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Lim J, Lilie H, Kalbacher H, Roos N, Frecot DI, Feige M, Conrady M, Votteler T, Cousido-Siah A, Corradini Bartoli G, Iftner T, Trave G, Simon C. Evidence for direct interaction between the oncogenic proteins E6 and E7 of high-risk human papillomavirus (HPV). J Biol Chem 2023; 299:104954. [PMID: 37354975 PMCID: PMC10372912 DOI: 10.1016/j.jbc.2023.104954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023] Open
Abstract
Human papillomaviruses (HPVs) are DNA tumor viruses that infect mucosal and cutaneous epithelial cells of more than 20 vertebrates. High-risk HPV causes about 5% of human cancers worldwide, and the viral proteins E6 and E7 promote carcinogenesis by interacting with tumor suppressors and interfering with many cellular pathways. As a consequence, they immortalize cells more efficiently in concert than individually. So far, the networks of E6 and E7 with their respective cellular targets have been studied extensively but independently. However, we hypothesized that E6 and E7 might also interact directly with each other in a novel interaction affecting HPV-related carcinogenesis. Here, we report a direct interaction between E6 and E7 proteins from carcinogenic HPV types 16 and 31. We demonstrated this interaction via cellular assays using two orthogonal methods: coimmunoprecipitation and flow cytometry-based FRET assays. Analytical ultracentrifugation of the recombinant proteins revealed that the stoichiometry of the E6/E7 complex involves two E7 molecules and two E6 molecules. In addition, fluorescence polarization showed that (I) E6 binds to E7 with a similar affinity for HPV16 and HPV31 (in the same micromolar range) and (II) that the binding interface involves the unstructured N-terminal region of E7. The direct interaction of these highly conserved papillomaviral oncoproteins may provide a new perspective for studying HPV-associated carcinogenesis and the overall viral life cycle.
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Affiliation(s)
- JiaWen Lim
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittemberg, Halle-Wittemberg, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
| | - Nora Roos
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Desiree Isabella Frecot
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Maximilian Feige
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcel Conrady
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Tobias Votteler
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Alexandra Cousido-Siah
- Equipe Labellisée Ligue 2015, Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, Illkirch, France
| | - Giada Corradini Bartoli
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.
| | - Gilles Trave
- Equipe Labellisée Ligue 2015, Department of Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, Illkirch, France
| | - Claudia Simon
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.
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2
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De Sio S, Waegele J, Bhatia T, Voigt B, Lilie H, Ott M. Inherent Adaptivity of Alzheimer Peptides to Crowded Environments. Macromol Biosci 2023; 23:e2200527. [PMID: 37066978 DOI: 10.1002/mabi.202200527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/30/2023] [Indexed: 04/18/2023]
Abstract
Amyloid β (Aβ) is the major constituent in senile plaques of Alzheimer's disease in which peptides initially undergo structural conversions to form elongated fibrils. The impact of crowding on the fibrillation pathways of Aβ40 and Aβ42 , the most common peptide isoforms are studied. PEG and Ficoll are used as model crowders to mimic a macromolecular enriched surrounding. The fibrillar growth is monitored with the help of ThT-fluorescence assays in order to extract two rates describing primary and secondary processes of nucleation and growth. Techniques as fluorescence correlation spectroscopy and analytical ultracentrifugation are used to discuss oligomeric states; fibril morphologies are investigated using negative-staining transmission electron microscopy. While excluded volume effects imposed by macromolecular crowding are expected to always increase rates of intermolecular interactions and structural conversion, a vast variety of effects are found depending on the peptide, the crowder, or ionic strength of the solution. While investigations of the obtained rates with respect to a reactant-occluded model are capable to display specific surface interactions with the crowder, the employment of crystallization-like models reveal the crowder-induced entropic gain withΔ Δ G fib crow = - 116 ± 21 k $\Delta \Delta G_{\text{fib}}^{\text{crow}}=-116\pm 21\; k$ J mol-1 per volume fraction of the crowder.
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Affiliation(s)
- Silvia De Sio
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Jana Waegele
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Twinkle Bhatia
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Bruno Voigt
- Department of Physics, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Strasse 7, Halle, 06120, Saxony-Anhalt, Germany
| | - Hauke Lilie
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Maria Ott
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
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Prasad A, Breithaupt C, Nguyen DA, Lilie H, Ziegler J, Stubbs MT. Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis. J Biol Chem 2022; 298:102601. [PMID: 36265588 PMCID: PMC9672406 DOI: 10.1016/j.jbc.2022.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
MqnA, the only chorismate dehydratase known so far, catalyzes the initial step in the biosynthesis of menaquinone via the futalosine pathway. Details of the MqnA reaction mechanism remain unclear. Here, we present crystal structures of Streptomyces coelicolor MqnA and its active site mutants in complex with chorismate and the product 3-enolpyruvyl-benzoate, produced during heterologous expression in Escherichia coli. Together with activity studies, our data are in line with dehydration proceeding via substrate assisted catalysis, with the enol pyruvyl group of chorismate acting as catalytic base. Surprisingly, structures of the mutant Asn17Asp with copurified ligand suggest that the enzyme converts to a hydrolase by serendipitous positioning of the carboxyl group. All complex structures presented here exhibit a closed Venus flytrap fold, with the enzyme exploiting the characteristic ligand binding properties of the fold for specific substrate binding and catalysis. The conformational rearrangements that facilitate complete burial of substrate/product, with accompanying topological changes to the enzyme surface, could foster substrate channeling within the biosynthetic pathway.
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Affiliation(s)
- Archna Prasad
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Constanze Breithaupt
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Duc-Anh Nguyen
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Hauke Lilie
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany
| | - Jörg Ziegler
- Abteilung Molekulare Signalverarbeitung, Leibniz-Institut für Pflanzenbiochemie, Halle/Saale, Germany
| | - Milton T. Stubbs
- Institut für Biochemie und Biotechnologie, Charles-Tanford-Proteinzentrum, Martin-Luther-Universität – Halle-Wittenberg, Halle/Saale, Germany,For correspondence: Milton T. Stubbs
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4
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Bock-Bierbaum T, Funck K, Wollweber F, Lisicki E, von der Malsburg K, von der Malsburg A, Laborenz J, Noel JK, Hessenberger M, Jungbluth S, Bernert C, Kunz S, Riedel D, Lilie H, Jakobs S, van der Laan M, Daumke O. Structural insights into crista junction formation by the Mic60-Mic19 complex. Sci Adv 2022; 8:eabo4946. [PMID: 36044574 PMCID: PMC9432830 DOI: 10.1126/sciadv.abo4946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Mitochondrial cristae membranes are the oxidative phosphorylation sites in cells. Crista junctions (CJs) form the highly curved neck regions of cristae and are thought to function as selective entry gates into the cristae space. Little is known about how CJs are generated and maintained. We show that the central coiled-coil (CC) domain of the mitochondrial contact site and cristae organizing system subunit Mic60 forms an elongated, bow tie-shaped tetrameric assembly. Mic19 promotes Mic60 tetramerization via a conserved interface between the Mic60 mitofilin and Mic19 CHCH (CC-helix-CC-helix) domains. Dimerization of mitofilin domains exposes a crescent-shaped membrane-binding site with convex curvature tailored to interact with the curved CJ neck. Our study suggests that the Mic60-Mic19 subcomplex traverses CJs as a molecular strut, thereby controlling CJ architecture and function.
