Foscari University of Venice, Venice, Italy
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24
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Abstract
Cell cycle progression is tightly controlled by many cell cycle-regulatory proteins that are in turn regulated by a family of cyclin-dependent kinases (CDKs) through protein phosphorylation. The peptidyl-prolyl cis/trans isomerase PIN1 provides a further post-phosphorylation modification and functional regulation of these CDK-phosphorylated proteins. PIN1 specifically binds the phosphorylated serine or threonine residue preceding a proline (pSer/Thr-Pro) motif of its target proteins and catalyzes the cis/trans isomerization on the pSer/Thr-Pro peptide bonds. Through this phosphorylation-dependent prolyl isomerization, PIN1 fine-tunes the functions of various cell cycle-regulatory proteins including retinoblastoma protein (Rb), cyclin D1, cyclin E, p27, Cdc25C, and Wee1. In this review, we discussed the essential roles of PIN1 in regulating cell cycle progression through modulating the functions of these cell cycle-regulatory proteins. Furthermore, the mechanisms underlying PIN1 overexpression in cancers were also explored. Finally, we examined and summarized the therapeutic potential of PIN1 inhibitors in cancer therapy.
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Affiliation(s)
- Chi-Wai Cheng
- Department of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Eric Tse
- Department of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
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25
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Lee YM, Liou YC. Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1. Front Oncol 2018; 8:469. [PMID: 30460195 PMCID: PMC6232885 DOI: 10.3389/fonc.2018.00469] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/04/2018] [Indexed: 01/22/2023] Open
Abstract
Pin1 belongs to the family of the peptidyl-prolyl cis-trans isomerase (PPIase), which is a class of enzymes that catalyze the cis/trans isomerization of the Proline residue. Pin1 is unique and only catalyzes the phosphorylated Serine/Threonine-Proline (S/T-P) motifs of a subset of proteins. Since the discovery of Pin1 as a key protein in cell cycle regulation, it has been implicated in numerous diseases, ranging from cancer to neurodegenerative diseases. The main features of Pin1 lies in its two main domains: the WW (two conserved tryptophan) domain and the PPIase domain. Despite extensive studies trying to understand the mechanisms of Pin1 functions, how these two domains contribute to the biological roles of Pin1 in cellular signaling requires more investigations. The WW domain of Pin1 is known to have a higher affinity to its substrate than that of the PPIase domain. Yet, the WW domain seems to prefer the trans configuration of phosphorylated S/T-P motif, while the PPIase catalyzes the cis to trans isomerasion. Such contradicting information has generated much confusion as to the actual mechanism of Pin1 function. In addition, dynamic allostery has been suggested to be important for Pin1 function. Henceforth, in this review, we will be looking at the progress made in understanding the function of Pin1, and how these understandings can aid us in overcoming the diseases implicated by Pin1 such as cancer during drug development.
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Affiliation(s)
- Yew Mun Lee
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yih-Cherng Liou
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
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26
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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27
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Cheng CW, Leong KW, Ng YM, Kwong YL, Tse E. The peptidyl-prolyl isomerase PIN1 relieves cyclin-dependent kinase 2 (CDK2) inhibition by the CDK inhibitor p27. J Biol Chem 2017; 292:21431-21441. [PMID: 29118189 DOI: 10.1074/jbc.m117.801373] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/27/2017] [Indexed: 01/22/2023] Open
Abstract
PIN1 is a peptidyl-prolyl isomerase that catalyzes the cis/trans isomerization of peptide bonds between proline and phosphorylated serine/threonine residues. By changing the conformation of its protein substrates, PIN1 increases the activities of key proteins that promote cell cycle progression and oncogenesis. Moreover, it has been shown that PIN1 stabilizes and increases the level of the cyclin-dependent kinase (CDK) inhibitor p27, which inhibits cell cycle progression by binding cyclin A- and cyclin E-CDK2. Notwithstanding the associated increase in the p27 level, PIN1 expression promotes rather than retards cell proliferation. To explain the paradoxical effects of PIN1 on p27 levels and cell cycle progression, we hypothesized that PIN1 relieves CDK2 inhibition by suppressing the CDK inhibitory activity of p27. Here, we confirmed that PIN1-expressing cells exhibit higher p27 levels but have increased CDK2 activities and higher proliferation rates in the S-phase compared with Pin1-null fibroblasts or PIN1-depleted hepatoma cells. Using co-immunoprecipitation and CDK kinase activity assays, we found that PIN1 binds the phosphorylated Thr187-Pro motif in p27 and reduces p27's interaction with cyclin A- or cyclin E-CDK2, leading to increased CDK2 kinase activity. In conclusion, our results indicate that although PIN1 increases p27 levels, it also attenuates p27's inhibitory activity on CDK2 and thereby contributes to increased G1-S phase transitions and cell proliferation.
