1
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Fu A, Luo Z, Ziv T, Bi X, Lulu-Shimron C, Cohen-Kaplan V, Ciechanover A. Nuclear p62 condensates stabilize the promyelocytic leukemia nuclear bodies by sequestering their ubiquitin ligase RNF4. Proc Natl Acad Sci U S A 2024; 121:e2414377121. [PMID: 39418304 DOI: 10.1073/pnas.2414377121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/06/2024] [Indexed: 10/19/2024] Open
Abstract
Liquid-liquid phase separation has emerged as a crucial mechanism driving the formation of membraneless biomolecular condensates, which play important roles in numerous cellular processes. These condensates, found both in the nucleus and cytoplasm, are formed through multivalent, low-affinity interactions between various molecules. P62-containing condensates serve, among other functions, as proteolytic hubs for the ubiquitin-proteasome system. In this study, we investigated the dynamic interplay between nuclear p62 condensates and promyelocytic nuclear bodies (PML-NBs). We show that p62 condensates stabilize PML-NBs under both basal conditions and following exposure to arsenic trioxide which stimulates their degradation. We further show that this effect on the stability of PML-NBs is due to sequestration of their ubiquitin E3 ligase RNF4 in the p62 condensates with subsequent rapid degradation of the ligase. The sequestration of the ligase is made possible by association between the proline-rich domain of the PML protein and the PB1 domain of p62, which results in the formation of a PML-NB shell around the p62 condensates. Importantly, these hybrid structures do not undergo fusion and mixing of their contents which leaves unsolved the mechanism of sequestration of RNF4 in the condensates. These findings suggest an additional possible mechanism of PML-NB as a tumor suppressor which is mediated via interactions between different biomolecular condensates.
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Affiliation(s)
- Afu Fu
- Rappaport-Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Zhiwen Luo
- Rappaport-Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Tamar Ziv
- Smoler Proteomic Center and Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Xinyu Bi
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Chen Lulu-Shimron
- Rappaport-Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Victoria Cohen-Kaplan
- Rappaport-Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
| | - Aaron Ciechanover
- Rappaport-Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109602, Israel
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2
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Umumararungu T, Gahamanyi N, Mukiza J, Habarurema G, Katandula J, Rugamba A, Kagisha V. Proline, a unique amino acid whose polymer, polyproline II helix, and its analogues are involved in many biological processes: a review. Amino Acids 2024; 56:50. [PMID: 39182198 PMCID: PMC11345334 DOI: 10.1007/s00726-024-03410-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/06/2024] [Indexed: 08/27/2024]
Abstract
Proline is a unique amino acid in that its side-chain is cyclised to the backbone, thus giving proline an exceptional rigidity and a considerably restricted conformational space. Polyproline forms two well-characterized helical structures: a left-handed polyproline helix (PPII) and a right-handed polyproline helix (PPI). Usually, sequences made only of prolyl residues are in PPII conformation, but even sequences not rich in proline but which are rich in glycine, lysine, glutamate, or aspartate have also a tendency to form PPII helices. Currently, the only way to study unambiguously PPII structure in solution is to use spectroscopies based on optical activity such as circular dichroism, vibrational circular dichroism and Raman optical activity. The importance of the PPII structure is emphasized by its ubiquitous presence in different organisms from yeast to human beings where proline-rich motifs and their binding domains are believed to be involved in vital biological processes. Some of the domains that are bound by proline-rich motifs include SH3 domains, WW domains, GYF domains and UEV domains, etc. The PPII structure has been demonstrated to be essential to biological activities such as signal transduction, transcription, cell motility, and immune response.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Industrial Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
| | - Noël Gahamanyi
- Department of Biology, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
- Rwanda Biomedical Center, Microbiology Unit, National Reference Laboratory, Kigali, Rwanda
| | - Janvier Mukiza
- Rwanda Food and Drugs Authority, Nyarutarama Plaza, KG 9 Avenue, Kigali, Rwanda
| | - Gratien Habarurema
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Jonathan Katandula
- Department of Pharmacology and Toxicology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Alexis Rugamba
- Department of Biochemistry, Molecular Biology and Genetics, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Vedaste Kagisha
- Department of Pharmaceuticals and Biomolecules Analysis, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
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3