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Affiliation(s)
- Tobias Bock-Bierbaum
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Kathrin Funck
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Wollweber
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Elisa Lisicki
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Karina von der Malsburg
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Janina Laborenz
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Jeffrey K. Noel
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Manuel Hessenberger
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sibylle Jungbluth
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Carola Bernert
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Séverine Kunz
- Technology Platform for Electron Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Stefan Jakobs
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
- Translational Neuroinflammation and Automated Microscopy, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University Medical School, Homburg, Saarland, Germany
| | - Oliver Daumke
- Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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5
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Dorner J, Korn P, Gruhle K, Ramsbeck D, Garamus VM, Lilie H, Meister A, Schwieger C, Ihling C, Sinz A, Drescher S. A Diazirine-Modified Membrane Lipid to Study Peptide/Lipid Interactions - Chances and Challenges. Chemistry 2021; 27:14586-14593. [PMID: 34406694 PMCID: PMC8597076 DOI: 10.1002/chem.202102048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 01/19/2023]
Abstract
Although incorporation of photo‐activatable lipids into membranes potentially opens up novel avenues for investigating interactions with proteins, the question of whether diazirine‐modified lipids are suitable for such studies, remains under debate. Focusing on the potential for studying lipid/peptide interactions by cross‐linking mass spectrometry (XL‐MS), we developed a diazirine‐modified lipid (DiazPC), and examined its behaviour in membranes incorporating the model α‐helical peptide LAVA20. We observed an unexpected backfolding of the diazirine‐containing stearoyl chain of the lipid. This surprising behaviour challenges the potential application of DiazPC for future XL‐MS studies of peptide and protein/lipid interactions. The observations made for DiazPC most likely represent a general phenomenon for any type of membrane lipids with a polar moiety incorporated into the alkyl chain. Our finding is therefore of importance for future protein/lipid interaction studies relying on modified lipid probes.
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Affiliation(s)
- Julia Dorner
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Weinbergweg 22, 06120, Halle (Saale), Germany.,Institute of Pharmacy, University Leipzig, Brüderstr. 34, 04103, Leipzig, Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502, Geesthacht, Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology-Technical Biochemistry, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Annette Meister
- Institute of Biochemistry and Biotechnology-Physical Biotechnology Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.,Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian Schwieger
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.,Phospholipid Research Center, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
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6
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Lehti TA, Pajunen MI, Jokilammi A, Korja M, Lilie H, Vettenranta K, Finne J. Design of a Cytotoxic Neuroblastoma-Targeting Agent Using an Enzyme Acting on Polysialic Acid Fused to a Toxin. Mol Cancer Ther 2021; 20:1996-2007. [PMID: 34315766 DOI: 10.1158/1535-7163.mct-20-1031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/26/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022]
Abstract
Polysialic acid, an abundant cell surface component of the developing nervous system, which declines rapidly postnatally to virtual absence in the majority of adult tissues, is highly expressed in some malignant tumors including neuroblastoma. We found that the binding of a noncatalytic endosialidase to polysialic acid causes internalization of the complex from the surface of neuroblastoma kSK-N-SH cells, a subline of SK-N-SH, and leads to a complete relocalization of polysialic acid to the intracellular compartment. The binding and uptake of the endosialidase is polysialic acid-dependent as it is inhibited by free excess ligand or removal of polysialic acid by active endosialidase, and does not happen if catalytic endosialidase is used in place of inactive endosialidase. A fusion protein composed of the noncatalytic endosialidase and the cytotoxic portion of diphtheria toxin was prepared to investigate whether the cellular uptake observed could be used for the specific elimination of polysialic acid-containing cells. The conjugate toxin was found to be toxic to polysialic acid-positive kSK-N-SH with an IC50 of 1.0 nmol/L. Replacing the noncatalytic endosialidase with active endosialidase decreased the activity to the level of nonconjugated toxin. Normal nonmalignant cells were selectively resistant to the toxin conjugate. The results demonstrate that noncatalytic endosialidase induces a quantitative removal and cellular uptake of polysialic acid from the cell surface which, by conjugation with diphtheria toxin fragment, can be exploited for the selective elimination of polysialic acid-containing tumor cells.
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Affiliation(s)
- Timo A Lehti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Maria I Pajunen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anne Jokilammi
- Institute of Biomedicine, Cancer Laboratories and Medicity Research Laboratories, Faculty of Medicine, University of Turku, Turku, Finland
| | - Miikka Korja
- Department of Neurosurgery, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kim Vettenranta
- University of Helsinki and Hospital for Children and Adolescents, Helsinki University Central Hospital, Helsinki, Finland
| | - Jukka Finne
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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7
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Roos N, Breiner B, Preuss L, Lilie H, Hipp K, Herrmann H, Horn T, Biener R, Iftner T, Simon C. Optimized production strategy of the major capsid protein HPV 16L1 non-assembly variant in E. coli. Protein Expr Purif 2020; 175:105690. [DOI: 10.1016/j.pep.2020.105690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/31/2022]
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8
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Sänger L, Bender J, Rostowski K, Golbik R, Lilie H, Schmidt C, Behrens SE, Friedrich S. Alternatively spliced isoforms of AUF1 regulate a miRNA-mRNA interaction differentially through their YGG motif. RNA Biol 2020; 18:843-853. [PMID: 32924750 DOI: 10.1080/15476286.2020.1822637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Proper base-pairing of a miRNA with its target mRNA is a key step in miRNA-mediated mRNA repression. RNA remodelling by RNA-binding proteins (RBPs) can improve access of miRNAs to their target mRNAs. The largest isoform p45 of the RBP AUF1 has previously been shown to remodel viral or AU-rich RNA elements. Here, we show that AUF1 is capable of directly promoting the binding of the miRNA let-7b to its target site within the 3'UTR of the POLR2D mRNA. Our data suggest this occurs in two ways. First, the helix-destabilizing RNA chaperone activity of AUF1 disrupts a stem-loop structure of the target mRNA and thus exposes the miRNA target site. Second, the RNA annealing activity of AUF1 drives hybridization of the miRNA and its target site within the mRNA. Interestingly, the RNA remodelling activities of AUF1 were found to be isoform-specific. AUF1 isoforms containing a YGG motif are competent RNA chaperones, whereas isoforms lacking the YGG motif are not. Overall, our study demonstrates that AUF1 has the ability to modulate a miRNA-target site interaction, thus revealing a new regulatory function for AUF1 proteins during post-transcriptional control of gene expression. Moreover, tests with other RBPs suggest the YGG motif acts as a key element of RNA chaperone activity.