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Affiliation(s)
- Chi-Wai Cheng
- From the Department of Medicine, The University of Hong Kong, Hong Kong
| | - Ka-Wai Leong
- From the Department of Medicine, The University of Hong Kong, Hong Kong
| | - Yiu-Ming Ng
- From the Department of Medicine, The University of Hong Kong, Hong Kong
| | - Yok-Lam Kwong
- From the Department of Medicine, The University of Hong Kong, Hong Kong
| | - Eric Tse
- From the Department of Medicine, The University of Hong Kong, Hong Kong
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28
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Wang J, Kawasaki R, Uewaki JI, Rashid AUR, Tochio N, Tate SI. Dynamic Allostery Modulates Catalytic Activity by Modifying the Hydrogen Bonding Network in the Catalytic Site of Human Pin1. Molecules 2017; 22:molecules22060992. [PMID: 28617332 PMCID: PMC6152768 DOI: 10.3390/molecules22060992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 02/01/2023] Open
Abstract
Allosteric communication among domains in modular proteins consisting of flexibly linked domains with complimentary roles remains poorly understood. To understand how complementary domains communicate, we have studied human Pin1, a representative modular protein with two domains mutually tethered by a flexible linker: a WW domain for substrate recognition and a peptidyl-prolyl isomerase (PPIase) domain. Previous studies of Pin1 showed that physical contact between the domains causes dynamic allostery by reducing conformation dynamics in the catalytic domain, which compensates for the entropy costs of substrate binding to the catalytic site and thus increases catalytic activity. In this study, the S138A mutant PPIase domain, a mutation that mimics the structural impact of the interdomain contact, was demonstrated to display dynamic allostery by rigidification of the α2-α3 loop that harbors the key catalytic residue C113. The reduced dynamics of the α2-α3 loop stabilizes the C113-H59 hydrogen bond in the hydrogen-bonding network of the catalytic site. The stabilized hydrogen bond between C113 and H59 retards initiation of isomerization, which explains the reduced isomerization rate by ~20% caused by the S138A mutation. These results provide new insight into the interdomain allosteric communication of Pin1.
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Affiliation(s)
- Jing Wang
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Jun-Ichi Uewaki
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Arif U R Rashid
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Naoya Tochio
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
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29
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Carnemolla A, Michelazzi S, Agostoni E. PIN1 Modulates Huntingtin Levels and Aggregate Accumulation: An In vitro Model. Front Cell Neurosci 2017; 11:121. [PMID: 28533744 PMCID: PMC5420564 DOI: 10.3389/fncel.2017.00121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022] Open
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder characterized by a polyglutamine expansion within the N-terminal region of huntingtin protein (HTT). Cellular mechanisms promoting mutant huntingtin (mHTT) clearance are of great interest in HD pathology as they can lower the level of the mutant protein and its toxic aggregated species, thus affecting disease onset and progression. We have previously shown that the prolyl-isomerase PIN1 represents a promising negative regulator of mHTT aggregate accumulation using a genetically precise HD mouse model, namely HdhQ111 mice. Therefore, the current study aims at underpinning the mechanism by which PIN1 affects huntingtin's aggregates. We found that PIN1 overexpression led to a reduction of mHTT aggregates in HEK293 cells, and that this could be linked to a negative regulation of mHTT half-life by PIN1. Furthermore, we show that PIN1 has the ability to stimulate the proteasome presenting evidence of a mechanism regulating this phenomenon. Our findings provide a rationale for future investigation into PIN1 with the potential for the development of novel therapeutic strategies.