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Garsi JB, Komjáti B, Cullia G, Fejes I, Sipos M, Sipos Z, Fördős E, Markacz P, Balázs B, Lancelot N, Berger S, Raimbaud E, Brown D, Vuillard LM, Haberkorn L, Cukier C, Szlávik Z, Hanessian S. Targeting NOX2 via p47/phox-p22/phox Inhibition with Novel Triproline Mimetics. ACS Med Chem Lett 2022; 13:949-954. [DOI: 10.1021/acsmedchemlett.2c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jean-Baptiste Garsi
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Station Centre-Ville, Montréal, QC H2V 0B3, Canada
| | - Balázs Komjáti
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Gregorio Cullia
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Station Centre-Ville, Montréal, QC H2V 0B3, Canada
| | - Imre Fejes
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Melinda Sipos
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Zoltán Sipos
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Eszter Fördős
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Piroska Markacz
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Barbara Balázs
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Nathalie Lancelot
- Institut de Recherche Servier, 125 Chemin de la Ronde, 78290 Croissy, France
| | - Sylvie Berger
- Institut de Recherche Servier, 125 Chemin de la Ronde, 78290 Croissy, France
| | - Eric Raimbaud
- Institut de Recherche Servier, 125 Chemin de la Ronde, 78290 Croissy, France
| | - David Brown
- Institut de Recherche Servier, 125 Chemin de la Ronde, 78290 Croissy, France
| | | | - Laure Haberkorn
- Institut de Recherche Servier, 125 Chemin de la Ronde, 78290 Croissy, France
| | - Cyprian Cukier
- Selvita S.A., ul. Bobrzyńskiego 14, 30-348 Kraków, Poland
| | - Zoltán Szlávik
- Servier Research Institute of Medicinal Chemistry, 1031 Záhony utca 7 Mb, Budapest 1031, Hungary
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Station Centre-Ville, Montréal, QC H2V 0B3, Canada
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92617, USA
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Prostaglandin A2 Interacts with Nurr1 and Ameliorates Behavioral Deficits in Parkinson's Disease Fly Model. Neuromolecular Med 2022; 24:469-478. [PMID: 35482177 DOI: 10.1007/s12017-022-08712-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/09/2022] [Indexed: 02/01/2023]
Abstract
The orphan nuclear receptor Nurr1 is critical for the development, maintenance, and protection of midbrain dopaminergic neurons. Recently, we demonstrated that prostaglandins E1 (PGE1) and PGA1 directly bind to the ligand-binding domain (LBD) of Nurr1 and stimulate its transcriptional activation function. In this direction, here we report the transcriptional activation of Nurr1 by PGA2, a dehydrated metabolite of PGE2, through physical binding ably supported by NMR titration and crystal structure. The co-crystal structure of Nurr1-LBD bound to PGA2 revealed the covalent coupling of PGA2 with Nurr1-LBD through Cys566. PGA2 binding also induces a 21° shift of the activation function 2 (AF-2) helix H12 away from the protein core, similar to that observed in the Nurr1-LBD-PGA1 complex. We also show that PGA2 can rescue the locomotor deficits and neuronal degeneration in LRRK2 G2019S transgenic fly models.
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Plambeck KE, He CW, Navarro HH, Díaz E. Mutually Dependent Clustering of SynDIG4/PRRT1 and AMPA Receptor Subunits GluA1 and GluA2 in Heterologous Cells and Primary Neurons. Front Mol Neurosci 2022; 15:788620. [PMID: 35465096 PMCID: PMC9024365 DOI: 10.3389/fnmol.2022.788620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs) at synapses is a predominant mechanism for regulating synaptic strength. We identified the transmembrane protein synapse differentiation-induced gene 1 (SynDIG1; SD1) as an AMPAR interacting protein that regulates excitatory synaptic strength and AMPAR number both in vitro and in vivo. The related protein SynDIG4 (SD4; also known as PRRT1) was identified in several independent proteomic screens in complex with AMPARs, suggesting that it may function as an AMPAR auxiliary factor. Here, we show that the co-expression of SD4 with GluA1 or GluA2 homomeric AMPARs in COS cells leads to a 50 or 33% increase in the mean area of AMPAR puncta, respectively. This effect is accentuated when AMPAR puncta are stratified for co-localization with SD4, resulting in a 100 and 65% increase in GluA1 and GluA2 puncta, respectively. Chimeric proteins expressing only the membrane bound domain of SD4 co-expressed with full-length GluA1 or GluA2 recapitulated the effects of wild-type (WT) SD4. Additionally, the mean puncta area of GluA1 or GluA2 chimeras expressing the membrane and C-terminal domains increased significantly when co-localized with WT SD4. Similarly, the co-expression of GluA1 or GluA2 with SD4 results in a significant increase in the mean area of SD4 puncta co-localized with GluA1 or GluA2, respectively. Last, we observed a significant increase in the co-localization of SD4 with GluA1 after glycine induced long-term potentiation (LTP). The mean size of GluA1 puncta was significantly increased when stratified, indicating that co-localization with SD4 increases synaptic GluA1 cluster size during LTP. These data indicate mutually dependent clustering of SD4 and AMPAR subunits both in COS cells and primary hippocampal neurons, suggesting a mechanism for increased synaptic strength during chemical LTP.
