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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [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: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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2
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Schiene‐Fischer C, Fischer G, Braun M. Non-Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022; 61:e202201597. [PMID: 35290695 PMCID: PMC9804594 DOI: 10.1002/anie.202201597] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 01/05/2023]
Abstract
Cyclophilins, enzymes with peptidyl-prolyl cis/trans isomerase activity, are relevant to a large variety of biological processes. The most abundant member of this enzyme family, cyclophilin A, is the cellular receptor of the immunosuppressive drug cyclosporine A (CsA). As a consequence of the pathophysiological role of cyclophilins, particularly in viral infections, there is a broad interest in cyclophilin inhibition devoid of immunosuppressive activity. This Review first gives an introduction into the physiological and pathophysiological roles of cyclophilins. The presentation of non-immunosuppressive cyclophilin inhibitors will commence with drugs based on chemical modifications of CsA. The naturally occurring macrocyclic sanglifehrins have become other lead structures for cyclophilin-inhibiting drugs. Finally, de novo designed compounds, whose structures are not derived from or inspired by natural products, will be presented. Relevant synthetic concepts will be discussed, but the focus will also be on biochemical studies, structure-activity relationships, and clinical studies.
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Affiliation(s)
- Cordelia Schiene‐Fischer
- Institute of Biochemistry and BiotechnologyMartin-Luther-University Halle-Wittenberg06099Halle (Saale)Germany
| | - Gunter Fischer
- Max Planck Institute for Biophysical Chemistry37077GöttingenGermany
| | - Manfred Braun
- Institute of Organic and Macromolecular ChemistryHeinrich-Heine-University Düsseldorf40225DüsseldorfGermany
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3
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Braun M, Schiene-Fischer C, Fischer G. Non‐Immunosuppressive Cyclophilin Inhibitors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Manfred Braun
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Organic CHemistry Universitätsstr. 1 40225 Düsseldorf GERMANY
| | - Cordelia Schiene-Fischer
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg Institute of Biochemistry and Biotechnology, GERMANY
| | - Gunter Fischer
- Max-Planck-Institut für Biophysikalische Chemie Abteilung Meiosis: Max-Planck-Institut fur Multidisziplinare Naturwissenschaften Abteilung Meiosis Max Planck Institute for Biophysical Chemistry GERMANY
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4
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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5
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Denic M, Turlin E, Michel V, Fischer F, Khorasani-Motlagh M, Zamble D, Vinella D, de Reuse H. A novel mode of control of nickel uptake by a multifunctional metallochaperone. PLoS Pathog 2021; 17:e1009193. [PMID: 33444370 PMCID: PMC7840056 DOI: 10.1371/journal.ppat.1009193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/27/2021] [Accepted: 11/26/2020] [Indexed: 01/08/2023] Open
Abstract
Cellular metal homeostasis is a critical process for all organisms, requiring tight regulation. In the major pathogen Helicobacter pylori, the acquisition of nickel is an essential virulence determinant as this metal is a cofactor for the acid-resistance enzyme, urease. Nickel uptake relies on the NixA permease and the NiuBDE ABC transporter. Till now, bacterial metal transporters were reported to be controlled at their transcriptional level. Here we uncovered post-translational regulation of the essential Niu transporter in H. pylori. Indeed, we demonstrate that SlyD, a protein combining peptidyl-prolyl isomerase (PPIase), chaperone, and metal-binding properties, is required for the activity of the Niu transporter. Using two-hybrid assays, we found that SlyD directly interacts with the NiuD permease subunit and identified a motif critical for this contact. Mutants of the different SlyD functional domains were constructed and used to perform in vitro PPIase activity assays and four different in vivo tests measuring nickel intracellular accumulation or transport in H. pylori. In vitro, SlyD PPIase activity is down-regulated by nickel, independently of its C-terminal region reported to bind metals. In vivo, a role of SlyD PPIase function was only revealed upon exposure to high nickel concentrations. Most importantly, the IF chaperone domain of SlyD was shown to be mandatory for Niu activation under all in vivo conditions. These data suggest that SlyD is required for the active functional conformation of the Niu permease and regulates its activity through a novel mechanism implying direct protein interaction, thereby acting as a gatekeeper of nickel uptake. Finally, in agreement with a central role of SlyD, this protein is essential for the colonization of the mouse model by H. pylori. Metal ions are essential for the viability of all living organisms. Indeed, more than one-third of all proteins need metal cofactors for their function. Intracellular metal concentrations require tight control as non-physiological amounts are very toxic. In particular, nickel plays a unique role in Helicobacter pylori, a bacterial pathogen that colonizes the stomach of about half of the human population worldwide and is associated with the development of gastric cancer. Nickel is essential for H. pylori as it is the cofactor of urease, an enzyme indispensable for resistance to the gastric acidity of the stomach and thus for in vivo colonization. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms. Till now, control of nickel uptake was only reported to rely on transcriptional regulators. In the present study, we uncovered a novel mechanism of regulation of nickel acquisition. SlyD, a multifunctional enzyme was found to control, by direct protein interaction, the activity of an essential nickel uptake system in H. pylori. We revealed that the SlyD chaperone activity is mandatory for the active conformation and thus functionality of the nickel permease.
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Affiliation(s)
- Milica Denic
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- Université de Paris, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Evelyne Turlin
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
| | - Valérie Michel
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, Strasbourg, France
| | | | - Deborah Zamble
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- * E-mail: (DV); (HDR)
| | - Hilde de Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, CNRS UMR 2001, Paris, France
- * E-mail: (DV); (HDR)
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6
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Singh H, Kaur K, Singh M, Kaur G, Singh P. Plant Cyclophilins: Multifaceted Proteins With Versatile Roles. FRONTIERS IN PLANT SCIENCE 2020; 11:585212. [PMID: 33193535 PMCID: PMC7641896 DOI: 10.3389/fpls.2020.585212] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.
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Affiliation(s)
- Harpreet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Kirandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Mangaljeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - Gundeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- William Harvey Heart Centre, Queen Mary University of London, London, United Kingdom
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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7
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Demetriou C, Chanudet E, Joseph A, Topf M, Thomas AC, Bitner-Glindzicz M, Regan L, Stanier P, Moore GE. Exome sequencing identifies variants in FKBP4 that are associated with recurrent fetal loss in humans. Hum Mol Genet 2020; 28:3466-3474. [PMID: 31504499 DOI: 10.1093/hmg/ddz203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/25/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is defined as two or more consecutive miscarriages and affects an estimated 1.5% of couples trying to conceive. RPL has been attributed to genetic, endocrine, immune and thrombophilic disorders, but many cases remain unexplained. We investigated a Bangladeshi family where the proband experienced 29 consecutive pregnancy losses with no successful pregnancies from three different marriages. Whole exome sequencing identified rare genetic variants in several candidate genes. These were further investigated in Asian and white European RPL cohorts, and in Bangladeshi controls. FKBP4, encoding the immunophilin FK506-binding protein 4, was identified as a plausible candidate, with three further novel variants identified in Asian patients. None were found in European patients or controls. In silico structural studies predicted damaging effects of the variants in the structure-function properties of the FKBP52 protein. These were located within domains reported to be involved in Hsp90 binding and peptidyl-prolyl cis-trans isomerase (PPIase) activity. Profound effects on PPIase activity were demonstrated in transiently transfected HEK293 cells comparing wild-type and mutant FKBP4 constructs. Mice lacking FKBP4 have been previously reported as infertile through implantation failure. This study therefore strongly implicates FKBP4 as associated with fetal losses in humans, particularly in the Asian population.