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Affiliation(s)
- Alisia Carnemolla
- International School for Advanced Studies, Area of NeuroscienceTrieste, Italy
| | - Silvia Michelazzi
- International School for Advanced Studies, Area of NeuroscienceTrieste, Italy
| | - Elena Agostoni
- International School for Advanced Studies, Area of NeuroscienceTrieste, Italy
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30
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Rogals MJ, Greenwood AI, Kwon J, Lu KP, Nicholson LK. Neighboring phosphoSer-Pro motifs in the undefined domain of IRAK1 impart bivalent advantage for Pin1 binding. FEBS J 2016; 283:4528-4548. [PMID: 27790836 DOI: 10.1111/febs.13943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023]
Abstract
The peptidyl prolyl isomerase Pin1 has two domains that are considered to be its binding (WW) and catalytic (PPIase) domains, both of which interact with phosphorylated Ser/Thr-Pro motifs. This shared specificity might influence substrate selection, as many known Pin1 substrates have multiple sequentially close phosphoSer/Thr-Pro motifs, including the protein interleukin-1 receptor-associated kinase-1 (IRAK1). The IRAK1 undefined domain (UD) contains two sets of such neighboring motifs (Ser131/Ser144 and Ser163/Ser173), suggesting possible bivalent interactions with Pin1. Using a series of NMR titrations with 15N-labeled full-length Pin1 (Pin1-FL), PPIase, or WW domain and phosphopeptides representing the Ser131/Ser144 and Ser163/Ser173 regions of IRAK1-UD, bivalent interactions were investigated. Binding studies using singly phosphorylated peptides showed that individual motifs displayed weak affinities (> 100 μm) for Pin1-FL and each isolated domain. Analysis of dually phosphorylated peptides binding to Pin1-FL showed that inclusion of bivalent states was necessary to fit the data. The resulting complex model and fitted parameters were applied to predict the impact of bivalent states at low micromolar concentrations, demonstrating significant affinity enhancement for both dually phosphorylated peptides (3.5 and 24 μm for peptides based on the Ser131/Ser144 and Ser163/Ser173 regions, respectively). The complementary technique biolayer interferometry confirmed the predicted affinity enhancement for a representative set of singly and dually phosphorylated Ser131/Ser144 peptides at low micromolar concentrations, validating model predictions. These studies provide novel insights regarding the complexity of interactions between Pin1 and activated IRAK1, and more broadly suggest that phosphorylation of neighboring Ser/Thr-Pro motifs in proteins might provide competitive advantage at cellular concentrations for engaging with Pin1.
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Affiliation(s)
- Monique J Rogals
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Alexander I Greenwood
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, IL, USA
| | - Jeahoo Kwon
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Kun Ping Lu
- Division of Translational Therapeutics, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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31
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Ikolo F, Zhang M, Harrington DJ, Robinson C, Waller AS, Sutcliffe IC, Black GW. Characterisation of SEQ0694 (PrsA/PrtM) of Streptococcus equi as a functional peptidyl-prolyl isomerase affecting multiple secreted protein substrates. MOLECULAR BIOSYSTEMS 2016; 11:3279-86. [PMID: 26466087 DOI: 10.1039/c5mb00543d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptidyl-prolyl isomerase (PPIase) lipoproteins have been shown to influence the virulence of a number of Gram-positive bacterial human and animal pathogens, most likely through facilitating the folding of cell envelope and secreted virulence factors. Here, we used a proteomic approach to demonstrate that the Streptococcus equi PPIase SEQ0694 alters the production of multiple secreted proteins, including at least two putative virulence factors (FNE and IdeE2). We demonstrate also that, despite some unusual sequence features, recombinant SEQ0694 and its central parvulin domain are functional PPIases. These data add to our knowledge of the mechanisms by which lipoprotein PPIases contribute to the virulence of streptococcal pathogens.
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Affiliation(s)
- Felicia Ikolo
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK. and Department of Biochemistry, School of Medicine, St. George's University, True Blue, St. George's, Grenada
| | - Meng Zhang
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
| | - Dean J Harrington
- Division of Biomedical Science, School of Life Sciences, University of Bradford, West Yorkshire, BD7 1DP, UK
| | - Carl Robinson
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Andrew S Waller
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk CB8 7UU, UK
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
| | - Gary W Black
- Department of Applied Sciences, Faculty of Health & Life Sciences, University of Northumbria at Newcastle, Newcastle upon Tyne, NE1 8ST, UK.
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32
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Dunyak BM, Gestwicki JE. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. J Med Chem 2016; 59:9622-9644. [PMID: 27409354 DOI: 10.1021/acs.jmedchem.6b00411] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptidyl-proline isomerases (PPIases) are a chaperone superfamily comprising the FK506-binding proteins (FKBPs), cyclophilins, and parvulins. PPIases catalyze the cis/trans isomerization of proline, acting as a regulatory switch during folding, activation, and/or degradation of many proteins. These "clients" include proteins with key roles in cancer, neurodegeneration, and psychiatric disorders, suggesting that PPIase inhibitors could be important therapeutics. However, the active site of PPIases is shallow, solvent-exposed, and well conserved between family members, making selective inhibitor design challenging. Despite these hurdles, macrocyclic natural products, including FK506, rapamycin, and cyclosporin, bind PPIases with nanomolar or better affinity. De novo attempts to derive new classes of inhibitors have been somewhat less successful, often showcasing the "undruggable" features of PPIases. Interestingly, the most potent of these next-generation molecules tend to integrate features of the natural products, including macrocyclization or proline mimicry strategies. Here, we review recent developments and ongoing challenges in the inhibition of PPIases, with a focus on how natural products might inform the creation of potent and selective inhibitors.