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Affiliation(s)
- Lennart Sänger
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Julian Bender
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Katja Rostowski
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ralph Golbik
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hauke Lilie
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sven-Erik Behrens
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susann Friedrich
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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9
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Faelber K, Dietrich L, Noel JK, Wollweber F, Pfitzner AK, Mühleip A, Sánchez R, Kudryashev M, Chiaruttini N, Lilie H, Schlegel J, Rosenbaum E, Hessenberger M, Matthaeus C, Kunz S, von der Malsburg A, Noé F, Roux A, van der Laan M, Kühlbrandt W, Daumke O. Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1. Nature 2019; 571:429-433. [PMID: 31292547 DOI: 10.1038/s41586-019-1372-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/13/2019] [Indexed: 12/25/2022]
Abstract
Balanced fusion and fission are key for the proper function and physiology of mitochondria1,2. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals3-5. Mgm1 is required for the preservation of mitochondrial DNA in yeast6, whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy-a genetic disorder that affects the optic nerve7,8. Mgm1 and OPA1 are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space. Yeast strains that express temperature-sensitive mutants of Mgm19,10 or mammalian cells that lack OPA1 display fragmented mitochondria11,12, which suggests that Mgm1 and OPA1 have an important role in inner-membrane fusion. Consistently, only the mitochondrial outer membrane-not the inner membrane-fuses in the absence of functional Mgm113. Mgm1 and OPA1 have also been shown to maintain proper cristae architecture10,14; for example, OPA1 prevents the release of pro-apoptotic factors by tightening crista junctions15. Finally, the short form of OPA1 localizes to mitochondrial constriction sites, where it presumably promotes mitochondrial fission16. How Mgm1 and OPA1 perform their diverse functions in membrane fusion, scission and cristae organization is at present unknown. Here we present crystal and electron cryo-tomography structures of Mgm1 from Chaetomium thermophilum. Mgm1 consists of a GTPase (G) domain, a bundle signalling element domain, a stalk, and a paddle domain that contains a membrane-binding site. Biochemical and cell-based experiments demonstrate that the Mgm1 stalk mediates the assembly of bent tetramers into helical filaments. Electron cryo-tomography studies of Mgm1-decorated lipid tubes and fluorescence microscopy experiments on reconstituted membrane tubes indicate how the tetramers assemble on positively or negatively curved membranes. Our findings convey how Mgm1 and OPA1 filaments dynamically remodel the mitochondrial inner membrane.
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Affiliation(s)
- Katja Faelber
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany.
| | - Lea Dietrich
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jeffrey K Noel
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Florian Wollweber
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | | | - Alexander Mühleip
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ricardo Sánchez
- Alexander von Humboldt - Sofja Kovalevskaja Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Misha Kudryashev
- Alexander von Humboldt - Sofja Kovalevskaja Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jeanette Schlegel
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Eva Rosenbaum
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Manuel Hessenberger
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Claudia Matthaeus
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Séverine Kunz
- EM facility, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Frank Noé
- Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, Geneva, Switzerland
| | - Martin van der Laan
- Medical Biochemistry & Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University Medical School, Homburg, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine, Berlin, Germany. .,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
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10
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Breiner B, Preuss L, Roos N, Conrady M, Lilie H, Iftner T, Simon C. Refolding and in vitro characterization of human papillomavirus 16 minor capsid protein L2. Biol Chem 2019; 400:513-522. [PMID: 30375341 DOI: 10.1515/hsz-2018-0311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/25/2018] [Indexed: 01/31/2023]
Abstract
The minor capsid protein L2 of papillomaviruses exhibits multiple functions during viral entry including membrane interaction. Information on the protein is scarce, because of its high tendency of aggregation. We determined suitable conditions to produce a functional human papillomavirus (HPV) 16 L2 protein and thereby provide the opportunity for extensive in vitro analysis with respect to structural and biochemical information on L2 proteins and mechanistic details in viral entry. We produced the L2 protein of high-risk HPV 16 in Escherichia coli as inclusion bodies and purified the protein under denaturing conditions. A successive buffer screen resulted in suitable conditions for the biophysical characterization of 16L2. Analytical ultracentrifugation of the refolded protein showed a homogenous monomeric species. Furthermore, refolded 16L2 shows secondary structure elements. The N-terminal region including the proposed transmembrane region of 16L2 shows alpha-helical characteristics. However, overall 16L2 appears largely unstructured. Refolded 16L2 is capable of binding to DNA indicating that the putative DNA-binding regions are accessible in refolded 16L2. Further the refolded protein interacts with liposomal membranes presumably via the proposed transmembrane region at neutral pH without structural changes. This indicates that 16L2 can initially interact with membranes via pre-existing structural features.
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Affiliation(s)
- Bastian Breiner
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
| | - Laura Preuss
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
| | - Nora Roos
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
| | - Marcel Conrady
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 03, D-06120, Halle/Saale, Germany
| | - Thomas Iftner
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
| | - Claudia Simon
- Institute of Medical Virology, University of Tübingen, Elfriede-Aulhorn-Str. 06, D-72076 Tuebingen, Germany
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11
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Pertermann R, Tamilarasan S, Gursinsky T, Gambino G, Schuck J, Weinholdt C, Lilie H, Grosse I, Golbik RP, Pantaleo V, Behrens SE. A Viral Suppressor Modulates the Plant Immune Response Early in Infection by Regulating MicroRNA Activity. mBio 2018; 9:e00419-18. [PMID: 29691336 PMCID: PMC5915741 DOI: 10.1128/mbio.00419-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Many viral suppressors (VSRs) counteract antiviral RNA silencing, a central component of the plant's immune response by sequestration of virus-derived antiviral small interfering RNAs (siRNAs). Here, we addressed how VSRs affect the activities of cellular microRNAs (miRNAs) during a viral infection by characterizing the interactions of two unrelated VSRs, the Tombusvirus p19 and the Cucumovirus 2b, with miRNA 162 (miR162), miR168, and miR403. These miRNAs regulate the expression of the important silencing factors Dicer-like protein 1 (DCL1) and Argonaute proteins 1 and 2 (AGO1 and AGO2), respectively. Interestingly, while the two VSRs showed similar binding profiles, the miRNAs were bound with significantly different affinities, for example, with the affinity of miR162 greatly exceeding that of miR168. In vitro silencing experiments revealed that p19 and 2b affect miRNA-mediated silencing of the DCL1, AGO1, and AGO2 mRNAs in strict accordance with the VSR's miRNA-binding profiles. In Tombusvirus-infected plants, the miRNA-binding behavior of p19 closely corresponded to that in vitro Most importantly, in contrast to controls with a Δp19 virus, infections with wild-type (wt) virus led to changes of the levels of the miRNA-targeted mRNAs, and these changes correlated with the miRNA-binding preferences of p19. This was observed exclusively in the early stage of infection when viral genomes are proposed to be susceptible to silencing and viral siRNA (vsiRNA) concentrations are low. Accordingly, our study suggests that differential binding of miRNAs by VSRs is a widespread viral mechanism to coordinately modulate cellular gene expression and the antiviral immune response during infection initiation.IMPORTANCE Plant viruses manipulate their hosts in various ways. Viral suppressor proteins (VSRs) interfere with the plant's immune response by sequestering small, antivirally acting vsiRNAs, which are processed from viral RNAs during the plant's RNA-silencing response. Here, we examined the effects of VSRs on cellular microRNAs (miRNAs), which show a high degree of similarity with vsiRNAs. Binding experiments with two unrelated VSRs and three important regulatory miRNAs revealed that the proteins exhibit similar miRNA-binding profiles but bind different miRNAs at considerably different affinities. Most interestingly, experiments in plants showed that in the early infection phase, the Tombusvirus VSR p19 modulates the activity of these miRNAs on their target mRNAs very differently and that this differential regulation strictly correlates with the binding affinities of p19 for the respective miRNAs. Our data suggest that VSRs may specifically control plant gene expression and the early immune response by differential sequestration of miRNAs.