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Affiliation(s)
- Charalambos Demetriou
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Estelle Chanudet
- Centre for Translational Omics-GOSgene, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Agnel Joseph
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Anna C Thomas
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Lesley Regan
- Department of Obstetrics and Gynaecology, St. Mary's Campus, Imperial College London, London, UK
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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8
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Acevedo LA, Korson NE, Williams JM, Nicholson LK. Tuning a timing device that regulates lateral root development in rice. JOURNAL OF BIOMOLECULAR NMR 2019; 73:493-507. [PMID: 31407206 PMCID: PMC7141409 DOI: 10.1007/s10858-019-00258-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Peptidyl Prolyl Isomerases (PPIases) accelerate cis-trans isomerization of prolyl peptide bonds. In rice, the PPIase LRT2 is essential for lateral root initiation. LRT2 displays in vitro isomerization of a highly conserved W-P peptide bond (104W-P105) in the natural substrate OsIAA11. OsIAA11 is a transcription repressor that, in response to the plant hormone auxin, is targeted to ubiquitin-mediated proteasomal degradation via specific recognition of the cis isomer of its 104W-P105 peptide bond. OsIAA11 controls transcription of specific genes, including its own, that are required for lateral root development. This auxin-responsive negative feedback circuit governs patterning and development of lateral roots along the primary root. The ability to tune LRT2 activity via mutagenesis is crucial for understanding and modeling the role of this bimodal switch in the auxin circuit and lateral root development. We present characterization of the thermal stability and isomerization rates of several LRT2 mutants acting on the OsIAA11 substrate. The thermally stable mutants display activities lower than that of wild-type (WT) LRT2. These include binding diminished but catalytically active P125K, binding incompetent W128A, and binding capable but catalytically incompetent H133Q mutations. Additionally, LRT2 homologs hCypA from human, TaCypA from Triticum aestivum (wheat) and PPIB from E. coli were shown to have 110, 50 and 60% of WT LRT2 activity on the OsIAA11 substrate. These studies identify several thermally stable LRT2 mutants with altered activities that will be useful for establishing relationships between cis-trans isomerization, auxin circuit dynamics, and lateral root development in rice.
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Affiliation(s)
- Lucila Andrea Acevedo
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan E Korson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Justin M Williams
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Linda K Nicholson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.
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9
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Wang C, Cui Y, Qu X. Identification of proteins regulated by acid adaptation related two component system HPK1/RR1 in Lactobacillus delbrueckii subsp. bulgaricus. Arch Microbiol 2018; 200:1381-1393. [PMID: 30022229 DOI: 10.1007/s00203-018-1552-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 11/25/2022]
Abstract
Lactobacillus delbrueckii subsp. bulgaricus is currently one of the most valuable lactic acid bacteria (LAB) and widely used in global dairy industry. The acid tolerance and adaptation ability of LAB is the key point of their survival and proliferation during fermentation process and in gastrointestinal tract of human body. Two component system (TCS) is one of the most important mechanisms to allow bacteria to sense and respond to changes of environmental conditions. TCS typically consists of a histidine protein kinase (HPK) and a corresponding response regulator (RR). Our previous study indicated a TCS (JN675228/JN675229) was involved in acid adaptation in L. bulgaricus. To reveal the role of JN675228 (HPK1)/JN675229 (RR1) in acid adaptation, the target genes of JN675228 (HPK1)/JN675229 (RR1) were identified by means of a proteomic approach complemented with transcription data in the present study. The results indicated that HPK1/RR1 regulated the acid adaptation ability of bacteria by means of many pathways, including the proton pump related protein, classical stress shock proteins, carbohydrate metabolism, nucleotide biosynthesis, DNA repair, transcription and translation, peptide transport and degradation, and cell wall biosynthesis, etc. To our knowledge, this is the first report with the effect of acid adaptation-related TCS HPK1/RR1 on its target genes. This study will offer experimental basis for clarifying the acid adaptation regulation mechanism of L. bulgaricus, and provide a theoretical basis for this bacterium in industry application.
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Affiliation(s)
- Chao Wang
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Yanhua Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150090, People's Republic of China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, People's Republic of China
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10
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Jiang Q, Li XR, Wang CK, Cheng J, Tan C, Cui TT, Lu NN, James TD, Han F, Li X. A fluorescent peptidyl substrate for visualizing peptidyl-prolyl cis/trans isomerase activity in live cells. Chem Commun (Camb) 2018; 54:1857-1860. [PMID: 29387835 DOI: 10.1039/c7cc09135d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This communication reports on a fluorescent probe (PPI-P) for imaging active peptidyl-prolyl cis/trans isomerases in live cells. PPI-P is capable of responding to both recombinant and cellular PPIases fluorogenically, and has been shown to specifically image active PPIases in live cells.
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Affiliation(s)
- Quan Jiang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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11
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Ettelaie C, Collier MEW, Featherby S, Greenman J, Maraveyas A. Peptidyl-prolyl isomerase 1 (Pin1) preserves the phosphorylation state of tissue factor and prolongs its release within microvesicles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:12-24. [PMID: 28962834 DOI: 10.1016/j.bbamcr.2017.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/07/2017] [Accepted: 09/24/2017] [Indexed: 01/23/2023]
Abstract
The exposure and release of TF is regulated by post-translational modifications of its cytoplasmic domain. Here, the potential of Pin1 to interact with the cytoplasmic domain of TF, and the outcome on TF function was examined. MDA-MB-231 and transfected-primary endothelial cells were incubated with either Pin1 deactivator Juglone, or its control Plumbagin, as well as transfected with Pin1-specific or control siRNA. TF release into microvesicles following activation, and also phosphorylation and ubiquitination states of cellular-TF were then assessed. Furthermore, the ability of Pin1 to bind wild-type and mutant forms of overexpressed TF-tGFP was investigated by co-immunoprecipitation. Additionally, the ability of recombinant or cellular Pin1 to bind to peptides of the C-terminus of TF, synthesised in different phosphorylation states was examined by binding assays and spectroscopically. Finally, the influence of recombinant Pin1 on the ubiquitination and dephosphorylation of the TF-peptides was examined. Pre-incubation of Pin1 with Juglone but not Plumbagin, reduced TF release as microvesicles and was also achievable following transfection with Pin1-siRNA. This was concurrent with early ubiquitination and dephosphorylation of cellular TF at Ser253. Pin1 co-immunoprecipitated with overexpressed wild-type TF-tGFP but not Ser258→Ala or Pro259→Ala substituted mutants. Pin1 did interact with Ser258-phosphorylated and double-phosphorylated TF-peptides, with the former having higher affinity. Finally, recombinant Pin1 was capable of interfering with the ubiquitination and dephosphorylation of TF-derived peptides. In conclusion, Pin1 is a fast-acting enzyme which may be utilised by cells to protect the phosphorylation state of TF in activated cells prolonging TF activity and release, and therefore ensuring adequate haemostasis.
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Affiliation(s)
- Camille Ettelaie
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK.
| | - Mary E W Collier
- Department of Cardiovascular Sciences, University of Leicester, Clinical Sciences Wing, Glenfield General Hospital, Leicester LE3 9QP, UK
| | - Sophie Featherby
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John Greenman
- Biomedical Section, Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - Anthony Maraveyas
- Division of Cancer, Hull York Medical School University of Hull, Cottingham Road, Hull HU6 7RX, UK
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12
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Vivoli M, Renou J, Chevalier A, Norville IH, Diaz S, Juli C, Atkins H, Holzgrabe U, Renard PY, Sarkar-Tyson M, Harmer NJ. A miniaturized peptidyl-prolyl isomerase enzyme assay. Anal Biochem 2017; 536:59-68. [PMID: 28803887 DOI: 10.1016/j.ab.2017.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/04/2017] [Accepted: 08/09/2017] [Indexed: 01/15/2023]
Abstract
Prolyl-peptidyl isomerases (PPIases) are enzymes that are found in all living organisms. They form an essential part of the cellular protein folding homeostasis machinery. PPIases are associated with many important human diseases, e.g. cardiovascular disease, cancer and Alzheimer's. The development of novel PPIase inhibitors has been limited by the lack of a rapid, laboratory-based assay for these enzymes, as their substrates and products are challenging to distinguish. A well described continuous assay, coupled with the hydrolysis of a peptide by chymotrypsin is highly effective, but comparatively slow. To address this, we developed an improved version of the traditional assay using a temperature controlled plate reader. This assay allows semi-automated medium throughput assays in an academic laboratory for 84 samples per day. The assay shows lower errors, with an average Z' of 0.72. We further developed the assay using a fluorogenic peptide-based FRET probe. This provides an extremely sensitive PPIase assay using substrate at 200 nM, which approaches single turnover conditions. The fluorescent probe achieves an excellent quenching efficiency of 98.6%, and initial experiments showed acceptable Z' of 0.31 and 0.30 for cyclophilin A and hFKBP12 respectively. The assays provide an improved toolset for the quantitative, biochemical analysis of PPIases.