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Affiliation(s)
- Bryan M Dunyak
- Department of Biological Chemistry, University of Michigan Medical School , 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
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33
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Wang J, Tochio N, Kawasaki R, Tamari Y, Xu N, Uewaki JI, Utsunomiya-Tate N, Tate SI. Allosteric Breakage of the Hydrogen Bond within the Dual-Histidine Motif in the Active Site of Human Pin1 PPIase. Biochemistry 2015; 54:5242-53. [PMID: 26226559 DOI: 10.1021/acs.biochem.5b00606] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intimate cooperativity among active site residues in enzymes is a key factor for regulating elaborate reactions that would otherwise not occur readily. Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is the phosphorylation-dependent cis-trans peptidyl-prolyl isomerase (PPIase) that specifically targets phosphorylated Ser/Thr-Pro motifs. Residues C113, H59, H157, and T152 form a hydrogen bond network in the active site, as in the noted connection. Theoretical studies have shown that protonation to thiolate C113 leads to rearrangement of this hydrogen bond network, with switching of the tautomeric states of adjacent histidines (H59 and H157) [Barman, A., and Hamelberg, D. (2014) Biochemistry 53, 3839-3850]. This is called the "dual-histidine motif". Here, C113A and C113S Pin1 mutants were found to alter the protonation states of H59 according to the respective residue type replaced at C113, and the mutations resulted in disruption of the hydrogen bond within the dual-histidine motif. In the C113A mutant, H59 was observed to be in exchange between ε- and δ-tautomers, which widened the entrance of the active site cavity, as seen by an increase in the distance between residues A113 and S154. The C113S mutant caused H59 to exchange between the ε-tautomer and imidazolium while not changing the active site structure. Moreover, the imidazole ring orientations of H59 and H157 were changed in the C113S mutant. These results demonstrated that a mutation at C113 modulates the hydrogen bond network dynamics. Thus, C113 acts as a pivot to drive the concerted function among the residues in the hydrogen bond network, as theoretically predicted.
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Affiliation(s)
- Jing Wang
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Naoya Tochio
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Yu Tamari
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Ning Xu
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Jun-Ichi Uewaki
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Naoko Utsunomiya-Tate
- Faculty of Pharma-Sciences, Teikyo University , 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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34
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The structural and functional role of the three tryptophan residues in Pin1. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 146:58-67. [DOI: 10.1016/j.jphotobiol.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/25/2015] [Accepted: 03/12/2015] [Indexed: 11/23/2022]
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35
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Innes BT, Sowole MA, Gyenis L, Dubinsky M, Konermann L, Litchfield DW, Brandl CJ, Shilton BH. Peroxide-mediated oxidation and inhibition of the peptidyl-prolyl isomerase Pin1. Biochim Biophys Acta Mol Basis Dis 2015; 1852:905-12. [DOI: 10.1016/j.bbadis.2014.12.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/18/2014] [Accepted: 12/23/2014] [Indexed: 12/31/2022]
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36
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Abstract
Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 consists of two tethered domains: a WW domain for substrate binding, and a catalytic domain for peptidyl-prolyl isomerase (PPIase) activity. Pin1 accelerates the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs within proteins regulating the cell cycle and neuronal development. The early x-ray (Ranganathan et al. 1997; Verdecia et al. 2000) and solution NMR studies (Bayer et al. 2003; Jacobs et al. 2003) of Pin1 indicated inter- and intradomain motion. We became interested in exploring how such motions might affect interdomain communication, using NMR. Our accumulated results indicate substrate binding to Pin1 WW domain changes the intra/inter domain mobility, thereby altering substrate activity in the distal PPIase domain catalytic site. Thus, Pin1 shows evidence of dynamic allostery, in the sense of Cooper and Dryden (Cooper and Dryden 1984). We highlight our results supporting this conclusion, and summarize them via a simple speculative model of conformational selection.
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37
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Ladani ST, Souffrant MG, Barman A, Hamelberg D. Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl cis-trans isomerases. Biochim Biophys Acta Gen Subj 2015; 1850:1994-2004. [PMID: 25585011 DOI: 10.1016/j.bbagen.2014.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND Peptidyl prolyl cis-trans isomerization of the protein backbone is involved in the regulation of many biological processes. Cis-trans isomerization is notoriously slow and is catalyzed by a family of cis-trans peptidyl prolyl isomerases (PPIases) that have been implicated in many diseases. A general consensus on how these enzymes speed up prolyl isomerization has not been reached after decades of both experimental and computational studies. SCOPE OF REVIEW Computational studies carried out to understand the catalytic mechanism of the prototypical FK506 binding protein 12, Cyclophilin A and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) are reviewed. A summary and an evaluation of the implications of the proposed mechanisms from computational studies are presented. MAJOR CONCLUSIONS The analysis of computational studies and evaluation of the proposed mechanisms provide a general consensus and a better understanding of PPIase catalysis. The speedup of the rate of peptidyl-prolyl isomerization by PPIases can be best described by a catalytic mechanism in which the substrate in transition state configuration is stabilized. The enzymes preferentially bind the transition state configuration of the substrate relative to the cis conformation, which in most cases is bound better than the trans conformation of the substrate. Stabilization of the transition state configuration of the substrate leads to a lower free energy barrier and a faster rate of isomerization when compared to the uncatalyzed isomerization reaction. GENERAL SIGNIFICANCE Fully understanding the catalytic mechanism of PPIases has broad implications for drug design, elucidation of the molecular basis of many diseases, protein engineering, and enzyme catalysis in general. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Safieh Tork Ladani
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Michael G Souffrant
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Arghya Barman
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA.