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Affiliation(s)
- Robert Pertermann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Selvaraj Tamilarasan
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection-Consiglio Nazionale delle Ricerche, Turin, Italy
| | - Jana Schuck
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Claus Weinholdt
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ivo Grosse
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection-Consiglio Nazionale delle Ricerche, Research Unit of Bari, Bari, Italy
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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12
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Buttstedt A, Mureşan CI, Lilie H, Hause G, Ihling CH, Schulze SH, Pietzsch M, Moritz RFA. How Honeybees Defy Gravity with Royal Jelly to Raise Queens. Curr Biol 2018; 28:1095-1100.e3. [PMID: 29551410 DOI: 10.1016/j.cub.2018.02.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Abstract
The female sex in honeybees (Apis spp.) comprises a reproductive queen and a sterile worker caste. Nurse bees feed all larvae progressively with a caste-specific food jelly until the prepupal stage. Only those larvae that are exclusively fed a large amount of royal jelly (RJ) develop into queens [1]. RJ is a composite secretion of two specialized head glands: the mandibular glands, which produce mainly fatty acids [2], and the hypopharyngeal glands, which contribute proteins, primarily belonging to the major royal jelly protein (MRJP) family [3]. Past research on RJ has focused on its nutritional function and overlooked its central role with regard to the orientation of the larva in the royal brood cell. Whereas workers are reared in the regular horizontal cells of the comb, the queen cells are specifically built outside of the normal comb area to accommodate for the larger queen [4, 5]. These cells hang freely along the bottom of the comb and are vertically oriented, opening downward [6]. Queen larvae are attached by their RJ diet to the cell ceiling. Thus, the physical properties of RJ are central to successful retention of larvae in the cell. Here, we show that the main protein of RJ (MRJP1) polymerizes in complex with another protein, apisimin, into long fibrous structures that build the basis for the high viscosity of RJ to hold queen larvae on the RJ surface.
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Affiliation(s)
- Anja Buttstedt
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany.
| | - Carmen I Mureşan
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany; Facultatea de Zootehnie şi Biotehnologii, Universitatea de Ştiinţe Agricole şi Medicină Veterinară, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania
| | - Hauke Lilie
- Institut für Biochemie und Biotechnologie-Technische Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Gerd Hause
- Biozentrum-Elektronenmikroskopie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Christian H Ihling
- Institut für Pharmazie-Pharmazeutische Chemie und Bioanalytik, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Stefan-H Schulze
- Fraunhofer Institut für Mikrostruktur von Werkstoffen und Systemen IMWS, Walter-Hülse-Str. 1, 06120 Halle (Saale), Germany
| | - Markus Pietzsch
- Institut für Pharmazie-Pharmazeutische Technologie und Biopharmazie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Robin F A Moritz
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany; Facultatea de Zootehnie şi Biotehnologii, Universitatea de Ştiinţe Agricole şi Medicină Veterinară, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania; Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa
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13
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Hunger D, Röcker M, Falke D, Lilie H, Sawers RG. The C-terminal Six Amino Acids of the FNT Channel FocA Are Required for Formate Translocation But Not Homopentamer Integrity. Front Microbiol 2017; 8:1616. [PMID: 28878762 PMCID: PMC5572259 DOI: 10.3389/fmicb.2017.01616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/08/2017] [Indexed: 01/27/2023] Open
Abstract
FocA is the archetype of the pentameric formate-nitrite transporter (FNT) superfamily of channels, members of which translocate small organic and inorganic anions across the cytoplasmic membrane of microorganisms. The N- and C-termini of each protomer are cytoplasmically oriented. A Y-L-R motif is found immediately after transmembrane helix 6 at the C-terminus of FNT proteins related to FocA, or those with a role in formate translocation. Previous in vivo studies had revealed that formate translocation through FocA was controlled by interaction with the formate-producing glycyl-radical enzyme pyruvate formate-lyase (PflB) or its structural and functional homolog, TdcE. In this study we analyzed the effect on in vivo formate export and import, as well as on the stability of the homopentamer in the membrane, of successively removing amino acid residues from the C-terminus of FocA. Removal of up to five amino acids was without consequence for either formate translocation or oligomer stability. Removal of a sixth residue (R280) prevented formate uptake by FocA in a strain lacking PflB and significantly reduced, but did not prevent, formate export. Sensitivity to the toxic formate analog hypophosphite, which is also transported into the cell by FocA, was also relieved. Circular dichroism spectroscopy and blue-native PAGE analysis revealed, however, that this variant had near identical secondary and quaternary structural properties to those of native FocA. Interaction with the glycyl radical enzyme, TdcE, was also unaffected by removal of the C-terminal 6 amino acid residues, indicating that impaired interaction with TdcE was not the reason for impaired formate translocation. Removal of a further residue (L279) severely restricted formate export, the stability of the protein and its ability to form homopentamers. Together, these studies revealed that the Y278-L279-R280 motif at the C-terminus is essential for bidirectional formate translocation by FocA, but that L279 is both necessary and sufficient for homopentamer integrity.