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High-valency Anti-CD99 Antibodies Toward the Treatment of T Cell Acute Lymphoblastic Leukemia. J Mol Biol 2022; 434:167402. [PMID: 34958778 PMCID: PMC8897262 DOI: 10.1016/j.jmb.2021.167402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/07/2021] [Indexed: 11/21/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive form of leukemia that currently requires intensive chemotherapy. While childhood T-ALL is associated with high cure rates, adult T-ALL is not, and both are associated with significant short- and long-term morbidities. Thus, less toxic and effective strategies to treat T-ALL are needed. CD99 is overexpressed on T-ALL blasts at diagnosis and at relapse. Although targeting CD99 with cytotoxic antibodies has been proposed, the molecular features required for their activity are undefined. We identified human antibodies that selectively bound to the extracellular domain of human CD99, and the most potent clone, 10A1, shared an epitope with a previously described cytotoxic IgM antibody. We engineered clone 10A1 in bivalent, trivalent, tetravalent, and dodecavalent formats. Increasing the antibody valency beyond two had no effects on binding to T-ALL cells. In contrast, a valency of ≥3 was required for cytotoxicity, suggesting a mechanism of action in which an antibody clusters ≥3 CD99 molecules to induce cytotoxicity. We developed a human IgG-based tetravalent version of 10A1 that exhibited cytotoxic activity to T-ALL cells but not to healthy peripheral blood cells. The crystal structure of the 10A1 Fab in complex with a CD99 fragment revealed that the antibody primarily recognizes a proline-rich motif (PRM) of CD99 in a manner reminiscent of SH3-PRM interactions. This work further validates CD99 as a promising therapeutic target in T-ALL and defines a pathway toward the development of a selective therapy against T-ALL.
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7
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Martinez JC, Castillo F, Ruiz-Sanz J, Murciano-Calles J, Camara-Artigas A, Luque I. Understanding binding affinity and specificity of modular protein domains: A focus in ligand design for the polyproline-binding families. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:161-188. [PMID: 35534107 DOI: 10.1016/bs.apcsb.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Within the modular protein domains there are five families that recognize proline-rich sequences: SH3, WW, EVH1, GYF and UEV domains. This chapter reviews the main strategies developed for the design of ligands for these families, including peptides, peptidomimetics and drugs. We also describe some studies aimed to understand the molecular reasons responsible for the intrinsic affinity and specificity of these domains.
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Affiliation(s)
- Jose C Martinez
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Castillo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Javier Ruiz-Sanz
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Javier Murciano-Calles
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Ana Camara-Artigas
- Departamento de Química Física, Universidad de Almería, Campus de Excelencia Internacional Agroalimentario ceiA3 y CIAMBITAL, Almeria, Spain
| | - Irene Luque
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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8
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Aung LHH, Jumbo JCC, Wang Y, Li P. Therapeutic potential and recent advances on targeting mitochondrial dynamics in cardiac hypertrophy: A concise review. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:416-443. [PMID: 34484866 PMCID: PMC8405900 DOI: 10.1016/j.omtn.2021.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pathological cardiac hypertrophy begins as an adaptive response to increased workload; however, sustained hemodynamic stress will lead it to maladaptation and eventually cardiac failure. Mitochondria, being the powerhouse of the cells, can regulate cardiac hypertrophy in both adaptive and maladaptive phases; they are dynamic organelles that can adjust their number, size, and shape through a process called mitochondrial dynamics. Recently, several studies indicate that promoting mitochondrial fusion along with preventing mitochondrial fission could improve cardiac function during cardiac hypertrophy and avert its progression toward heart failure. However, some studies also indicate that either hyperfusion or hypo-fission could induce apoptosis and cardiac dysfunction. In this review, we summarize the recent knowledge regarding the effects of mitochondrial dynamics on the development and progression of cardiac hypertrophy with particular emphasis on the regulatory role of mitochondrial dynamics proteins through the genetic, epigenetic, and post-translational mechanisms, followed by discussing the novel therapeutic strategies targeting mitochondrial dynamic pathways.