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38
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Sowole MA, Innes BT, Amunugama M, Litchfield DW, Brandl CJ, Shilton BH, Konermann L. Noncovalent binding of a cyclic peptide inhibitor to the peptidyl-prolyl isomerase Pin1, explored by hydrogen exchange mass spectrometry. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pin1 is a peptidyl-prolyl isomerase (PPIase) that plays a central role in eukaryotic cell cycle regulation, making this protein an interesting target for cancer therapy. Pin1 exhibits high specificity for substrates where proline is preceded by phosphoserine or phosphothreonine. The protein comprises an N-terminal WW (tryptophan–tryptophan) domain and a C-terminal PPIase domain. The cyclic peptide [CRYPEVEIC] (square brackets are used to denote the cyclic structure) represents a lead compound for a new class of nonphosphorylated Pin1 inhibitors. Unfortunately, it has not been possible thus far to characterize the Pin1–[CRYPEVEIC] complex by X-ray crystallography. Thus, the exact binding mode remains unknown. The current work employs hydrogen/deuterium exchange mass spectrometry for gaining insights into the Pin1–[CRYPEVEIC] interactions. The WW domain shows extensive conformational dynamics, both in the presence and in the absence of ligand. In contrast, profound changes in deuteration kinetics are observed in the PPIase domain after the addition of [CRYPEVEIC]. The secondary structure elements β2, α3, and α4 exhibit markedly reduced deuteration, consistent with their postulated involvement in ligand binding. Unexpectedly, [CRYPEVEIC] destabilizes the range of residues 61–86, a segment that comprises basic side chains that normally interact with the substrate phosphate. This destabilization is likely caused by steric clashes with Y3 or E5 of the inhibitor. Ligand-induced destabilization has previously been reported for a few other proteins, but effects of this type are not very common. Our findings suggest that future crystallization trials on Pin1 variants deleted for residues in the 61–86 range might provide a path towards high-resolution X-ray structures of Pin1 bound to cyclic peptide inhibitors.
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Affiliation(s)
- Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Brendan T. Innes
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mahasilu Amunugama
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - David W. Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J. Brandl
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Brian H. Shilton
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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39
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Xu N, Tochio N, Wang J, Tamari Y, Uewaki JI, Utsunomiya-Tate N, Igarashi K, Shiraki T, Kobayashi N, Tate SI. The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif. Biochemistry 2014; 53:5568-78. [PMID: 25100325 DOI: 10.1021/bi5007817] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pin1 peptidyl-prolyl isomerase (PPIase) catalyzes specifically the pSer/pThr-Pro motif. The cis-trans isomerization mechanism has been studied by various approaches, including X-ray crystallography, site-directed mutagenesis, and the kinetic isotope effect on isomerization. However, a complete picture of the reaction mechanism remains elusive. On the basis of the X-ray structure of Pin1, residue C113 was proposed to play a nucleophile attacker to catalyze the isomerization. The controversial result that the C113D Pin1 mutant retains the activity, albeit at a reduced level, challenges the importance of C113 as a catalyst. To facilitate our understanding of the Pin1 isomerization process, we compared the structures and dynamics of the wild type with those of the C113D mutant Pin1 PPIase domains (residues 51-163). We found the C113D mutation disturbed the hydrogen bonds between the conserved histidine residues, H59 and H157 ("dual-histidine motif"); H59 imidazole forms a stable hydrogen bond to H157 in the wild type, whereas it has a strong hydrogen bond to D113 with weakened bonding to H157 in the C113D mutant. The C113D mutation unbalanced the hydrogen bonding tug of war for H59 between C113/D113 and H157 and destabilized the catalytic site structure, which eventually resulted in an altered conformation of the basic triad (K63, R68, and R69) that binds to the phosphate group in a substrate. The change in the basic triad structure could explain the severely weakened substrate binding ability of the C113D mutant. Overall, this work demonstrated that C113 plays a role in keeping the catalytic site in an active fold, which has never before been described.