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Affiliation(s)
- Doreen Hunger
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Marie Röcker
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Dörte Falke
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
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14
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Annamalai K, Liberta F, Vielberg MT, Close W, Lilie H, Gührs KH, Schierhorn A, Koehler R, Schmidt A, Haupt C, Hegenbart U, Schönland S, Schmidt M, Groll M, Fändrich M. Common Fibril Structures Imply Systemically Conserved Protein Misfolding Pathways In Vivo. Angew Chem Int Ed Engl 2017; 56:7510-7514. [DOI: 10.1002/anie.201701761] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/15/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Karthikeyan Annamalai
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Falk Liberta
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich (CIPSM); Technische Universität München, Department Chemie; 85748 Garching Germany
| | - William Close
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology/Technical Biochemistry; 06120 Halle (Saale) Germany
| | - Karl-Heinz Gührs
- CF Protemics; Leibniz Institute on Aging-, Fritz Lipmann Institute (FLI); Beutenbergstraße 11 07745 Jena Germany
| | - Angelika Schierhorn
- Institut für Biochemie und Biotechnologie; Serviceeinheit für Massenspektrometrie; 06120 Halle (Saale) Germany
| | - Rolf Koehler
- Institute of Human Genetics; Im Neuenheimer Feld 366 69120 Heidelberg Germany
| | - Andreas Schmidt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Christian Haupt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Ute Hegenbart
- Amyloidosis Center; Department of Internal Medicine V; Im Neuenheimer Feld 410 69120 Heidelberg Germany
| | - Stefan Schönland
- Amyloidosis Center; Department of Internal Medicine V; Im Neuenheimer Feld 410 69120 Heidelberg Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM); Technische Universität München, Department Chemie; 85748 Garching Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
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15
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Annamalai K, Liberta F, Vielberg MT, Close W, Lilie H, Gührs KH, Schierhorn A, Koehler R, Schmidt A, Haupt C, Hegenbart U, Schönland S, Schmidt M, Groll M, Fändrich M. Common Fibril Structures Imply Systemically Conserved Protein Misfolding Pathways In Vivo. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701761] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Karthikeyan Annamalai
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Falk Liberta
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich (CIPSM); Technische Universität München, Department Chemie; 85748 Garching Germany
| | - William Close
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology/Technical Biochemistry; 06120 Halle (Saale) Germany
| | - Karl-Heinz Gührs
- CF Protemics; Leibniz Institute on Aging-, Fritz Lipmann Institute (FLI); Beutenbergstraße 11 07745 Jena Germany
| | - Angelika Schierhorn
- Institut für Biochemie und Biotechnologie; Serviceeinheit für Massenspektrometrie; 06120 Halle (Saale) Germany
| | - Rolf Koehler
- Institute of Human Genetics; Im Neuenheimer Feld 366 69120 Heidelberg Germany
| | - Andreas Schmidt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Christian Haupt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Ute Hegenbart
- Amyloidosis Center; Department of Internal Medicine V; Im Neuenheimer Feld 410 69120 Heidelberg Germany
| | - Stefan Schönland
- Amyloidosis Center; Department of Internal Medicine V; Im Neuenheimer Feld 410 69120 Heidelberg Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM); Technische Universität München, Department Chemie; 85748 Garching Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry; Ulm University; Helmholtzstrasse 8/1 89081 Ulm Germany
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16
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Friedrich S, Schmidt T, Schierhorn A, Lilie H, Szczepankiewicz G, Bergs S, Liebert UG, Golbik RP, Behrens SE. Arginine methylation enhances the RNA chaperone activity of the West Nile virus host factor AUF1 p45. RNA 2016; 22:1574-1591. [PMID: 27520967 PMCID: PMC5029455 DOI: 10.1261/rna.055269.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/07/2016] [Indexed: 06/06/2023]
Abstract
A prerequisite for the intracellular replication process of the Flavivirus West Nile virus (WNV) is the cyclization of the viral RNA genome, which enables the viral replicase to initiate RNA synthesis. Our earlier studies indicated that the p45 isoform of the cellular AU-rich element binding protein 1 (AUF1) has an RNA chaperone activity, which supports RNA cyclization and viral RNA synthesis by destabilizing a stem structure at the WNV RNA's 3'-end. Here we show that in mammalian cells, AUF1 p45 is consistently modified by arginine methylation of its C terminus. By a combination of different experimental approaches, we can demonstrate that the methyltransferase PRMT1 is necessary and sufficient for AUF1 p45 methylation and that PRMT1 is required for efficient WNV replication. Interestingly, in comparison to the nonmethylated AUF1 p45, the methylated AUF1 p45(aDMA) exhibits a significantly increased affinity to the WNV RNA termini. Further data also revealed that the RNA chaperone activity of AUF1 p45(aDMA) is improved and the methylated protein stimulates viral RNA synthesis considerably more efficiently than the nonmethylated AUF1 p45. In addition to its destabilizing RNA chaperone activity, we identified an RNA annealing activity of AUF1 p45, which is not affected by methylation. Arginine methylation of AUF1 p45 thus represents a specific determinant of its RNA chaperone activity while functioning as a WNV host factor. Our data suggest that the methylation modifies the conformation of AUF1 p45 and in this way affects its RNA binding and restructuring activities.
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Affiliation(s)
- Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | | | - Sandra Bergs
- Institute of Virology, Leipzig University, 04130 Leipzig, Germany
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04130 Leipzig, Germany
| | - Ralph P Golbik
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Martin Luther University Halle-Wittenberg, 60120 Halle, Germany
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17
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Schmidt T, Knick P, Lilie H, Friedrich S, Golbik RP, Behrens SE. Coordinated Action of Two Double-Stranded RNA Binding Motifs and an RGG Motif Enables Nuclear Factor 90 To Flexibly Target Different RNA Substrates. Biochemistry 2016; 55:948-59. [PMID: 26795062 DOI: 10.1021/acs.biochem.5b01072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanisms of how RNA binding proteins (RBP) bind to and distinguish different RNA molecules are yet uncertain. Here, we performed a comprehensive analysis of the RNA binding properties of multidomain RBP nuclear factor 90 (NF90) by investigating specifically the functional activities of two double-stranded RNA binding motifs (dsRBM) and an RGG motif in the protein's unstructured C-terminus. By comparison of the RNA binding affinities of several NF90 variants and their modes of binding to a set of defined RNA molecules, the activities of the motifs turned out to be very different. While dsRBM1 contributes little to RNA binding, dsRBM2 is essential for effective binding of double-stranded RNA. The protein's immediate C-terminus, including the RGG motif, is indispensable for interactions of the protein with single-stranded RNA, and the RGG motif decisively contributes to NF90's overall RNA binding properties. Conformational studies, which compared wild-type NF90 with a variant that contains a pseudophosphorylated residue in the RGG motif, suggest that the NF90 C-terminus is involved in conformational changes in the protein after RNA binding, with the RGG motif acting as a central regulatory element. In summary, our data propose a concerted action of all RNA binding motifs within the frame of the full-length protein, which may be controlled by regulation of the activity of the RGG motif, e.g., by phosphorylation. This multidomain interplay enables the RBP NF90 to discriminate RNA features by dynamic and adaptable interactions.
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Affiliation(s)
- Tobias Schmidt
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Paul Knick
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Susann Friedrich
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Ralph Peter Golbik
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI), Section of Microbial Biotechnology, and ‡Section of Protein Biochemistry, Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3, D-06120 Halle/Saale, Germany
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18
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Osadnik H, Schöpfel M, Heidrich E, Mehner D, Lilie H, Parthier C, Risselada HJ, Grubmüller H, Stubbs MT, Brüser T. PspF-binding domain PspA1-144and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins. Mol Microbiol 2015; 98:743-59. [DOI: 10.1111/mmi.13154] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Hendrik Osadnik
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Michael Schöpfel
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Eyleen Heidrich
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Denise Mehner
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Christoph Parthier
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - H. Jelger Risselada
- Max Planck Institute for Biophysical Chemistry; Am Fassberg 11 Göttingen 37077 Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry; Am Fassberg 11 Göttingen 37077 Germany
| | - Milton T. Stubbs
- Institute of Biochemistry and Biotechnology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Straße 3 Halle (Saale) 06120 Germany
| | - Thomas Brüser
- Institute of Microbiology; Leibniz Universität Hannover; Herrenhäuser Str. 2 Hannover 30419 Germany
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Job F, Settele F, Lorey S, Rundfeldt C, Baumann L, Beck-Sickinger AG, Haupts U, Lilie H, Bosse-Doenecke E. Ubiquitin is a versatile scaffold protein for the generation of molecules with de novo binding and advantageous drug-like properties. FEBS Open Bio 2015; 5:579-93. [PMID: 26258013 PMCID: PMC4522466 DOI: 10.1016/j.fob.2015.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 01/17/2023] Open
Abstract
In the search for effective therapeutic strategies, protein-based biologicals are under intense development. While monoclonal antibodies represent the majority of these drugs, other innovative approaches are exploring the use of scaffold proteins for the creation of binding molecules with tailor-made properties. Ubiquitin is especially suited for this strategy due to several key characteristics. Ubiquitin is a natural serum protein, 100% conserved across the mammalian class and possesses high thermal, structural and proteolytic stability. Because of its small size and lack of posttranslational modifications, it can be easily produced in Escherichia coli. In this work we provide evidence that ubiquitin is safe as tested experimentally in vivo. In contrast to previously published results, we show that, in our hands, ubiquitin does not act as a functional ligand of the chemokine receptor CXCR4. Cellular assays based on different signaling pathways of the receptor were conducted with the natural agonist SDF-1 as a benchmark. In none of the assays could a response to ubiquitin treatment be elicited. Furthermore, intravenous application to mice at high concentrations did not induce any detectable effect on cytokine levels or hematological parameters.