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Affiliation(s)
- Lynn Htet Htet Aung
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.,Center for Bioinformatics, Institute for Translational Medicine, School of Basic Science, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Juan Carlos Cueva Jumbo
- School of Preclinical Medicine, Nanobody Research Center, Guangxi Medical University, Nanning 530021, China
| | - Yin Wang
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Peifeng Li
- Center for Molecular Genetics, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.,Center for Bioinformatics, Institute for Translational Medicine, School of Basic Science, College of Medicine, Qingdao University, Qingdao 266021, China
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9
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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10
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Teplyakov A, Obmolova G, Malia TJ, Gilliland GL. Crystal structure of CD27 in complex with a neutralizing noncompeting antibody. Acta Crystallogr F Struct Biol Commun 2017; 73:294-299. [PMID: 28471362 PMCID: PMC5417320 DOI: 10.1107/s2053230x17005957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/19/2017] [Indexed: 11/21/2022] Open
Abstract
CD27 is a T-cell and B-cell co-stimulatory glycoprotein of the tumor necrosis factor (TNF) receptor superfamily that is dependent on the availability of the TNF-like ligand CD70. Therapeutic approaches to treating autoimmune diseases and cancers with antagonistic and agonistic anti-CD27 monoclonal antibodies (mAbs), respectively, have recently been developed. Mouse anti-human CD27 mAb 2177 shows potency in neutralizing CD70-induced signaling; however, it does not block the binding of soluble CD70. To provide insight into the mechanism of action of the mAb, the crystal structure of the CD27 extracellular domain in complex with the Fab fragment of mAb 2177 was determined at 1.8 Å resolution. CD27 exhibits the assembly of cysteine-rich domains characteristic of the TNF receptor superfamily. The structure reveals a unique binding site of mAb 2177 at the edge of the receptor molecule, which allows the mAb to sterically block the cell-bound form of CD70 from reaching CD27 while leaving the ligand epitope clear. This mode of action suggests a potential dual use of mAb 2177 either as an antagonist or as an agonist.
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MESH Headings
- Amino Acid Motifs
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/genetics
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/genetics
- Baculoviridae/genetics
- Baculoviridae/metabolism
- Binding Sites
- CD27 Ligand/chemistry
- CD27 Ligand/genetics
- CD27 Ligand/immunology
- Cloning, Molecular
- Crystallography, X-Ray
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Ligands
- Mice
- Models, Molecular
- Protein Binding
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- Sequence Alignment
- Sf9 Cells
- Spodoptera
- Tumor Necrosis Factor Receptor Superfamily, Member 7/chemistry
- Tumor Necrosis Factor Receptor Superfamily, Member 7/genetics
- Tumor Necrosis Factor Receptor Superfamily, Member 7/immunology
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Affiliation(s)
- Alexey Teplyakov
- Janssen Research and Development LLC, 1400 McKean Road, Spring House, PA 19477, USA
| | - Galina Obmolova
- Janssen Research and Development LLC, 1400 McKean Road, Spring House, PA 19477, USA
| | - Thomas J. Malia
- Janssen Research and Development LLC, 1400 McKean Road, Spring House, PA 19477, USA
| | - Gary L. Gilliland
- Janssen Research and Development LLC, 1400 McKean Road, Spring House, PA 19477, USA
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11
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Imran QM, Falak N, Hussain A, Mun BG, Sharma A, Lee SU, Kim KM, Yun BW. Nitric Oxide Responsive Heavy Metal-Associated Gene AtHMAD1 Contributes to Development and Disease Resistance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:1712. [PMID: 27917181 PMCID: PMC5116471 DOI: 10.3389/fpls.2016.01712] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/31/2016] [Indexed: 05/29/2023]
Abstract
Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.
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Affiliation(s)
- Q. Muhammad Imran
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Noreen Falak
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan UniversityMardan, Pakistan
| | - Bong-Gyu Mun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Arti Sharma
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Sang-Uk Lee
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Kyung-Min Kim
- Laboratory of Plant Molecular Breeding, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National UniversityDaegu, South Korea
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12
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Righino B, Pirolli D, Radicioni G, Marzano V, Longhi R, Arcovito A, Sanna MT, De Rosa MC, Paoluzi S, Cesareni G, Messana I, Castagnola M, Vitali A. Structural studies and SH3 domain binding properties of a human antiviral salivary proline-rich peptide. Biopolymers 2016; 106:714-25. [DOI: 10.1002/bip.22889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/01/2016] [Accepted: 06/04/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Benedetta Righino
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
| | - Davide Pirolli
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
| | - Giorgia Radicioni
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
| | - Valeria Marzano
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare; C.N.R, via Mario Bianco, 9 Milan 20100 Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Monserrato, 09042, Italy, Università di Cagliari, Cittadella Universitaria; Cagliari
| | - Maria Cristina De Rosa
- Istituto di Chimica di Riconoscimento Molecolare; C.N.R. Rome, L.Go F. Vito, 1 Rome 00168 Italy
| | - Serena Paoluzi
- Dipartimento di Biologia; Università di Tor Vergata; Rome 00173 Italy
| | - Gianni Cesareni
- Dipartimento di Biologia; Università di Tor Vergata; Rome 00173 Italy
| | - Irene Messana
- Dipartimento di Scienze della Vita e dell'Ambiente, Monserrato, 09042, Italy, Università di Cagliari, Cittadella Universitaria; Cagliari
| | - Massimo Castagnola
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica; L.Go F. Vito, 1 Rome 00168 Italy
- Istituto di Chimica di Riconoscimento Molecolare; C.N.R. Rome, L.Go F. Vito, 1 Rome 00168 Italy
| | - Alberto Vitali
- Istituto di Chimica di Riconoscimento Molecolare; C.N.R. Rome, L.Go F. Vito, 1 Rome 00168 Italy
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13