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Affiliation(s)
- Ning Xu
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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40
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Di Martino GP, Masetti M, Cavalli A, Recanatini M. Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations. Proteins 2014; 82:2943-56. [PMID: 25066180 DOI: 10.1002/prot.24650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/25/2014] [Accepted: 07/15/2014] [Indexed: 12/22/2022]
Abstract
The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier.
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Affiliation(s)
- Giovanni Paolo Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, 40126, Bologna, Italy
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41
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Barman A, Hamelberg D. Cysteine-mediated dynamic hydrogen-bonding network in the active site of Pin1. Biochemistry 2014; 53:3839-50. [PMID: 24840168 DOI: 10.1021/bi5000977] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Enzymes catalyze a plethora of chemical reactions that are tightly regulated and intricately coupled in biology. Catalysis of phosphorylation-dependent cis-trans isomerization of peptidyl-prolyl bonds, which act as conformational switches in regulating many post-phosphorylation processes, is considered to be one of the most critical. Pin1 is a cis-trans isomerase of peptidyl-prolyl(ω-) bonds of phosphorylated-Ser/Thr-Pro motifs and has been implicated in many diseases. Structural and experimental studies are still unable to resolve the mechanistic role and protonation states of two adjacent histidines (His59 and His157) and a cysteine (Cys113) in the active site of Pin1. Here, we show that the protonation state of Cys113 mediates a dynamic hydrogen-bonding network in the active site of Pin1, involving the two adjacent histidines and several other residues that are highly conserved and necessary for catalysis. We have used detailed free energy calculations and molecular dynamics simulations, complementing previous experiments, to resolve the ambiguities in the orientations of the histidines and protonation states of these key active site residues, details that are critical for fully understanding the mechanism of Pin1 and necessary for developing potent inhibitors. Importantly, Cys113 is shown to alternate between the unprotonated and neutral states, unprotonated in free Pin1 and neutral in substrate-bound Pin1. Our results are consistent with experiments and provide an explanation for the chemical reactivity of free Pin1 that is suggested to be necessary for the regulation of the enzyme.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-4098, United States
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The Ess1 prolyl isomerase: traffic cop of the RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:316-33. [PMID: 24530645 DOI: 10.1016/j.bbagrm.2014.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 02/01/2014] [Accepted: 02/03/2014] [Indexed: 11/23/2022]
Abstract
Ess1 is a prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II. Ess1 works by catalyzing the cis/trans conversion of pSer5-Pro6 bonds, and to a lesser extent pSer2-Pro3 bonds, within the carboxy-terminal domain (CTD) of Rpb1, the largest subunit of RNA pol II. Ess1 is conserved in organisms ranging from yeast to humans. In budding yeast, Ess1 is essential for growth and is required for efficient transcription initiation and termination, RNA processing, and suppression of cryptic transcription. In mammals, Ess1 (called Pin1) functions in a variety of pathways, including transcription, but it is not essential. Recent work has shown that Ess1 coordinates the binding and release of CTD-binding proteins that function as co-factors in the RNA pol II complex. In this way, Ess1 plays an integral role in writing (and reading) the so-called CTD code to promote production of mature RNA pol II transcripts including non-coding RNAs and mRNAs.
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43
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Mercedes-Camacho AY, Mullins AB, Mason MD, Xu GG, Mahoney BJ, Wang X, Peng JW, Etzkorn FA. Kinetic isotope effects support the twisted amide mechanism of Pin1 peptidyl-prolyl isomerase. Biochemistry 2013; 52:7707-13. [PMID: 24116866 DOI: 10.1021/bi400700b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Pin1 peptidyl-prolyl isomerase catalyzes isomerization of pSer/pThr-Pro motifs in regulating the cell cycle. Peptide substrates, Ac-Phe-Phe-phosphoSer-Pro-Arg-p-nitroaniline, were synthesized in unlabeled form, and with deuterium-labeled Ser-d3 and Pro-d7 amino acids. Kinetic data were collected as a function of Pin1 concentration to measure kinetic isotope effects (KIEs) on catalytic efficiency (kcat/Km). The normal secondary (2°) KIE value measured for the Ser-d3 substrate (kH/kD = 1.6 ± 0.2) indicates that the serine carbonyl does not rehybridize from sp(2) to sp(3) in the rate-determining step, ruling out a nucleophilic addition mechanism. The normal 2° KIE can be explained by hyperconjugation between Ser α-C-H/D and C═O and release of steric strain upon rotation of the amide bond from cis to syn-exo. The inverse 2° KIE value (kH/kD = 0.86 ± 0.08) measured for the Pro-d7 substrate indicates rehybridization of the prolyl nitrogen from sp(2) to sp(3) during the rate-limiting step of isomerization. No solvent kinetic isotope was measured by NMR exchange spectroscopy (kH2O/kD2O = 0.92 ± 0.12), indicating little or no involvement of exchangeable protons in the mechanism. These results support the formation of a simple twisted amide transition state as the mechanism for peptidyl prolyl isomerization catalyzed by Pin1. A model of the reaction mechanism is presented using crystal structures of Pin1 with ground state analogues and an inhibitor that resembles a twisted amide transition state.