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Affiliation(s)
- Florian Job
- Institute for Biochemistry and Biotechnology/Technical Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Florian Settele
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Susan Lorey
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Chris Rundfeldt
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Lars Baumann
- Institute of Biochemistry, University of Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
| | | | - Ulrich Haupts
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology/Technical Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Eva Bosse-Doenecke
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
- Corresponding author. Tel.: +49 345 4780 365; fax: +49 345 27996 332.
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20
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Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TMD, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JGH, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BDE, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SFW, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 2015; 10:e0126420. [PMID: 25997164 PMCID: PMC4440767 DOI: 10.1371/journal.pone.0126420] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carlos Alfonso
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Fumio Arisaka
- Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252–0880, Japan
| | - Ilan Attali
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David L. Bain
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Marina M. Bakhtina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Donald F. Becker
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Ahmet Bekdemir
- Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Tabot M. D. Besong
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - William Brennerman
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Jonathan B. Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Catherine T. Chaton
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Keith D. Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Kimberly A. Crowley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Tina Daviter
- Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom
| | - William L. Dean
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Ana I. Díez
- Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain
| | - Christine Ebel
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Debra M. Eckert
- Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America
| | - Patrick England
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Carlos Escalante
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America
| | - Jeffrey A. Fagan
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Ron M. Finn
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Jayesh Gor
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | | | - Damien Hall
- Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Andrew B. Herr
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Elizabeth E. Howell
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Richard S. Isaac
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Muan, 534–729, Korea
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Jack A. Kornblatt
- Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Dalibor Kosek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daniel Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Eric A. Kusznir
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - Hyewon Kwon
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Adam Larson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Aline Le Roy
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Andrew P. Leech
- Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Juan R. Luque-Ortega
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Ernest L. Maynard
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | | | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Chad K. Park
- Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America
| | - Jin-Ku Park
- Central Instrument Center, Mokpo National University, Muan, 534–729, Korea
| | - Peter D. Pawelek
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Erby E. Perdue
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Martin G. Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Bertrand D. E. Raynal
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Klaus Richter
- Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany
| | - Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Rose Rosenberg
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Arthur J. Rowe
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Arne C. Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - David J. Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Javier G. Seravalli
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Alexandra S. Solovyova
- Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Renjie Song
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - David Staunton
- Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom
| | - Caitlin Stoddard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Katherine Stott
- Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | | | - Werner W. Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark
| | - John P. Sumida
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Sarah G. Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Roman H. Szczepanowski
- Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02–109, Poland
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Ronald T. Toth
- Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Stephan F. W. Uebel
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230–0045, Japan
| | - Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter H. von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Christine Wandrey
- Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Szu-Huan Wang
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Steven E. Weitzel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Martin Wolff
- ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany
| | - Edward Wright
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Yu-Sung Wu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America
| | - Jacinta M. Wubben
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
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Dinesh DC, Kovermann M, Gopalswamy M, Hellmuth A, Calderón Villalobos LIA, Lilie H, Balbach J, Abel S. Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response. Proc Natl Acad Sci U S A 2015; 112:6230-5. [PMID: 25918389 PMCID: PMC4434759 DOI: 10.1073/pnas.1424077112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plant hormone auxin activates primary response genes by facilitating proteolytic removal of auxin/indole-3-acetic acid (AUX/IAA)-inducible repressors, which directly bind to transcriptional auxin response factors (ARF). Most AUX/IAA and ARF proteins share highly conserved C-termini mediating homotypic and heterotypic interactions within and between both protein families. The high-resolution NMR structure of C-terminal domains III and IV of the AUX/IAA protein PsIAA4 from pea (Pisum sativum) revealed a globular ubiquitin-like β-grasp fold with homologies to the Phox and Bem1p (PB1) domain. The PB1 domain of wild-type PsIAA4 features two distinct surface patches of oppositely charged amino acid residues, mediating front-to-back multimerization via electrostatic interactions. Mutations of conserved basic or acidic residues on either face suppressed PsIAA4 PB1 homo-oligomerization in vitro and confirmed directional interaction of full-length PsIAA4 in vivo (yeast two-hybrid system). Mixing of oppositely mutated PsIAA4 PB1 monomers enabled NMR mapping of the negatively charged interface of the reconstituted PsIAA4 PB1 homodimer variant, whose stoichiometry (1:1) and equilibrium binding constant (KD ∼ 6.4 μM) were determined by isothermal titration calorimetry. In silico protein-protein docking studies based on NMR and yeast interaction data derived a model of the PsIAA4 PB1 homodimer, which is comparable with other PB1 domain dimers, but indicated considerable differences between the homodimeric interfaces of AUX/IAA and ARF PB1 domains. Our study provides an impetus for elucidating the molecular determinants that confer specificity to complex protein-protein interaction circuits between members of the two central families of transcription factors important to the regulation of auxin-responsive gene expression.
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Affiliation(s)
| | - Michael Kovermann
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine
| | - Mohanraj Gopalswamy
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine
| | - Antje Hellmuth
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, D-06120 Halle, Germany
| | | | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany; and
| | - Jochen Balbach
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine;
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, D-06120 Halle, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany; and Department of Plant Sciences, University of California, Davis, CA 95616
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Burkert O, Kreßner S, Sinn L, Giese S, Simon C, Lilie H. Biophysical characterization of polyomavirus minor capsid proteins. Biol Chem 2015; 395:871-80. [PMID: 24713574 DOI: 10.1515/hsz-2014-0114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/01/2014] [Indexed: 11/15/2022]
Abstract
The murine polyomavirus encodes three structural proteins, VP1, VP2 and VP3, which together form the viral capsid. The outer shell of this capsid is composed of the major capsid protein VP1, the inner shell consists of VP2 and its N-terminally truncated form VP3. These two minor capsid proteins interact with their identical C-terminal part in the central cavity of VP1 pentamers, building the capsid assembly unit. While the VP1 structure and functions are well studied, VP2 and VP3 are poorly understood. In order to get a detailed insight into the structure and function of the minor capsid proteins, they were produced recombinantly in Escherichia coli as inclusion bodies and refolded in vitro. The success of refolding was strictly dependent on the presence of detergent in the refolding buffer. VP2 and VP3 are monomeric and their structures exhibit a high α-helical content. The function of both proteins could be monitored by complex formation with VP1. Furthermore, we could demonstrate a hemolytic activity of VP2/VP3 in vitro, which fits well into a postulated membrane interaction of VP2 during viral infection.