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Affiliation(s)
- Mirella Vivoli
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Julien Renou
- Normandie Univ, UNIROUEN, CNRS, INSAREOUEN, COBRA, UMR 6014 & FR 3038, 1 rue Tesnière 76000 Rouen, France
| | - Arnaud Chevalier
- Normandie Univ, UNIROUEN, CNRS, INSAREOUEN, COBRA, UMR 6014 & FR 3038, 1 rue Tesnière 76000 Rouen, France
| | - Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down SP4 0JQ, United Kingdom
| | - Suraya Diaz
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Christina Juli
- Institute of Pharmacy, University of Würzburg, Am Hubland, 970074 Würzburg, Germany
| | - Helen Atkins
- Defence Science and Technology Laboratory, Porton Down SP4 0JQ, United Kingdom
| | - Ulrike Holzgrabe
- Institute of Pharmacy, University of Würzburg, Am Hubland, 970074 Würzburg, Germany
| | - Pierre-Yves Renard
- Normandie Univ, UNIROUEN, CNRS, INSAREOUEN, COBRA, UMR 6014 & FR 3038, 1 rue Tesnière 76000 Rouen, France
| | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down SP4 0JQ, United Kingdom; Marshall Centre for Infectious Diseases, School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia
| | - Nicholas J Harmer
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
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Steadman VA, Pettit SB, Poullennec KG, Lazarides L, Keats AJ, Dean DK, Stanway SJ, Austin CA, Sanvoisin JA, Watt GM, Fliri HG, Liclican AC, Jin D, Wong MH, Leavitt SA, Lee YJ, Tian Y, Frey CR, Appleby TC, Schmitz U, Jansa P, Mackman RL, Schultz BE. Discovery of Potent Cyclophilin Inhibitors Based on the Structural Simplification of Sanglifehrin A. J Med Chem 2017; 60:1000-1017. [DOI: 10.1021/acs.jmedchem.6b01329] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Victoria A. Steadman
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Simon B. Pettit
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Karine G. Poullennec
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Linos Lazarides
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Andrew J. Keats
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - David K. Dean
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Steven J. Stanway
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Carol A. Austin
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Jonathan A. Sanvoisin
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Gregory M. Watt
- Selcia Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, United Kingdom
| | - Hans G. Fliri
- Cypralis Ltd., Babraham Research
Campus, Cambridge CB22
3AT, United Kingdom
| | - Albert C. Liclican
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Debi Jin
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Melanie H. Wong
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Stephanie A. Leavitt
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Yu-Jen Lee
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Yang Tian
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Christian R. Frey
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Todd C. Appleby
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Uli Schmitz
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Petr Jansa
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Richard L. Mackman
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
| | - Brian E. Schultz
- Gilead Sciences, 333 Lakeside
Drive, Foster City, California 94404, United States
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14
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Schumann M, Ihling CH, Prell E, Schierhorn A, Sinz A, Fischer G, Schiene-Fischer C, Malešević M. Identification of low abundance cyclophilins in human plasma. Proteomics 2016; 16:2815-2826. [PMID: 27586231 DOI: 10.1002/pmic.201600221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 11/08/2022]
Abstract
Cylophilins (Cyps) belong to the ubiquitously distributed enzyme class of peptidyl prolyl cis/trans isomerases (EC5.2.1.8), which are foldases capable of accelerating slow steps in the refolding of denatured proteins. At least 20 different Cyp isoenzymes are broadly distributed among all organs and cellular compartments in humans. Extracellularly localized Cyps came into the scientific focus recently because of their involvement in the control of inflammatory diseases, as well as viral and bacterial infections. However, detailed insights into Cyp functions are often hampered by the lack of sensitive detection methods. We present an improved method for affinity purification and detection of Cyp in biotic samples in this manuscript. The procedure takes advantage of two novel cyclosporine A derivatives. Derivative 1 was used to capture Cyps from the sample while derivative 2 was applied for selective release from the affinity matrix. Using this approach, eight different Cyp (CypA, CypB, CypC, Cyp40 (PPID), CypE, CypD (PPIF), CypH, and CypL1) were unambiguously detected in healthy human blood plasma. Moreover, extracellular CypA was found to be partially modified by Nε acetylation on residues Lys44, Lys133, Lys155, as well as Nα acetylation at the N-terminal Val residue. Nα acetylation of Ser2 residue was also found for Cyp40.
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Affiliation(s)
- Michael Schumann
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Erik Prell
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Gunter Fischer
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Miroslav Malešević
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
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15
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Rios-Covián D, Sánchez B, Martínez N, Cuesta I, Hernández-Barranco AM, de Los Reyes-Gavilán CG, Gueimonde M. A proteomic approach towards understanding the cross talk between Bacteroides fragilis and Bifidobacterium longum in coculture. Can J Microbiol 2016; 62:623-8. [PMID: 27156738 DOI: 10.1139/cjm-2015-0804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A better understanding of the interactions among intestinal microbes is needed to decipher the complex cross talk that takes place within the human gut. Bacteroides and Bifidobacterium genera are among the most relevant intestinal bacteria, and it has been previously reported that coculturing of these 2 microorganisms affects their survival. Therefore, coculturing of Bifidobacterium longum NB667 and Bacteroides fragilis DSMZ2151 was performed with the aim of unravelling the mechanisms involved in their interaction. To this end, we applied proteomic (2D-DIGE) analyses, and by chromatographic techniques we quantified the bacterial metabolites produced during coincubation. Coculture stimulated the growth of B. longum, retarding that of B. fragilis, with concomitant changes in the production of some proteins and metabolites of both bacteria. The combined culture promoted upregulation of the bifidobacterial pyruvate kinase and downregulation of the Bacteroides phosphoenolpyruvate carboxykinase - 2 enzymes involved in the catabolism of carbohydrates. Moreover, B. fragilis FKBP-type peptidyl-prolyl cis-trans isomerase, a protein with chaperone-like activity, was found to be overproduced in coculture, suggesting the induction of a stress response in this microorganism. This study provides mechanistic data to deepen our understanding of the interaction between Bacteroides and Bifidobacterium intestinal populations.
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Affiliation(s)
- David Rios-Covián
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Noelia Martínez
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Isabel Cuesta
- b Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Ana M Hernández-Barranco
- b Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- a Probiotics and Prebiotics Group, Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain
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16
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Schmidpeter PAM, Schmid FX. Prolyl isomerization and its catalysis in protein folding and protein function. J Mol Biol 2015; 427:1609-31. [PMID: 25676311 DOI: 10.1016/j.jmb.2015.01.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 12/20/2022]
Abstract
Prolyl isomerizations are intrinsically slow processes. They determine the rates of many protein folding reactions and control regulatory events in folded proteins. Prolyl isomerases are able to catalyze these isomerizations, and thus, they have the potential to assist protein folding and to modulate protein function. Here, we provide examples for how prolyl isomerizations limit protein folding and are accelerated by prolyl isomerases and how native-state prolyl isomerizations regulate protein functions. The roles of prolines in protein folding and protein function are closely interrelated because both of them depend on the coupling between cis/trans isomerization and conformational changes that can involve extended regions of a protein.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biologie, Universität Bayreuth, 95440 Bayreuth, Germany.
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17
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Schmidpeter PAM, Koch JR, Schmid FX. Control of protein function by prolyl isomerization. Biochim Biophys Acta Gen Subj 2014; 1850:1973-82. [PMID: 25542300 DOI: 10.1016/j.bbagen.2014.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 01/12/2023]
Abstract
BACKGROUND Prolyl cis/trans isomerizations have long been known as critical and rate-limiting steps in protein folding. RESULTS Now it is clear that they are also used as slow conformational switches and molecular timers in the regulation of protein activity. Here we describe several such proline switches and how they are regulated. CONCLUSIONS AND GENERAL SIGNIFICANCE Prolyl isomerizations can function as attenuators and provide allosteric systems with a molecular memory. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Philipp A M Schmidpeter
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Johanna R Koch
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95440 Bayreuth, Germany.