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Wilson KA, Bouchard JJ, Peng JW. Interdomain interactions support interdomain communication in human Pin1. Biochemistry 2013; 52:6968-81. [PMID: 24020391 PMCID: PMC3794440 DOI: 10.1021/bi401057x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
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Pin1 is an essential mitotic regulator
consisting of a peptidyl–prolyl
isomerase (PPIase) domain flexibly tethered to a smaller Trp–Trp
(WW) binding domain. Communication between these domains is important
for Pin1 in vivo activity; however, the atomic basis for this communication
has remained elusive. Our previous nuclear magnetic resonance (NMR)
studies of Pin1 functional dynamics suggested that weak interdomain
contacts within Pin1 enable allosteric communication between the domain
interface and the distal active site of the PPIase domain.1,2 A necessary condition for this hypothesis is that the intrinsic
properties of the PPIase domain should be sensitive to interdomain
contact. Here, we test this sensitivity by generating a Pin1 mutant,
I28A, which weakens the wild-type interdomain contact while maintaining
the overall folds of the two domains. Using NMR, we show that I28A
leads to altered substrate binding affinity and isomerase activity.
Moreover, I28A causes long-range perturbations to conformational flexibility
in both domains, for both the apo and substrate-complexed states of
the protein. These results show that the distribution of conformations
sampled by the PPIase domain is sensitive to interdomain contact and
strengthen the hypothesis that such contact supports interdomain allosteric
communication in Pin1. Other modular systems may exploit interdomain
interactions in a similar manner.
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Affiliation(s)
- Kimberly A Wilson
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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45
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Velazquez HA, Hamelberg D. Conformation-Directed Catalysis and Coupled Enzyme–Substrate Dynamics in Pin1 Phosphorylation-Dependent Cis–Trans Isomerase. J Phys Chem B 2013; 117:11509-17. [DOI: 10.1021/jp405271s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hector A. Velazquez
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Donald Hamelberg
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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46
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Aluminum(III) interferes with the structure and the activity of the peptidyl-prolyl cis-trans isomerase (Pin1): A new mechanism contributing to the pathogenesis of Alzheimer's disease and cancers? J Inorg Biochem 2013; 126:111-7. [DOI: 10.1016/j.jinorgbio.2013.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 12/25/2022]
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47
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The activity and specificity of the outer membrane protein chaperone SurA are modulated by a proline isomerase domain. mBio 2013; 4:mBio.00540-13. [PMID: 23943764 PMCID: PMC3747590 DOI: 10.1128/mbio.00540-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED SurA is a component of the periplasmic chaperone network that plays a central role in biogenesis of integral outer membrane β-barrel proteins (OMPs) in Escherichia coli. Although SurA contains two well-conserved proline isomerase (PPIase) domains, the contribution of these domains to SurA function is unclear. In the present work, we show that defects in OMP assembly caused by mutation of the β-barrel assembly factors BamA or BamB can be corrected by gain-of-function mutations in SurA that map to the first PPIase domain. These mutations apparently bypass the requirement for a stable interaction between SurA and the Bam complex and enhance SurA chaperone activity in vivo despite destabilization of the protein in vitro. Our findings suggest an autoinhibitory mechanism for regulation of SurA chaperone activity through interdomain interactions involving a PPIase domain. We propose a model in which SurA activity is modulated by an interaction between SurA and the Bam complex that alters the substrate specificity of the chaperone. IMPORTANCE The dominant surA mutations described here alter amino acid residues that are highly conserved in eukaryotic homologs of SurA, including Pin 1, the human proline isomerase (PPIase) implicated in Alzheimer's disease and certain cancers. Consequently, a mechanistic description of SurA function may enhance our understanding of clinically important PPIases and their role(s) in disease. In addition, the virulence of Gram-negative bacterial pathogens, such as Salmonella, Shigella, and Escherichia coli O157:H7, is largely dependent on SurA, making this PPIase/chaperone an attractive antibiotic target. Investigating the function of SurA in outer membrane (OM) biogenesis will be useful in the development of novel therapeutic strategies for the disruption of the OM or the processes that are essential for its assembly.