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Schlundt A, Niessing D, Heissmeyer V, Sattler M. RNA recognition by Roquin in posttranscriptional gene regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:455-69. [PMID: 26844532 DOI: 10.1002/wrna.1333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 11/08/2022]
Abstract
Posttranscriptional regulation of gene expression plays a central role in the initiation of innate and adaptive immune responses. This is exemplified by the protein Roquin, which has attracted great interest during the past decade owing to its ability to prevent autoimmunity. Roquin controls T-cell activation and T helper cell differentiation by limiting the induced expression of costimulatory receptors on the surface of T cells. It does so by recognizing cis regulatory RNA-hairpin elements in the 3' UTR of target transcripts via its ROQ domain-a novel RNA-binding fold-and triggering their degradation through recruitment of factors that mediate deadenylation and decapping. Recent structural studies have revealed molecular details of the recognition of RNA hairpin structures by the ROQ domain. Surprisingly, it was found that Roquin mainly relies on shape-specific recognition of the RNA. This observation implies that a much broader range of RNA motifs could interact with the protein, but it also complicates systematic searches for novel mRNA targets of Roquin. Thus, large-scale approaches, such as crosslinking and immunoprecipitation or systematic evolution of ligands by exponential enrichment experiments coupled with next-generation sequencing, will be required to identify the complete spectrum of its target RNAs. Together with structural analyses of their binding modes, this will enable us to unravel the intricate complexity of 3' UTR regulation by Roquin and other trans-acting factors. Here, we review our current understanding of Roquin-RNA interactions and their role for Roquin function. WIREs RNA 2016, 7:455-469. doi: 10.1002/wrna.1333 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Andreas Schlundt
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Cell Biology, Biomedical Center of the Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute of Molecular Immunology, Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, München, Germany.,Institute for Immunology, Biomedical Center of the Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
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14
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Kirk LM, Ti SW, Bishop HI, Orozco-Llamas M, Pham M, Trimmer JS, Díaz E. Distribution of the SynDIG4/proline-rich transmembrane protein 1 in rat brain. J Comp Neurol 2015; 524:2266-80. [PMID: 26660156 DOI: 10.1002/cne.23945] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 11/17/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022]
Abstract
The modulation of AMPA receptor (AMPAR) content at synapses is thought to be an underlying molecular mechanism of memory and learning. AMPAR content at synapses is highly plastic and is regulated by numerous AMPAR accessory transmembrane proteins such as TARPs, cornichons, and CKAMPs. SynDIG (synapse differentiation-induced gene) defines a family of four genes (SynDIG1-4) expressed in distinct and overlapping patterns in the brain. SynDIG1 was previously identified as a novel transmembrane AMPAR-associated protein that regulates synaptic strength. The related protein SynDIG4 [also known as Prrt1 (proline-rich transmembrane protein 1)] has recently been identified as a component of AMPAR complexes. In this study, we show that SynDIG1 and SynDIG4 have distinct yet overlapping patterns of expression in the central nervous system, with SynDIG4 having especially prominent expression in the hippocampus and particularly within CA1. In contrast to SynDIG1 and other traditional AMPAR auxiliary subunits, SynDIG4 is de-enriched at the postsynaptic density and colocalizes with extrasynaptic GluA1 puncta in primary dissociated neuron culture. These results indicate that, although SynDIG4 shares sequence similarity with SynDIG1, it might act through a unique mechanism as an auxiliary factor for extrasynaptic GluA1-containing AMPARs. J. Comp. Neurol. 524:2266-2280, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Lyndsey M Kirk
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, 95616
| | - Shu W Ti
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, 95616
| | - Hannah I Bishop
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, 95616
| | - Mayra Orozco-Llamas
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, 95616
| | - Michelle Pham
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, 95616
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, 95616.,Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, California, 95616
| | - Elva Díaz
- Department of Pharmacology, University of California Davis School of Medicine, Davis, California, 95616
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15
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Zuckerman DM, Boucher LE, Xie K, Engelhardt H, Bosch J, Hoiczyk E. The bactofilin cytoskeleton protein BacM of Myxococcus xanthus forms an extended β-sheet structure likely mediated by hydrophobic interactions. PLoS One 2015; 10:e0121074. [PMID: 25803609 PMCID: PMC4372379 DOI: 10.1371/journal.pone.0121074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/29/2015] [Indexed: 11/18/2022] Open
Abstract
Bactofilins are novel cytoskeleton proteins that are widespread in Gram-negative bacteria. Myxococcus xanthus, an important predatory soil bacterium, possesses four bactofilins of which one, BacM (Mxan_7475) plays an important role in cell shape maintenance. Electron and fluorescence light microscopy, as well as studies using over-expressed, purified BacM, indicate that this protein polymerizes in vivo and in vitro into ~3 nm wide filaments that further associate into higher ordered fibers of about 10 nm. Here we use a multipronged approach combining secondary structure determination, molecular modeling, biochemistry, and genetics to identify and characterize critical molecular elements that enable BacM to polymerize. Our results indicate that the bactofilin-determining domain DUF583 folds into an extended β-sheet structure, and we hypothesize a left-handed β-helix with polymerization into 3 nm filaments primarily via patches of hydrophobic amino acid residues. These patches form the interface allowing head-to-tail polymerization during filament formation. Biochemical analyses of these processes show that folding and polymerization occur across a wide variety of conditions and even in the presence of chaotropic agents such as one molar urea. Together, these data suggest that bactofilins are comprised of a structure unique to cytoskeleton proteins, which enables robust polymerization.