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18
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Lonati E, Brambilla A, Milani C, Masserini M, Palestini P, Bulbarelli A. Pin1, a new player in the fate of HIF-1α degradation: an hypothetical mechanism inside vascular damage as Alzheimer's disease risk factor. Front Cell Neurosci 2014; 8:1. [PMID: 24478626 PMCID: PMC3894457 DOI: 10.3389/fncel.2014.00001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 01/01/2014] [Indexed: 11/16/2022] Open
Abstract
Aetiology of neurodegenerative mechanisms underlying Alzheimer’s disease (AD) are still under elucidation. The contribution of cerebrovascular deficiencies (such as cerebral ischemia/stroke) has been strongly endorsed in recent years. Reduction of blood supply leading to hypoxic condition is known to activate cellular responses mainly controlled by hypoxia-inducible transcription factor-1 (HIF-1). Thus alterations of oxygen responsive HIF-1α subunit in the central nervous system may contribute to the cognitive decline, especially influencing mechanisms associated to amyloid precursor protein (APP) amyloidogenic metabolism. Although HIF-1α protein level is known to be regulated by von Hippel-Lindau (VHL) ubiquitin-proteasome system, it has been recently suggested that glycogen synthase kinase-3β (Gsk-3β) promotes a VHL-independent HIF-1α degradation. Here we provide evidences that in rat primary hippocampal cell cultures, HIF-1α degradation might be mediated by a synergic action of Gsk-3β and peptidyl-prolyl cis/trans isomerase (Pin1). In post-ischemic conditions, such as those mimicked with oxygen glucose deprivation (OGD), HIF-1α protein level increases remaining unexpectedly high for long time after normal condition restoration jointly with the increase of lactate dehydrogenase (LDH) and β-secretase 1 (BACE1) protein expression (70 and 140% respectively). Interestingly the Pin1 activity decreases about 40–60% and Pin1S16 inhibitory phosphorylation significantly increases, indicating that Pin1 binding to its substrate and enzymatic activity are reduced by treatment. Co-immunoprecipitation experiments demonstrate that HIF-1α/Pin1 in normoxia are associated, and that in presence of specific Pin1 and Gsk-3β inhibitors their interaction is reduced in parallel to an increase of HIF-1α protein level. Thus we suggest that in post-OGD neurons the high level of HIF-1α might be due to Pin1 binding ability and activity reduction which affects HIF-1α degradation: an event that may highlight the relevance of ischemia/HIF-1α as a risk factor in AD pathogenesis.
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Affiliation(s)
- Elena Lonati
- Department of Health Science, University of Milano-Bicocca Monza (MI), Italy
| | - Anna Brambilla
- Department of Health Science, University of Milano-Bicocca Monza (MI), Italy
| | - Chiara Milani
- Department of Health Science, University of Milano-Bicocca Monza (MI), Italy
| | - Massimo Masserini
- Department of Health Science, University of Milano-Bicocca Monza (MI), Italy
| | - Paola Palestini
- Department of Health Science, University of Milano-Bicocca Monza (MI), Italy
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19
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Linnert M, Lin YJ, Manns A, Haupt K, Paschke AK, Fischer G, Weiwad M, Lücke C. The FKBP-type domain of the human aryl hydrocarbon receptor-interacting protein reveals an unusual Hsp90 interaction. Biochemistry 2013; 52:2097-107. [PMID: 23418784 DOI: 10.1021/bi301649m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aryl hydrocarbon receptor-interacting protein (AIP) has been predicted to consist of an N-terminal FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) domain and a C-terminal tetratricopeptide repeat (TPR) domain, as typically found in FK506-binding immunophilins. AIP, however, exhibited no inherent FK506 binding or PPIase activity. Alignment with the prototypic FKBP12 showed a high sequence homology but indicated inconsistencies with regard to the secondary structure prediction derived from chemical shift analysis of AIP(2-166). NMR-based structure determination of AIP(2-166) now revealed a typical FKBP fold with five antiparallel β-strands forming a half β-barrel wrapped around a central α-helix, thus permitting AIP to be also named FKBP37.7 according to FKBP nomenclature. This PPIase domain, however, features two structure elements that are unusual for FKBPs: (i) an N-terminal α-helix, which additionally stabilizes the domain, and (ii) a rather long insert, which connects the last two β-strands and covers the putative active site. Diminution of the latter insert did not generate PPIase activity or FK506 binding capability, indicating that the lack of catalytic activity in AIP is the result of structural differences within the PPIase domain. Compared to active FKBPs, a diverging conformation of the loop connecting β-strand C' and the central α-helix apparently is responsible for this inherent lack of catalytic activity in AIP. Moreover, Hsp90 was identified as potential physiological interaction partner of AIP, which revealed binding contacts not only at the TPR domain but uncommonly also at the PPIase domain.
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Affiliation(s)
- Miriam Linnert
- Max Planck Research Unit for Enzymology of Protein Folding , Weinbergweg 22, 06120 Halle (Saale), Germany
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20
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Gregory MA, Kaja AL, Kendrew SG, Coates NJ, Warneck T, Nur-e-Alam M, Lill RE, Sheehan LS, Chudley L, Moss SJ, Sheridan RM, Quimpere M, Zhang MQ, Martin CJ, Wilkinson B. Structure guided design of improved anti-proliferative rapalogs through biosynthetic medicinal chemistry. Chem Sci 2013. [DOI: 10.1039/c2sc21833j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Hediger T, Frank W, Schumann M, Fischer G, Braun M. Aryl Hetaryl Ketones and Thioketones as Efficient Inhibitors of Peptidyl-Prolylcis-transIsomerases. Chem Biodivers 2012; 9:2618-34. [DOI: 10.1002/cbdv.201200275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Indexed: 01/29/2023]
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22
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PpiA, a surface PPIase of the cyclophilin family in Lactococcus lactis. PLoS One 2012; 7:e33516. [PMID: 22442694 PMCID: PMC3307742 DOI: 10.1371/journal.pone.0033516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/10/2012] [Indexed: 12/05/2022] Open
Abstract
Background Protein folding in the envelope is a crucial limiting step of protein export and secretion. In order to better understand this process in Lactococcus lactis, a lactic acid bacterium, genes encoding putative exported folding factors like Peptidyl Prolyl Isomerases (PPIases) were searched for in lactococcal genomes. Results In L. lactis, a new putative membrane PPIase of the cyclophilin subfamily, PpiA, was identified and characterized. ppiA gene was found to be constitutively expressed under normal and stress (heat shock, H2O2) conditions. Under normal conditions, PpiA protein was synthesized and released from intact cells by an exogenously added protease, showing that it was exposed at the cell surface. No obvious phenotype could be associated to a ppiA mutant strain under several laboratory conditions including stress conditions, except a very low sensitivity to H2O2. Induction of a ppiA copy provided in trans had no effect i) on the thermosensitivity of an mutant strain deficient for the lactococcal surface protease HtrA and ii) on the secretion and stability on four exported proteins (a highly degraded hybrid protein and three heterologous secreted proteins) in an otherwise wild-type strain background. However, a recombinant soluble form of PpiA that had been produced and secreted in L. lactis and purified from a culture supernatant displayed both PPIase and chaperone activities. Conclusions Although L. lactis PpiA, a protein produced and exposed at the cell surface under normal conditions, displayed a very moderate role in vivo, it was found, as a recombinant soluble form, to be endowed with folding activities in vitro.
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23
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Budiman C, Tadokoro T, Angkawidjaja C, Koga Y, Kanaya S. Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1. FEBS J 2012; 279:976-86. [PMID: 22244380 DOI: 10.1111/j.1742-4658.2012.08483.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FKBP22 from the psychotropic bacterium Shewanella sp. SIB1 is a homodimeric protein with peptidyl prolyl cis-trans isomerase (PPIase) activity. According to a tertiary model, several nonpolar residues including Trp157 and Phe197 form a substrate-binding cavity, and Asp137 and Arg142, which form a salt bridge, are located at the edge of this cavity. To analyze the role of these residues, nine single (D137A, R142A, W157A/F/Y, F197A/L/Y/W) and one double (D137A/R142A) mutant protein of SIB1 FKBP22 were constructed. The far- and near-UV CD spectra of these mutant proteins suggest that the mutations at Asp137 and Arg142 do not seriously affect the protein structure, while those at Trp157 and Phe197 cause a local conformational change around the mutation site. Each mutation decreased the PPIase activities of SIB1 FKBP22 for peptide and protein substrates similarly without seriously affecting chaperone function. This result indicates that SIB1 FKBP22 does not require PPIase activity for chaperone function. The PPIase activities of R142A, D137A and D137A/R142A decreased in this order, suggesting that Asp137 and Arg142 play a principal and auxiliary role in catalytic function, respectively, but Arg142 can function as a substitute of Asp137. Because the PPIase activity of SIB1 FKBP22 was not fully lost by the removal of all polar residues around the active site, the desolvation effect may also contribute to the enzymatic activity. However, the mutations of Trp157 to Phe or Phe197 to Leu greatly decrease the enzymatic activity, suggesting that the shape of the substrate-binding cavity is also important for enzymatic activity.