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Moritz B, Lilie H, Naarmann-de Vries IS, Urlaub H, Wahle E, Ostareck-Lederer A, Ostareck DH. Biophysical and biochemical analysis of hnRNP K: arginine methylation, reversible aggregation and combinatorial binding to nucleic acids. Biol Chem 2015; 395:837-53. [PMID: 25003387 DOI: 10.1515/hsz-2014-0146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/20/2014] [Indexed: 12/17/2022]
Abstract
Abstract Analysis of arginine methylation, which affects specific protein interactions in eukaryotic cells, requires access to methylated protein for biophysical and biochemical studies. Methylation of heterogeneous nuclear ribonucleoprotein K (hnRNP K) upon co-expression with protein arginine methyltransferase 1 in E. coli was monitored by mass spectrometry and found to be identical to the modification of hnRNP K purified from mammalian cells. Recombinant non-methylated and arginine-methylated hnRNP K (MethnRNP K) were used to characterize self-aggregation and nucleic acid binding. Analytical ultracentrifugation and static light scattering experiments revealed that hnRNP K methylation does not impact reversible self-aggregation, which can be prevented by high ionic strength and organic additives. Filter binding assays were used to compare the binding of non-methylated and MethnRNP K to the pyrimidine repeat-containing differentiation control element (DICE) of reticulocyte 15-lipoxygenase mRNA 3' UTR. No affinity differences were detected for both hnRNP K variants. A series of oligonucleotides carrying various numbers of C4 motifs at different positions was used in steady state competition assays with fluorescently-labeled functional differentiation control element (2R). Quantitative evaluation indicated that all hnRNP K homology domains of hnRNP K contribute differentially to RNA binding, with KH1-KH2 acting as a tandem domain and KH3 as an individual binding domain.
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Blüher D, Reinhardt-Tews A, Hey M, Lilie H, Golbik R, Breunig KD, Anders A. An ancient oxidoreductase making differential use of its cofactors. Biol Chem 2015; 395:855-69. [PMID: 25003388 DOI: 10.1515/hsz-2014-0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/01/2014] [Indexed: 11/15/2022]
Abstract
Abstract Many transcription factors contribute to cellular homeostasis by integrating multiple signals. Signaling via the yeast Gal80 protein, a negative regulator of the prototypic transcription activator Gal4, is primarily regulated by galactose. ScGal80 from Saccharomyces cerevisiae has been reported to bind NAD(P). Here, we show that the ability to bind these ligands is conserved in KlGal80, a Gal80 homolog from the distantly related yeast Kluyveromyces lactis. However, the homologs apparently have diverged with respect to response to the dinucleotide. Strikingly, ScGal80 binds NAD(P) and NAD(P)H with more than 50-fold higher affinity than KlGal80. In contrast to ScGal80, where NAD is neutral, NAD and NADP have a negative effect in KlGal80 on its interaction with a KlGal4-peptide in vitro. Swapping a loop in the NAD(P) binding Rossmann-fold of ScGal80 into KlGal80 increases the affinity for NAD(P) and has a significant impact on KlGal4 regulation in vivo. Apparently, dinucleotide binding allows coupling of the metabolic state of the cell to regulation of the GAL/LAC genes. The particular sequences involved in binding determine how exactly the metabolic state is sensed and integrated by Gal80 to regulate Gal4.
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Reich S, Kovermann M, Lilie H, Knick P, Geissler R, Golbik RP, Balbach J, Behrens SE. Initiation of RNA synthesis by the hepatitis C virus RNA-dependent RNA polymerase is affected by the structure of the RNA template. Biochemistry 2014; 53:7002-12. [PMID: 25310724 PMCID: PMC4230328 DOI: 10.1021/bi5006656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is
a central enzyme of the intracellular replication of the viral (+)RNA
genome. Here, we studied the individual steps of NS5B-catalyzed RNA
synthesis by a combination of biophysical methods, including real-time
1D 1H NMR spectroscopy. NS5B was found to bind to a nonstructured
and a structured RNA template in different modes. Following NTP binding
and conversion to the catalysis-competent ternary complex, the polymerase
revealed an improved affinity for the template. By monitoring the
folding/unfolding of 3′(−)SL by 1H NMR, the
base pair at the stem’s edge was identified as the most stable
component of the structure. 1H NMR real-time analysis of
NS5B-catalyzed RNA synthesis on 3′(−)SL showed that
a pronounced lag phase preceded the processive polymerization reaction.
The presence of the double-stranded stem with the edge base pair acting
as the main energy barrier impaired RNA synthesis catalyzed by NS5B.
Our observations suggest a crucial role of RNA-modulating factors
in the HCV replication process.
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Affiliation(s)
- Stefan Reich
- Institute of Biochemistry and Biotechnology, Section of Microbial Biotechnology, ‡Institute of Physics, Section of Biophysics, §Institute of Biochemistry and Biotechnology, Section of Technical Biochemistry, Martin Luther University Halle-Wittenberg , D-06120 Halle/Saale, Germany
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Thieme T, Patzschke R, Job F, Liebold J, Seemann P, Lilie H, Balbach J, Schwarz E. Biophysical and structural characterization of a folded core domain within the proregion of growth and differentiation factor-5. FEBS J 2014; 281:4866-77. [DOI: 10.1111/febs.13025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/17/2014] [Accepted: 08/26/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Tino Thieme
- Technical Biochemistry; Martin-Luther-University Halle-Wittenberg; Germany
| | - Rica Patzschke
- Institute of Physics; Martin-Luther-University Halle-Wittenberg; Germany
| | - Florian Job
- Technical Biochemistry; Martin-Luther-University Halle-Wittenberg; Germany
| | - Jens Liebold
- Technical Biochemistry; Martin-Luther-University Halle-Wittenberg; Germany
| | - Petra Seemann
- Berlin Brandenburg Center for Regenerative Therapies (BCRT); Charité-Universitätsmedizin Berlin; Germany
- Berlin Brandenburg School for Regenerative Therapies (BSRT); Charité-Universitätsmedizin Berlin; Germany
| | - Hauke Lilie
- Technical Biochemistry; Martin-Luther-University Halle-Wittenberg; Germany
| | - Jochen Balbach
- Institute of Physics; Martin-Luther-University Halle-Wittenberg; Germany
| | - Elisabeth Schwarz
- Technical Biochemistry; Martin-Luther-University Halle-Wittenberg; Germany
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Tischer A, Lilie H, Auton M, Lange C. Oxidative refolding of rPA in l
-ArgHCl and in ionic liquids: A correlation between hydrophobicity, salt effects, and refolding yield. Biopolymers 2014; 101:1129-40. [DOI: 10.1002/bip.22518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/09/2014] [Accepted: 06/10/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine; Biochemistry and Molecular Biology, Mayo Clinic; Rochester MN
| | - Hauke Lilie
- Institut für Biochemie und Biotechnologie; Martin-Luther-Universität Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle (Saale) Germany
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine; Biochemistry and Molecular Biology, Mayo Clinic; Rochester MN
| | - Christian Lange
- Scil Proteins GmbH; Heinrich Damerow Str. 1 06120 Halle (Saale) Germany
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Poenick S, Jahnke HG, Eichler M, Frost S, Lilie H, Robitzki AA. Comparative label-free monitoring of immunotoxin efficacy in 2D and 3D mamma carcinoma in vitro models by impedance spectroscopy. Biosens Bioelectron 2014; 53:370-6. [DOI: 10.1016/j.bios.2013.09.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 01/18/2023]
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Simon C, Klose T, Herbst S, Han BG, Sinz A, Glaeser RM, Stubbs MT, Lilie H. Disulfide linkage and structure of highly stable yeast-derived virus-like particles of murine polyomavirus. J Biol Chem 2014; 289:10411-10418. [PMID: 24567335 DOI: 10.1074/jbc.m113.484162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
VP1 is the major coat protein of murine polyomavirus and forms virus-like particles (VLPs) in vitro. VLPs consist of 72 pentameric VP1 subunits held together by a terminal clamp structure that is further stabilized by disulfide bonds and chelation of calcium ions. Yeast-derived VLPs (yVLPs) assemble intracellularly in vivo during recombinant protein production. These in vivo assembled yVLPs differ in several properties from VLPs assembled in vitro from bacterially produced pentamers. We found several intermolecular disulfide linkages in yVLPs involving 5 of the 6 cysteines of VP1 (Cys(115)-Cys(20), Cys(12)-Cys(20), Cys(16)-Cys(16), Cys(12)/ Cys(16)-Cys(115), and Cys(274)-Cys(274)), indicating a highly coordinated disulfide network within the in vivo assembled particles involving the N-terminal region of VP1. Cryoelectron microscopy revealed structured termini not resolved in the published crystal structure of the bacterially expressed VLP that appear to clamp the pentameric subunits together. These structural features are probably the reason for the observed higher stability of in vivo assembled yVLPs compared with in vitro assembled bacterially expressed VLPs as monitored by increased thermal stability, higher resistance to trypsin cleavage, and a higher activation enthalpy of the disassembly reaction. This high stability is decreased following disassembly of yVLPs and subsequent in vitro reassembly, suggesting a role for cellular components in optimal assembly.