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Affiliation(s)
- David M. Zuckerman
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Lauren E. Boucher
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Malaria Research Institute, Baltimore, Maryland, United States of America
| | - Kefang Xie
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Harald Engelhardt
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Jürgen Bosch
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Malaria Research Institute, Baltimore, Maryland, United States of America
| | - Egbert Hoiczyk
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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16
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Schatz O, Langer E, Ben-Arie N. Gene dosage of the transcription factor Fingerin (bHLHA9) affects digit development and links syndactyly to ectrodactyly. Hum Mol Genet 2014; 23:5394-401. [PMID: 24852374 DOI: 10.1093/hmg/ddu257] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Distal limb deformities are congenital malformations with phenotypic variability, genetic heterogeneity and complex inheritance. Among these, split-hand/foot malformation is an ectrodactyly with missing central fingers, yielding a lobster claw-like hand, which when combined with long-bone deficiency is defined as split-hand/foot malformation and long-bone deficiency (SHFLD) that is genetically heterogeneous. Copy number variation (CNV) consisting of 17p13.3 duplication was identified in unrelated pedigrees, underlying SHFLD3 (OMIM 612576). Although the transcription factor Fingerin (bHLHA9) is the only complete gene in the critical region, its biological role is not yet known and there are no data supporting its involvement in mammalian limb development. We have generated knockout mice in which only the entire coding region of Fingerin was deleted, and indeed found that most null mice display some limb defects. These include various levels of simple asymmetrical syndactyly, characterized by webbed fingers, generated by incomplete separation of soft, but not skeletal, tissues between forelimb digits 2 and 3. As expected, hand pads of Fingerin null embryos exhibited reduced apoptosis between digital rays 2 and 3. This defect was shown to cause syndactyly when the same limbs were grown ex vivo following the apoptosis assay. Extrapolating from mouse data, we suggest that Fingerin loss-of-function in humans may underlie MSSD syndactyly (OMIM 609432), which was mapped to the same locus. Taken together, Fingerin gene dosage links two different congenital limb malformations, syndactyly and ectrodactyly, which were previously postulated to share a common etiology. These results add limb disorders to the growing list of diseases resulting from CNV.
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Affiliation(s)
- Omri Schatz
- Department of Cell and Developmental Biology, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Erez Langer
- Department of Cell and Developmental Biology, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nissim Ben-Arie
- Department of Cell and Developmental Biology, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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17
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Sharma R, Lomash S, Salunke DM. Putative bioactive motif of tritrpticin revealed by an antibody with biological receptor-like properties. PLoS One 2013; 8:e75582. [PMID: 24086578 PMCID: PMC3782441 DOI: 10.1371/journal.pone.0075582] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 08/16/2013] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial peptides represent one of the most promising future strategies for combating infections and microbial drug resistance. Tritrpticin is a 13mer tryptophan-rich cationic antimicrobial peptide with a broad spectrum of activity whose application in antimicrobial therapy has been hampered by ambiguity about its biological target and consequently the molecular interactions necessary for its antimicrobial activity. The present study provides clues about the mechanism of action of tritripticin by using a unique monoclonal antibody (mAb) as a 'physiological' structural scaffold. A pool of mAbs were generated against tritrpticin and based on its high affinity and ability to bind tritrpticin analogs, mAb 6C6D7 was selected and characterized further. In a screening of phage displayed random peptides, this antibody was able to identify a novel antimicrobial peptide with low sequence homology to tritrpticin, suggesting that the mAb possessed the physico-chemical characteristics mimicking the natural receptor. Subsequently, thermodynamics and molecular modeling identified a core group of hydrophobic residues in tritrpticin arranged in a distorted's' shaped conformation as critical for antibody binding. Comparison of the mAb induced conformation with the micelle bound structure of tritrpticin reveals how a common motif may be able to interact with multiple classes of biomolecules thus extending the target range of this innate immune peptide. Based on the concurrence between thermodynamic and structural data our results reveal a template that can be used to design novel antimicrobial pharmacophores while simultaneously demonstrating at a more fundamental level the potential of mAbs to act as receptor surrogates.