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Affiliation(s)
- Cahyo Budiman
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
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24
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Arosio B, Bulbarelli A, Bastias Candia S, Lonati E, Mastronardi L, Romualdi P, Candeletti S, Gussago C, Galimberti D, Scarpini E, DellOsso B, Altamura C, Maccarrone M, Bergamaschini L, DAddario C, Mari D. Pin1 Contribution to Alzheimers Disease: Transcriptional and Epigenetic Mechanisms in Patients with Late-Onset Alzheimers Disease. NEURODEGENER DIS 2012; 10:207-11. [DOI: 10.1159/000333799] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/27/2011] [Indexed: 11/19/2022] Open
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25
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Oligopeptide cyclophilin inhibitors: A reassessment. Eur J Med Chem 2011; 46:5556-61. [DOI: 10.1016/j.ejmech.2011.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/12/2011] [Accepted: 09/14/2011] [Indexed: 11/24/2022]
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26
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Norville IH, Breitbach K, Eske-Pogodda K, Harmer NJ, Sarkar-Tyson M, Titball RW, Steinmetz I. A novel FK-506-binding-like protein that lacks peptidyl-prolyl isomerase activity is involved in intracellular infection and in vivo virulence of Burkholderia pseudomallei. MICROBIOLOGY-SGM 2011; 157:2629-2638. [PMID: 21680634 DOI: 10.1099/mic.0.049163-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia pseudomallei is a facultative intracellular bacterial pathogen causing melioidosis, an often fatal infectious disease that is endemic in several tropical and subtropical areas around the world. We previously described a Ptk2 cell-based plaque assay screening system of B. pseudomallei transposon mutants that led to the identification of several novel virulence determinants. Using this approach we identified a mutant with reduced plaque formation in which the BPSL0918 gene was disrupted. BPSL0918 encodes a putative FK-506-binding protein (FKBP) representing a family of proteins that typically possess peptidyl-prolyl isomerase (PPIase) activity. A B. pseudomallei ΔBPSL0918 mutant showed a severely impaired ability to resist intracellular killing and to replicate within primary macrophages. Complementation of the mutant fully restored its ability to grow intracellularly. Moreover, B. pseudomallei ΔBPSL0918 was significantly attenuated in a murine model of infection. Structural modelling confirmed a modified FKBP fold of the BPSL0918-encoded protein but unlike virulence-associated FKBPs from other pathogenic bacteria, recombinant BPSL0918 protein did not possess PPIase activity in vitro. In accordance with this observation BPSL0918 exhibits several mutations in residues that have been proposed to mediate PPIase activity in other FKBPs. To our knowledge this B. pseudomallei FKBP represents the first example of this protein family which lacks PPIase activity but is important in intracellular infection of a bacterial pathogen.
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Affiliation(s)
- Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Katrin Breitbach
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | - Kristin Eske-Pogodda
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
| | | | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | | | - Ivo Steinmetz
- Friedrich Loeffler Institute of Medical Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
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Nacev BA, Low WK, Huang Z, Su TT, Su Z, Alkuraya H, Kasuga D, Sun W, Träger M, Braun M, Fischer G, Zhang K, Liu JO. A calcineurin-independent mechanism of angiogenesis inhibition by a nonimmunosuppressive cyclosporin A analog. J Pharmacol Exp Ther 2011; 338:466-75. [PMID: 21562139 DOI: 10.1124/jpet.111.180851] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cyclosporin A (CsA) is a widely used immunosuppressant drug. Its immunosuppressive activity occurs through the inhibition of the protein phosphatase calcineurin via formation of a ternary complex with cyclophilin A (CypA). CsA also inhibits endothelial cell proliferation and angiogenesis. This has been thought to occur through calcineurin inhibition as well. However, CsA is also a potent inhibitor of cyclophilins, a class of prolyl isomerases. Because calcineurin inhibition requires binding, and therefore inhibition of CypA, the relative contributions of calcineurin and cyclophilin inhibition in antiangiogenesis have not been addressed. We have taken a chemical biology approach to explore this question by dissociating the two activities of CsA at the molecular level. We have identified a nonimmunosuppressive analog of CsA that does not inhibit calcineurin but maintains inhibition of endothelial cell proliferation and in vivo angiogenesis. The same analog also maintains inhibition of all cyclophilin isoforms tested. We also show that a second, structurally distinct, cyclophilin inhibitor is sufficient to block endothelial cell proliferation. These results suggest that the inhibition of cyclophilins may play a larger role in the antiangiogenic activity of CsA than previously believed, and that cyclophilins may be potential antiangiogenic drug targets.
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Affiliation(s)
- Benjamin A Nacev
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA
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28
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Kunzmann MH, Staub I, Böttcher T, Sieber SA. Protein reactivity of natural product-derived γ-butyrolactones. Biochemistry 2011; 50:910-6. [PMID: 21188974 DOI: 10.1021/bi101858g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The discovery of novel and unique target-drug pairs for the treatment of human diseases such as cancer and bacterial infections is an urgent goal of chemical and pharmaceutical sciences. Natural products represent an inspiring source of compounds for designing chemical biology methods with applications in target identification and characterization. Inspired by the huge structural diversity of γ-butyrolactones, which constitute up to 10% of all known compounds of natural origin, we extended the "activity-based protein profiling" (ABPP) target identification technology to this promising and so far unexplored natural compound class. We designed and synthesized a comprehensive set of natural product-derived γ-lactones and thiolactones that varied in protein reactivity. Several important bacterial enzymes that are involved in diverse cellular functions such as metabolism (dihydrolipoyl dehydrogenase and 6-phosphofructokinase), cell wall biosynthesis (MurA1 and MurA2), and protein folding (trigger factors) were obtained. Especially protein folding in bacteria could represent a novel strategy for antibiotic intervention and requires chemical tools for characterization and inhibition. Future studies that extend structural modifications to protein reactive α-methylene-γ-butyrolactone as well as to reversible binding γ-lactones and thiolactones will reveal if this premise holds true.
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Affiliation(s)
- Martin H Kunzmann
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 81377 Munich, Germany
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29
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Malešević M, Poehlmann A, Hernandez Alvarez B, Diessner A, Träger M, Rahfeld JU, Jahreis G, Liebscher S, Bordusa F, Fischer G, Lücke C. The Protein-Free IANUS Peptide Array Uncovers Interaction Sites between Escherichia coli Parvulin 10 and Alkyl Hydroperoxide Reductase. Biochemistry 2010; 49:8626-35. [DOI: 10.1021/bi101015p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miroslav Malešević
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Angela Poehlmann
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Birte Hernandez Alvarez
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - André Diessner
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straβe 3, 06120 Halle/Saale, Germany
| | - Mario Träger
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Jens-Ulrich Rahfeld
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Günther Jahreis
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Sandra Liebscher
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straβe 3, 06120 Halle/Saale, Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straβe 3, 06120 Halle/Saale, Germany
| | - Gunter Fischer
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Christian Lücke
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
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30
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Identification of an atypical peptidyl-prolyl cis/trans isomerase from trypanosomatids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1028-37. [DOI: 10.1016/j.bbamcr.2010.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 04/30/2010] [Accepted: 05/17/2010] [Indexed: 11/24/2022]
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31
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Davis TL, Walker JR, Campagna-Slater V, Finerty PJ, Paramanathan R, Bernstein G, MacKenzie F, Tempel W, Ouyang H, Lee WH, Eisenmesser EZ, Dhe-Paganon S. Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. PLoS Biol 2010; 8:e1000439. [PMID: 20676357 PMCID: PMC2911226 DOI: 10.1371/journal.pbio.1000439] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 06/16/2010] [Indexed: 11/29/2022] Open
Abstract
Peptidyl-prolyl isomerases catalyze the conversion between cis and trans isomers of proline. The cyclophilin family of peptidyl-prolyl isomerases is well known for being the target of the immunosuppressive drug cyclosporin, used to combat organ transplant rejection. There is great interest in both the substrate specificity of these enzymes and the design of isoform-selective ligands for them. However, the dearth of available data for individual family members inhibits attempts to design drug specificity; additionally, in order to define physiological functions for the cyclophilins, definitive isoform characterization is required. In the current study, enzymatic activity was assayed for 15 of the 17 human cyclophilin isomerase domains, and binding to the cyclosporin scaffold was tested. In order to rationalize the observed isoform diversity, the high-resolution crystallographic structures of seven cyclophilin domains were determined. These models, combined with seven previously solved cyclophilin isoforms, provide the basis for a family-wide structure:function analysis. Detailed structural analysis of the human cyclophilin isomerase explains why cyclophilin activity against short peptides is correlated with an ability to ligate cyclosporin and why certain isoforms are not competent for either activity. In addition, we find that regions of the isomerase domain outside the proline-binding surface impart isoform specificity for both in vivo substrates and drug design. We hypothesize that there is a well-defined molecular surface corresponding to the substrate-binding S2 position that is a site of diversity in the cyclophilin family. Computational simulations of substrate binding in this region support our observations. Our data indicate that unique isoform determinants exist that may be exploited for development of selective ligands and suggest that the currently available small-molecule and peptide-based ligands for this class of enzyme are insufficient for isoform specificity.