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Moore JD, Potter A. Pin1 inhibitors: Pitfalls, progress and cellular pharmacology. Bioorg Med Chem Lett 2013; 23:4283-91. [PMID: 23796453 DOI: 10.1016/j.bmcl.2013.05.088] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 01/12/2023]
Abstract
Compelling data supports the hypothesis that Pin1 inhibitors will be useful for the therapy of cancer: Pin1 deficient mice resist the induction of breast cancers normally evoked by expression of MMTV-driven Ras or Erb2 alleles. While Pin1 poses challenges for drug discovery, several groups have identified potent antagonists by structure based drug design, significant progress has been made designing peptidic inhibitors and a number of natural products have been found that blockade Pin1, notably epigallocatchechin gallate (EGCG), a major flavonoid in green tea. Here we critically discuss the modes of action and likely specificity of these compounds, concluding that a suitable chemical biology tool for probing the function of Pin1 has yet to be found. We conclude by outlining some open questions regarding the target validation of Pin1 and the prospects for identification of improved inhibitors in the future.
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Affiliation(s)
- Jonathan D Moore
- Horizon Discovery, Cambridge Research Park, Cambridge CB25 9TL, UK.
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49
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Innes BT, Bailey ML, Brandl CJ, Shilton BH, Litchfield DW. Non-catalytic participation of the Pin1 peptidyl-prolyl isomerase domain in target binding. Front Physiol 2013; 4:18. [PMID: 23407864 PMCID: PMC3571201 DOI: 10.3389/fphys.2013.00018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 01/24/2013] [Indexed: 01/19/2023] Open
Abstract
Pin1 is a phosphorylation-dependent peptidyl-prolyl isomerase (PPIase) that has the potential to add an additional level of regulation within protein kinase mediated signaling pathways. Furthermore, there is a mounting body of evidence implicating Pin1 in the emergence of pathological phenotypes in neurodegeneration and cancer through the isomerization of a wide variety of substrates at peptidyl-prolyl bonds where the residue preceding proline is a phosphorylated serine or threonine residue (i.e., pS/T-P motifs). A key step in this regulatory process is the interaction of Pin-1 with its substrates. This is a complex process since Pin1 is composed of two domains, the catalytic PPIase domain, and a type IV WW domain, both of which recognize pS/T-P motifs. The observation that the WW domain exhibits considerably higher binding affinity for pS/T-P motifs has led to predictions that the two domains may have distinct roles in mediating the actions of Pin1 on its substrates. To evaluate the participation of its individual domains in target binding, we performed GST pulldowns to monitor interactions between various forms of Pin1 and mitotic phospho-proteins that revealed two classes of Pin-1 interacting proteins, differing in their requirement for residues within the PPIase domain. From these observations, we consider models for Pin1-substrate interactions and the potential functions of the different classes of Pin1 interacting proteins. We also compare sequences that are recognized by Pin1 within its individual interaction partners to investigate the underlying basis for its different types of interactions.
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Affiliation(s)
- Brendan T Innes
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario London, ON, Canada
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50
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Aluise CD, Rose K, Boiani M, Reyzer ML, Manna JD, Tallman K, Porter NA, Marnett LJ. Peptidyl-prolyl cis/trans-isomerase A1 (Pin1) is a target for modification by lipid electrophiles. Chem Res Toxicol 2012; 26:270-9. [PMID: 23231502 PMCID: PMC3579456 DOI: 10.1021/tx300449g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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Oxidation of membrane phospholipids is associated with
inflammation,
neurodegenerative disease, and cancer. Oxyradical damage to phospholipids
results in the production of reactive aldehydes that adduct proteins
and modulate their function. 4-Hydroxynonenal (HNE), a common product
of oxidative damage to lipids, adducts proteins at exposed Cys, His,
or Lys residues. Here, we demonstrate that peptidyl-prolyl cis/trans-isomerase A1 (Pin1), an enzyme
that catalyzes the conversion of the peptide bond of pSer/pThr-Pro
moieties in signaling proteins from cis to trans, is highly susceptible
to HNE modification. Incubation of purified Pin1 with HNE followed
by MALDI-TOF/TOF mass spectrometry resulted in detection of Michael
adducts at the active site residues His-157 and Cys-113. Time and
concentration dependencies indicate that Cys-113 is the primary site
of HNE modification. Pin1 was adducted in MDA-MB-231 breast cancer
cells treated with 8-alkynyl-HNE as judged by click chemistry conjugation
with biotin followed by streptavidin-based pulldown and Western blotting
with anti-Pin1 antibody. Furthermore, orbitrap MS data support the
adduction of Cys-113 in the Pin1 active site upon HNE treatment of
MDA-MB-231 cells. siRNA knockdown of Pin1 in MDA-MB-231 cells partially
protected the cells from HNE-induced toxicity. Recent studies indicate
that Pin1 is an important molecular target for the chemopreventive
effects of green tea polyphenols. The present study establishes that
it is also a target for electrophilic modification by products of
lipid peroxidation.
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Affiliation(s)
- Christopher D Aluise
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
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