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Affiliation(s)
| | | | - Dinakar M. Salunke
- National Institute of Immunology, New Delhi, India
- Regional Centre for Biotechnology, Gurgaon, India
- * E-mail:
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18
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Polyproline-II Helix in Proteins: Structure and Function. J Mol Biol 2013; 425:2100-32. [DOI: 10.1016/j.jmb.2013.03.018] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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19
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Dreumont N, Séraphin B. Rapid screening of yeast mutants with reporters identifies new splicing phenotypes. FEBS J 2013; 280:2712-26. [PMID: 23560879 DOI: 10.1111/febs.12277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 11/29/2022]
Abstract
Nuclear precursor mRNA splicing requires the stepwise assembly of a large complex, the spliceosome. Recent large-scale analyses, including purification of splicing complexes, high-throughput genetic screens and interactomic studies, have linked numerous factors to this dynamic process, including a well-defined core conserved from yeast to human. Intriguingly, despite extensive studies, no splicing defects were reported for some of the corresponding yeast mutants. To resolve this paradox, we screened a collection of viable yeast strains carrying mutations in splicing-related factors with a set of reporters including artificial constructs carrying competing splice sites. Previous analyses have indeed demonstrated that this strategy identifies yeast factors able to regulate alternative splicing and whose properties are conserved in human cells. The method, sensitive to subtle defects, revealed new splicing phenotypes for most analyzed factors such as the Urn1 protein. Interestingly, a mutant of PRP8 specifically lacking an N-terminal proline-rich region stimulated the splicing of a reporter containing competing branchpoint/3' splice site regions. Thus, using appropriate reporters, yeast can be used to quickly delineate the effect of various factors on splicing and identify those with the propensity to regulate alternative splicing events.
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Affiliation(s)
- Natacha Dreumont
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67404 Illkirch, France
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20
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Mischo A, Ohlenschläger O, Hortschansky P, Ramachandran R, Görlach M. Structural insights into a wildtype domain of the oncoprotein E6 and its interaction with a PDZ domain. PLoS One 2013; 8:e62584. [PMID: 23638119 PMCID: PMC3640046 DOI: 10.1371/journal.pone.0062584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 03/22/2013] [Indexed: 12/17/2022] Open
Abstract
The high-risk human papilloma virus (HPV) oncoproteins E6 and E7 interact with key cellular regulators and are etiological agents for tumorigenesis and tumor maintenance in cervical cancer and other malignant conditions. E6 induces degradation of the tumor suppressor p53, activates telomerase and deregulates cell polarity. Analysis of E6 derived from a number of high risk HPV finally yielded the first structure of a wild-type HPV E6 domain (PDB 2M3L) representing the second zinc-binding domain of HPV 51 E6 (termed 51Z2) determined by NMR spectroscopy. The 51Z2 structure provides clues about HPV-type specific structural differences between E6 proteins. The observed temperature sensitivity of the well-folded wild-type E6 domain implies a significant malleability of the oncoprotein in vivo. Hence, the structural differences between individual E6 and their malleability appear, together with HPV type-specific surface exposed side-chains, to provide the structural basis for the different interaction networks reported for individual E6 proteins. Furthermore, the interaction of 51Z2 with a PDZ domain of hDlg was analyzed. Human Dlg constitutes a prototypic representative of the large family of PDZ proteins regulating cell polarity, which are common targets of high-risk HPV E6. Nine C-terminal residues of 51Z2 interact with the second PDZ domain of hDlg2. Surface plasmon resonance in conjunction with the NMR spectroscopy derived complex structure (PDB 2M3M) indicate that E6 residues N-terminal to the canonical PDZ-BM of E6 significantly contribute to this interaction and increase affinity. The structure of the complex reveals how residues outside of the classical PDZ-BM enhance the affinity of E6 towards PDZ domains. Such mechanism facilitates successful competition of E6 with cellular PDZ-binding proteins and may apply to PDZ-binding proteins of other viruses as well.