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Affiliation(s)
- Tara L. Davis
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - John R. Walker
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Patrick J. Finerty
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Ragika Paramanathan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Galina Bernstein
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Farrell MacKenzie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Hui Ouyang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- University of Oxford, Headington, United Kingdom
| | - Elan Z. Eisenmesser
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Sirano Dhe-Paganon
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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32
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Westmark PR, Westmark CJ, Wang S, Levenson J, O'Riordan KJ, Burger C, Malter JS. Pin1 and PKMzeta sequentially control dendritic protein synthesis. Sci Signal 2010; 3:ra18. [PMID: 20215645 DOI: 10.1126/scisignal.2000451] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Some forms of learning and memory and their electrophysiologic correlate, long-term potentiation (LTP), require dendritic translation. We demonstrate that Pin1 (protein interacting with NIMA 1), a peptidyl-prolyl isomerase, is present in dendritic spines and shafts and inhibits protein synthesis induced by glutamatergic signaling. Pin1 suppression increased dendritic translation, possibly through eukaryotic translation initiation factor 4E (eIF4E) and eIF4E binding proteins 1 and 2 (4E-BP1/2). Consistent with increased protein synthesis, hippocampal slices from Pin(-/-) mice had normal early LTP (E-LTP) but significantly enhanced late LTP (L-LTP) compared to wild-type controls. Protein kinase C zeta (PKCzeta) and protein kinase M zeta (PKMzeta) were increased in Pin1(-/-) mouse brain, and their activity was required to maintain dendritic translation. PKMzeta interacted with and inhibited Pin1 by phosphorylating serine 16. Therefore, glutamate-induced, dendritic protein synthesis is sequentially regulated by Pin1 and PKMzeta signaling.
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Affiliation(s)
- Pamela R Westmark
- Department of Pathology and Laboratory Medicine and Waisman Center for Developmental Disabilities, University of Wisconsin, Madison, WI 53705, USA
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33
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Zoldák G, Aumüller T, Lücke C, Hritz J, Oostenbrink C, Fischer G, Schmid FX. A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases. Biochemistry 2009; 48:10423-36. [PMID: 19785464 DOI: 10.1021/bi9014242] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To fully explore the substrate specificities of prolyl isomerases, we synthesized a library of 20 tetrapeptides that are labeled with a 2-aminobenzoyl (Abz) group at the amino terminus and a p-nitroanilide (pNA) group at the carboxy terminus. In this peptide library of the general formula Abz-Ala-Xaa-Pro-Phe-pNA, the position Xaa before the proline is occupied by all 20 proteinogenic amino acids. A conformational analysis of the peptide by molecular dynamics simulations and by NMR spectroscopy showed that the mutual distance between the Abz and pNA moieties in the peptides depends on the isomeric state of the Xaa-Pro bond. In the cis, but not in the trans form, there are significant chemical shift changes of the Abz and pNA moieties, because their aromatic rings are close to each other. This proximity also leads to a strong quenching of Abz fluorescence, which, in combination with a solvent jump, was used to devise a sensitive assay for prolyl isomerases. Unlike the traditional assay, it is not coupled with peptide proteolysis and thus can be employed for protease-sensitive prolyl isomerases as well. The peptide library was used to provide a complete set of P1-site specificities for prototypic human members of the three prolyl isomerase families, FKBP12, cyclophilin 18, and parvulin 14. In a second application, the substrate specificity of SlyD, a protease-sensitive prolyl isomerase from Escherichia coli, was characterized and compared with that of human FKBP12 as well as with homologues from other bacteria.
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Affiliation(s)
- Gabriel Zoldák
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
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34
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Daum S, Schumann M, Mathea S, Aumüller T, Balsley MA, Constant SL, de Lacroix BF, Kruska F, Braun M, Schiene-Fischer C. Isoform-specific inhibition of cyclophilins. Biochemistry 2009; 48:6268-77. [PMID: 19480458 DOI: 10.1021/bi9007287] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cyclophilins belong to the enzyme class of peptidyl prolyl cis-trans isomerases which catalyze the cis-trans isomerization of prolyl bonds in peptides and proteins in different folding states. Cyclophilins have been shown to be involved in a multitude of cellular functions like cell growth, proliferation, and motility. Among the 20 human cyclophilin isoenzymes, the two most abundant members of the cyclophilin family, CypA and CypB, exhibit specific cellular functions in several inflammatory diseases, cancer development, and HCV replication. A small-molecule inhibitor on the basis of aryl 1-indanylketones has now been shown to discriminate between CypA and CypB in vitro. CypA binding of this inhibitor has been characterized by fluorescence anisotropy- and isothermal titration calorimetry-based cyclosporin competition assays. Inhibition of CypA- but not CypB-mediated chemotaxis of mouse CD4(+) T cells by the inhibitor provided biological proof of discrimination in vivo.
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Affiliation(s)
- Sebastian Daum
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
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35
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Mori T, Itami S, Yanagi T, Tatara Y, Takamiya M, Uchida T. Use of a real-time fluorescence monitoring system for high-throughput screening for prolyl isomerase inhibitors. ACTA ACUST UNITED AC 2009; 14:419-24. [PMID: 19403925 DOI: 10.1177/1087057109333979] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cyclophilin is a ubiquitous peptidyl prolyl cis/trans isomerase that plays critical roles in many biological processes. A number of cyclophilin inhibitors have been designed based on the structure of the immunosuppressant cyclosporin A. To discover inhibitors that have other structures, the authors established the high-throughput screening (HTS) method using FDSS6000 real-time fluorescence detector. The inhibitors identified with this HTS showed significant correlation with direct interaction as measured by surface plasmon resonance. This high-throughput assay system is a powerful tool for the discovery of peptidylprolyl isomerase inhibitors.
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Affiliation(s)
- Tadashi Mori
- Molecular Enzymology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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36
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Smajlović A, Berbić S, Schiene-Fischer C, Tušek-Žnidarič M, Taler A, Jenko-Kokalj S, Turk D, Žerovnik E. Essential role of Pro 74 in stefin B amyloid-fibril formation: Dual action of cyclophilin A on the process. FEBS Lett 2009; 583:1114-20. [DOI: 10.1016/j.febslet.2009.02.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/16/2009] [Accepted: 02/26/2009] [Indexed: 01/05/2023]
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37
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Zoldák G, Carstensen L, Scholz C, Schmid FX. Consequences of domain insertion on the stability and folding mechanism of a protein. J Mol Biol 2008; 386:1138-52. [PMID: 19136015 DOI: 10.1016/j.jmb.2008.12.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/17/2008] [Accepted: 12/18/2008] [Indexed: 11/30/2022]
Abstract
SlyD, the sensitive-to-lysis protein from Escherichia coli, consists of two domains. They are not arranged successively along the protein chain, but one domain, the "insert-in-flap" (IF) domain, is inserted internally as a guest into a surface loop of the host domain, which is a prolyl isomerase of the FK506 binding protein (FKBP) type. We used SlyD as a model to elucidate how such a domain insertion affects the stability and folding mechanism of the host and the guest domain. For these studies, the two-domain protein was compared with a single-domain variant SlyDDeltaIF, SlyD* without the chaperone domain (residues 1-69 and 130-165) in which the IF domain was removed and replaced by a short loop, as present in human FKBP12. Equilibrium unfolding and folding kinetics followed an apparent two-state mechanism in the absence and in the presence of the IF domain. The inserted domain decreased, however, the stability of the host domain in the transition region and decelerated its refolding reaction by about 10-fold. This originates from the interruption of the chain connectivity by the IF domain and its inherent instability. To monitor folding processes in this domain selectively, a Trp residue was introduced as fluorescent probe. Kinetic double-mixing experiments revealed that, in intact SlyD, the IF domain folds and unfolds about 1000-fold more rapidly than the FKBP domain, and that it is strongly stabilized when linked with the folded FKBP domain. The unfolding limbs of the kinetic chevrons of SlyD show a strong downward curvature. This deviation from linearity is not caused by a transition-state movement, as often assumed, but by the accumulation of a silent unfolding intermediate at high denaturant concentrations. In this kinetic intermediate, the FKBP domain is still folded, whereas the IF domain is already unfolded.