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Affiliation(s)
- André Mischo
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Oliver Ohlenschläger
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Peter Hortschansky
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Ramadurai Ramachandran
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
| | - Matthias Görlach
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research - Fritz Lipmann Institute, Jena, Germany
- * E-mail:
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21
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de Abreu-Neto JB, Turchetto-Zolet AC, de Oliveira LFV, Zanettini MHB, Margis-Pinheiro M. Heavy metal-associated isoprenylated plant protein (HIPP): characterization of a family of proteins exclusive to plants. FEBS J 2013; 280:1604-16. [PMID: 23368984 DOI: 10.1111/febs.12159] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 12/15/2012] [Accepted: 01/29/2013] [Indexed: 11/29/2022]
Abstract
Metallochaperones are key proteins for the safe transport of metallic ions inside the cell. HIPPs (heavy metal-associated isoprenylated plant proteins) are metallochaperones that contain a metal binding domain (HMA) and a C-terminal isoprenylation motif. In this study, we provide evidence that proteins of this family are found only in vascular plants and may be separated into five distinct clusters. HIPPs may be involved in (a) heavy metal homeostasis and detoxification mechanisms, especially those involved in cadmium tolerance, (b) transcriptional responses to cold and drought, and (c) plant-pathogen interactions. In particular, our results show that the rice (Oryza sativa) HIPP OsHIPP41 gene is highly expressed in response to cold and drought stresses, and its product is localized in the cytosol and the nucleus. The results suggest that HIPPs play an important role in the development of vascular plants and in plant responses to environmental changes.
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Affiliation(s)
- João Braga de Abreu-Neto
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil
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22
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Kolesinska B, Podwysocka DJ, Rueping MA, Seebach D, Kamena F, Walde P, Sauer M, Windschiegl B, Meyer-Ács M, Vor der Brüggen M, Giehring S. Permeation through Phospholipid Bilayers, Skin-Cell Penetration, Plasma Stability, and CD Spectra ofα- andβ-Oligoproline Derivatives. Chem Biodivers 2013; 10:1-38. [DOI: 10.1002/cbdv.201200393] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Indexed: 11/06/2022]
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23
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011; 50:12201-4. [DOI: 10.1002/anie.201106177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 01/23/2023]
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25
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Borja MS, Piotukh K, Freund C, Gross JD. Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition. RNA (NEW YORK, N.Y.) 2011; 17:278-90. [PMID: 21148770 PMCID: PMC3022277 DOI: 10.1261/rna.2382011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/08/2010] [Indexed: 05/20/2023]
Abstract
Cap hydrolysis is a critical step in several eukaryotic mRNA decay pathways and is carried out by the evolutionarily conserved decapping complex containing Dcp2 at the catalytic core. In yeast, Dcp1 is an essential activator of decapping and coactivators such as Edc1 and Edc2 are thought to enhance activity, though their mechanism remains elusive. Using kinetic analysis we show that a crucial function of Dcp1 is to couple the binding of coactivators of decapping to activation of Dcp2. Edc1 and Edc2 bind Dcp1 via its EVH1 proline recognition site and stimulate decapping by 1000-fold, affecting both the K(M) for mRNA and rate of the catalytic step. The C-terminus of Edc1 is necessary and sufficient to enhance the catalytic step, while the remainder of the protein likely increases mRNA binding to the decapping complex. Lesions in the Dcp1 EVH1 domain or the Edc1 proline-rich sequence are sufficient to block stimulation. These results identify a new role of Dcp1, which is to link the binding of coactivators to substrate recognition and activation of Dcp2.
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Affiliation(s)
- Mark S Borja
- Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94158, USA
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27
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Zaminer J, Brockmann C, Huy P, Opitz R, Reuter C, Beyermann M, Freund C, Müller M, Oschkinat H, Kühne R, Schmalz HG. Addressing protein-protein interactions with small molecules: a Pro-Pro dipeptide mimic with a PPII helix conformation as a module for the synthesis of PRD-binding ligands. Angew Chem Int Ed Engl 2011; 49:7111-5. [PMID: 20803590 DOI: 10.1002/anie.201001739] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jan Zaminer
- Universität zu Köln, Department für Chemie, Greinstrasse 4, 50939 Köln, Germany
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28
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Huy P, Neudörfl JM, Schmalz HG. A practical synthesis of trans-3-substituted proline derivatives through 1,4-addition. Org Lett 2010; 13:216-9. [PMID: 21158419 DOI: 10.1021/ol102613z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A practical four-step synthesis of 3-alkyl-, vinyl-, and aryl-substituted proline derivatives, which are important building blocks for conformationally restrained peptide analogs, was developed. The method relies on a Cu-catalyzed 1,4-addition of Grignard reagents to N-protected 2,3-dehydroproline esters, efficiently prepared in a new one-pot protocol. The 1,4-addition products are obtained with good trans-selectivity (dr 5:1 to 25:1). A nonracemic sample of N-Cbz-3-vinylproline (74% ee) was obtained using Evans oxazolidinone as a chiral auxiliary.
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Affiliation(s)
- Peter Huy
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939 Köln, Germany
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29
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Zaminer J, Brockmann C, Huy P, Opitz R, Reuter C, Beyermann M, Freund C, Müller M, Oschkinat H, Kühne R, Schmalz HG. Adressierung von Protein-Protein-Wechselwirkungen durch niedermolekulare Verbindungen: ein Pro-Pro-Dipeptidmimetikum mit PPII-Helixkonformation als Modul für die Synthese PRD-bindender Liganden. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001739] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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