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Affiliation(s)
- Gabriel Zoldák
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
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38
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Wehofsky N, Wespe C, Cerovsky V, Pech A, Hoess E, Rudolph R, Bordusa F. Ionic liquids and proteases: a clean alliance for semisynthesis. Chembiochem 2008; 9:1493-9. [PMID: 18509837 DOI: 10.1002/cbic.200800025] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Herein we present the first report on protease-catalysed ligation of cleavage-sensitive peptide and protein fragments in ionic-liquid-containing solvent systems. By applying the newly established [MMIM][Me2PO4]/buffer mixture as a reaction medium, significant advantages over purely aqueous or conventional organic solvent-containing media could be identified, including in particular the use of active wild-type proteases as biocatalysts, the suppression of any competitive proteolytic side reactions, the high turnover rates compared to classical organic solvents and the high stability of chemically labile reactants.
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Affiliation(s)
- Nicole Wehofsky
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
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39
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Novel spiroannulated 3-benzofuranones. Synthesis and inhibition of the human peptidyl prolyl cis/trans isomerase Pin1. Molecules 2008; 13:995-1003. [PMID: 18463601 PMCID: PMC6245329 DOI: 10.3390/molecules13040995] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 04/22/2007] [Accepted: 04/23/2008] [Indexed: 11/17/2022] Open
Abstract
The novel 3H-spiro[1-benzofuran-2-cyclopentan]-3-one skeleton has been made accessible by different routes. One- and two-step protocols lead to tricyclic and tetracyclic benzofuranones 2 and 3, respectively. A four-step synthesis to spirocompound 4 is described. The novel spirocyclic benzofuranones display modest to no inhibition of the human peptidyl prolyl cis/trans isomerase Pin1.
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40
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Daum S, Lücke C, Wildemann D, Schiene-Fischer C. On the benefit of bivalency in peptide ligand/pin1 interactions. J Mol Biol 2007; 374:147-61. [PMID: 17931657 DOI: 10.1016/j.jmb.2007.09.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 07/31/2007] [Accepted: 09/05/2007] [Indexed: 11/17/2022]
Abstract
The human peptidyl prolyl cis/trans isomerase (PPIase) Pin1 has a key role in developmental processes and cell proliferation. Pin1 consists of an N-terminal WW domain and a C-terminal catalytic PPIase domain both targeted specifically to Ser(PO(3)H(2))/Thr(PO(3)H(2))-Pro sequences. Here, we report the enhanced affinity originating from bivalent binding of ligands toward Pin1 compared to monovalent binding. We developed composite peptides where an N-terminal segment represents a catalytic site-directed motif and a C-terminal segment exhibits a predominant affinity to the WW domain of Pin1 tethered by polyproline linkers of different chain length. We used NMR shift perturbation experiments to obtain information on the specific interaction of a bivalent ligand to both targeted sites of Pin1. The bivalent ligands allowed a considerable range of thermodynamic investigations using isothermal titration calorimetry and PPIase activity assays. They expressed up to 350-fold improved affinity toward Pin1 in the nanomolar range in comparison to the monovalent peptides. The distance between the two binding motifs was highly relevant for affinity. The optimum in affinity manifested by a linker length of five prolyl residues between active site- and WW domain-directed peptide fragments suggests that the corresponding domains in Pin1 are allowed to adopt preferred spatial arrangement upon ligand binding.
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Affiliation(s)
- Sebastian Daum
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
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41
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Zhang JW, Leach MR, Zamble DB. The peptidyl-prolyl isomerase activity of SlyD is not required for maturation of Escherichia coli hydrogenase. J Bacteriol 2007; 189:7942-4. [PMID: 17720786 PMCID: PMC2168748 DOI: 10.1128/jb.00922-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli SlyD, which is involved in the biosynthesis of the metal cluster in the [NiFe]-hydrogenase enzymes, exhibits several activities including that of a peptidyl-prolyl isomerase (PPIase). Mutations that result in deficient PPIase activity do not produce corresponding decreases in the other activities of SlyD in vitro or in hydrogenase production levels in vivo.
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Affiliation(s)
- Jie Wei Zhang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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42
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Leach MR, Zhang JW, Zamble DB. The Role of Complex Formation between the Escherichia coli Hydrogenase Accessory Factors HypB and SlyD. J Biol Chem 2007; 282:16177-86. [PMID: 17426034 DOI: 10.1074/jbc.m610834200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli protein SlyD is a member of the FK-506-binding protein family of peptidylprolyl isomerases. In addition to its peptidylprolyl isomerase domain, SlyD is composed of a molecular chaperone domain and a C-terminal tail rich in potential metal-binding residues. SlyD interacts with the [NiFe]-hydrogenase accessory protein HypB and contributes to nickel insertion during biosynthesis of the hydrogenase metallocenter. This study examines the HypB-SlyD complex and its significance in hydrogenase activation. Protein variants were prepared to delineate the interface between HypB and SlyD. Complex formation requires the HypB linker region located between the high affinity N-terminal Ni(II) site and the GTPase domain of the protein. In the case of SlyD, the deletion of a short loop in the chaperone domain abrogates the interaction with HypB. Mutations in either protein that disrupt complex formation in vitro also result in deficient hydrogenase production in vivo, indicating that the contact between HypB and SlyD is important for hydrogenase maturation. Surprisingly, SlyD stimulates release of nickel from the high affinity Ni(II)-binding site of HypB, an activity that is also disrupted by mutations that affect complex formation. Furthermore, a SlyD truncation lacking the C-terminal metal-binding tail still interacts with HypB but is deficient in stimulating metal release and is not functional in vivo. These results suggest that SlyD could activate metal release from HypB during metallation of the [NiFe] hydrogenase.
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Affiliation(s)
- Michael R Leach
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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43
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Zhang Y, Daum S, Wildemann D, Zhou XZ, Verdecia MA, Bowman ME, Lücke C, Hunter T, Lu KP, Fischer G, Noel JP. Structural basis for high-affinity peptide inhibition of human Pin1. ACS Chem Biol 2007; 2:320-8. [PMID: 17518432 PMCID: PMC2692202 DOI: 10.1021/cb7000044] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human Pin1 is a key regulator of cell-cycle progression and plays growth-promoting roles in human cancers. High-affinity inhibitors of Pin1 may provide a unique opportunity for disrupting oncogenic pathways. Here we report two high-resolution X-ray crystal structures of human Pin1 bound to non-natural peptide inhibitors. The structures of the bound high-affinity peptides identify a type-I beta-turn conformation for Pin1 prolyl peptide isomerase domain-peptide binding and an extensive molecular interface for high-affinity recognition. Moreover, these structures suggest chemical elements that may further improve the affinity and pharmacological properties of future peptide-based Pin inhibitors. Finally, an intramolecular hydrogen bond observed in both peptide complexes mimics the cyclic conformation of FK506 and rapamycin. Both FK506 and rapamycin are clinically important inhibitors of other peptidyl-prolyl cis-trans isomerases. This comparative discovery suggests that a cyclic peptide polyketide bridge, like that found in FK506 and rapamycin or a similar linkage, may significantly improve the binding affinity of structure-based Pin1 inhibitors.
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Affiliation(s)
- Yan Zhang
- Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Sebastian Daum
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Dirk Wildemann
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Xiao Zhen Zhou
- Cancer Biology Program, Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215
| | - Mark A. Verdecia
- Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Christian Lücke
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Kun-Ping Lu
- Cancer Biology Program, Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215
| | - Gunter Fischer
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Joseph P. Noel
- Howard Hughes Medical Institute, The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
- Corresponding author,
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44
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Knappe TA, Eckert B, Schaarschmidt P, Scholz C, Schmid FX. Insertion of a Chaperone Domain Converts FKBP12 into a Powerful Catalyst of Protein Folding. J Mol Biol 2007; 368:1458-68. [PMID: 17397867 DOI: 10.1016/j.jmb.2007.02.097] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Accepted: 02/28/2007] [Indexed: 11/28/2022]
Abstract
The catalytic activity of human FKBP12 as a prolyl isomerase is high towards short peptides, but very low in proline-limited protein folding reactions. In contrast, the SlyD proteins, which are members of the FKBP family, are highly active as folding enzymes. They contain an extra "insert-in-flap" or IF domain near the prolyl isomerase active site. The excision of this domain did not affect the prolyl isomerase activity of SlyD from Escherichia coli towards short peptide substrates but abolished its catalytic activity in proline-limited protein folding reactions. The reciprocal insertion of the IF domain of SlyD into human FKBP12 increased its folding activity 200-fold and generated a folding catalyst that is more active than SlyD itself. The IF domain binds to refolding protein chains and thus functions as a chaperone module. A prolyl isomerase catalytic site and a separate chaperone site with an adapted affinity for refolding protein chains are the key elements for a productive coupling between the catalysis of prolyl isomerization and conformational folding in the enzymatic mechanisms of SlyD and other prolyl isomerases, such as trigger factor and FkpA.
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Affiliation(s)
- Thomas A Knappe
- Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany
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45
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A Novel Synthesis of Highly Substituted Perhydropyrrolizines, Perhydroindolizines, and Pyrrolidines: Inhibition of the Peptidyl-Prolylcis/trans Isomerase (PPIase) Pin1. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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46
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Wagner C, Khan AS, Kamphausen T, Schmausser B, Unal C, Lorenz U, Fischer G, Hacker J, Steinert M. Collagen binding protein Mip enables Legionella pneumophila to transmigrate through a barrier of NCI-H292 lung epithelial cells and extracellular matrix. Cell Microbiol 2007; 9:450-62. [PMID: 16953800 DOI: 10.1111/j.1462-5822.2006.00802.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guinea pigs are highly susceptible to Legionella pneumophila infection and therefore have been the preferred animal model for studies of legionellosis. In this study guinea pig infections revealed that the Legionella virulence factor Mip (macrophage infectivity potentiator) contributes to the bacterial dissemination within the lung tissue and the spread of Legionella to the spleen. Histopathology of infected animals, binding assays with components of the extracellular matrix (ECM), bacterial transmigration experiments across an artificial lung epithelium barrier, inhibitor studies and ECM degradation assays were used to elucidate the underlying mechanism of the in vivo observation. The Mip protein, which belongs to the enzyme family of FK506-binding proteins (FKBP), was shown to bind to the ECM protein collagen (type I, II, III, IV, V, VI). Transwell assays with L. pneumophila and recombinant Escherichia coli HB101 strains revealed that Mip enables these bacteria to transmigrate across a barrier of NCI-H292 lung epithelial cells and ECM (NCI-H292/ECM barrier). Mip-specific monoclonal antibodies and the immunosuppressants rapamycin and FK506, which inhibit the peptidyl prolyl cis/trans isomerase (PPIase) activity of Mip, were able to inhibit this transmigration. By using protease inhibitors we found that the penetration of the NCI-H292/ECM barrier additionally requires a serine protease activity. Degradation assays with (35)S-labelled ECM proteins supported the finding of a concerted action of Mip and a serine protease. The described synergism between the activity of the collagen binding Mip protein and the serine protease activity represents an entirely new mechanism for bacterial penetration of the lung epithelial barrier and has implications for other prokaryotic and eukaryotic pathogens.
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Affiliation(s)
- Carina Wagner
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, D-97070 Würzburg, Germany
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47
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Esnault S, Shen ZJ, Whitesel E, Malter JS. The peptidyl-prolyl isomerase Pin1 regulates granulocyte-macrophage colony-stimulating factor mRNA stability in T lymphocytes. THE JOURNAL OF IMMUNOLOGY 2007; 177:6999-7006. [PMID: 17082615 DOI: 10.4049/jimmunol.177.10.6999] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cytokine production is associated with both the normal and pathologic inflammatory response to injury. Previous studies have shown that the immunosuppressants cyclosporin A or FK506, which interact with the peptidyl-propyl isomerases cyclophilin A and FK506-binding protein (FKBP12), respectively, block cytokine expression. A third member of the peptidyl-propyl isomerase family, Pin1 is expressed by immune and other cells. Pin1 has been implicated in cell cycle progression, is overexpressed in human tumors, and may rescue neurons from tau-associated degeneration. However, the role of Pin1 in the immune system remains largely unknown. In this study, we analyze the role of Pin1 in GM-CSF expression by human PBMC and CD4+ lymphocytes. We show that Pin1 isomerase activity is necessary for activation-dependent, GM-CSF mRNA stabilization, accumulation, and protein secretion, but not non-AU-rich elements containing cytokine mRNAs, including TGF-beta and IL-4. Mechanistically, Pin1 mediated the association of the AU-rich element-binding protein, AUF1, with GM-CSF mRNA, which determined the rate of decay by the exosome.
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Affiliation(s)
- Stephane Esnault
- Waisman Center for Developmental Disabilities, Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine, Madison, WI 53705, USA
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48
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Daum S, Erdmann F, Fischer G, Féaux de Lacroix B, Hessamian-Alinejad A, Houben S, Frank W, Braun M. Arylindanylketone: effiziente Inhibitoren der humanen Peptidyl-Prolyl-cis/trans-Isomerase Pin1. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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49
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Daum S, Erdmann F, Fischer G, Féaux de Lacroix B, Hessamian-Alinejad A, Houben S, Frank W, Braun M. Aryl Indanyl Ketones: Efficient Inhibitors of the Human Peptidyl Prolylcis/trans Isomerase Pin1. Angew Chem Int Ed Engl 2006; 45:7454-8. [PMID: 17048295 DOI: 10.1002/anie.200601569] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sebastian Daum
- Max-Planck-Forschungsstelle für Enzymologie der Proteinfaltung, Weinbergweg 22, 06120 Halle, Germany
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50
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Manteca A, Pelaez AI, Zardoya R, Sanchez J. Actinobacteria cyclophilins: phylogenetic relationships and description of new class- and order-specific paralogues. J Mol Evol 2006; 63:719-32. [PMID: 17103061 DOI: 10.1007/s00239-005-0130-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 06/30/2006] [Indexed: 10/23/2022]
Abstract
Cyclophilins are folding helper enzymes belonging to the class of peptidyl-prolyl cis-trans isomerases (PPIases; EC 5.2.1.8) that catalyze the cis-trans isomerization of peptidyl-prolyl bonds in proteins. They are ubiquitous proteins present in almost all living organisms analyzed to date, with extremely rare exceptions. Few cyclophilins have been described in Actinobacteria, except for three reported in the genus Streptomyces and another one in Mycobacterium tuberculosis. In this study, we performed a complete phylogenetic analysis of all Actinobacteria cyclophilins available in sequence databases and new Streptomyces cyclophilin genes sequenced in our laboratory. Phylogenetic analyses of cyclophilins recovered six highly supported groups of paralogy. Streptomyces appears as the bacteria having the highest cyclophilin diversity, harboring proteins from four groups. The first group was named "A" and is made up of highly conserved cytosolic proteins of approximately 18 kDa present in all Actinobacteria. The second group, "B," includes cytosolic proteins widely distributed throughout the genus Streptomyces and closely related to eukaryotic cyclophilins. The third group, "M" cyclophilins, consists of high molecular mass cyclophilins ( approximately 30 kDa) that contain putative membrane binding domains and would constitute the only membrane cyclophilins described to date in bacteria. The fourth group, named "C" cyclophilins, is made up of proteins of approximately 18 kDa that are orthologous to Gram-negative proteobacteria cyclophilins. Ancestral character reconstruction under parsimony was used to identify shared-derived (and likely functionally important) amino acid residues of each paralogue. Southern and Western blot experiments were performed to determine the taxonomic distribution of the different cyclophilins in Actinobacteria.
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Affiliation(s)
- Angel Manteca
- Area de Microbiologia, Departamento de Biologia Funcional and IUBA, Universidad de Oviedo, Julian Claveria s/n, Oviedo, 33006, Spain
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