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Affiliation(s)
- Claudia Simon
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Strasse 03, 06120 Halle, Germany
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Sabine Herbst
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck Strasse 04, 06120 Halle, Germany
| | - Bong Gyoon Han
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720
| | - Andrea Sinz
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck Strasse 04, 06120 Halle, Germany
| | - Robert M Glaeser
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720
| | - Milton T Stubbs
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Strasse 03, 06120 Halle, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Strasse 03, 06120 Halle, Germany.
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Tischer A, Pultke H, Topf A, Auton M, Lange C, Lilie H. The effects ofN-ethyl-N′-methyl imidazolium chloride on the solubility, stability and aggregation of tc-rPA. FEBS J 2014; 281:1738-49. [DOI: 10.1111/febs.12736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/18/2014] [Accepted: 01/29/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Tischer
- Division of Hematology; Departments of Internal Medicine, Biochemistry and Molecular Biology; Mayo Clinic; Rochester MN USA
| | | | - Andrea Topf
- Institut für Biophysikalische Chemie; Medizinische Hochschule Hannover; Germany
| | - Matthew Auton
- Division of Hematology; Departments of Internal Medicine, Biochemistry and Molecular Biology; Mayo Clinic; Rochester MN USA
| | | | - Hauke Lilie
- Institut für Biochemie und Biotechnologie; Martin-Luther-Universität Halle-Wittenberg; Halle (Saale) Germany
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Lilie H, Richter S, Bergelt S, Frost S, Gehle F. Polyionic and cysteine-containing fusion peptides as versatile protein tags. Biol Chem 2014; 394:995-1004. [PMID: 23629522 DOI: 10.1515/hsz-2013-0116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/24/2013] [Indexed: 11/15/2022]
Abstract
In response to advances in proteomics research and the use of proteins in medical and biotechnological applications, recombinant protein production and the design of specific protein characteristics and functions has become a widely used technology. In this context, protein fusion tags have been developed as indispensable tools for protein expression, purification, and the design of functionalized surfaces or artificially bifunctional proteins. Here we summarize how positively or negatively charged polyionic fusion peptides with or without an additional cysteine can be used as protein tags for protein expression and purification, for matrix-assisted refolding of aggregated protein, and for coupling of proteins either to technologically relevant matrices or to other proteins. In this context we used cysteine-containing polyionic fusion peptides for the design of immunotoxins. In general, polyionic fusion tags can be considered as a multifunctional module in protein technology.
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Affiliation(s)
- Hauke Lilie
- Institut fur Biochemie und Biotechnologie, Martin-Luther-Universit at Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany.
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Pettelkau J, Thondorf I, Theisgen S, Lilie H, Schröder T, Arlt C, Ihling CH, Sinz A. Structural analysis of guanylyl cyclase-activating protein-2 (GCAP-2) homodimer by stable isotope-labeling, chemical cross-linking, and mass spectrometry. J Am Soc Mass Spectrom 2013; 24:1969-1979. [PMID: 24026978 DOI: 10.1007/s13361-013-0734-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
The topology of the GCAP-2 homodimer was investigated by chemical cross-linking and high resolution mass spectrometry. Complementary conducted size-exclusion chromatography and analytical ultracentrifugation studies indicated that GCAP-2 forms a homodimer both in the absence and in the presence of Ca(2+). In-depth MS and MS/MS analysis of the cross-linked products was aided by (15)N-labeled GCAP-2. The use of isotope-labeled protein delivered reliable structural information on the GCAP-2 homodimer, enabling an unambiguous discrimination between cross-links within one monomer (intramolecular) or between two subunits (intermolecular). The limited number of cross-links obtained in the Ca(2+)-bound state allowed us to deduce a defined homodimeric GCAP-2 structure by a docking and molecular dynamics approach. In the Ca(2+)-free state, GCAP-2 is more flexible as indicated by the higher number of cross-links. We consider stable isotope-labeling to be indispensable for deriving reliable structural information from chemical cross-linking data of multi-subunit protein assemblies.
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Affiliation(s)
- Jens Pettelkau
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
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Kettner K, Kuettner EB, Otto A, Lilie H, Golbik RP, Sträter N, Kriegel TM. In vivo phosphorylation and in vitro autophosphorylation-inactivation of Kluyveromyces lactis hexokinase KlHxk1. Biochem Biophys Res Commun 2013; 435:313-8. [PMID: 23583397 DOI: 10.1016/j.bbrc.2013.03.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 11/16/2022]
Abstract
The bifunctional hexokinase KlHxk1 is a key component of glucose-dependent signal transduction in Kluyveromyces lactis. KlHxk1 is phosphorylated in vivo and undergoes ATP-dependent autophosphorylation-inactivation in vitro. This study identifies serine-15 as the site of in vivo phosphorylation and serine-157 as the autophosphorylation-inactivation site. X-ray crystallography of the in vivo phosphorylated enzyme indicates the existence of a ring-shaped symmetrical homodimer carrying two phosphoserine-15 residues. In contrast, small-angle X-ray scattering and equilibrium sedimentation analyses reveal the existence of monomeric phosphoserine-15 KlHxk1 in solution. While phosphorylation at serine-15 and concomitant homodimer dissociation are likely to be involved in glucose signalling, mechanism and putative physiological significance of KlHxk1 inactivation by autophosphorylation at serine-157 remain to be established.
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Affiliation(s)
- Karina Kettner
- Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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Funkner A, Parthier C, Schutkowski M, Zerweck J, Lilie H, Gyrych N, Fischer G, Stubbs MT, Ferrari DM. Peptide binding by catalytic domains of the protein disulfide isomerase-related protein ERp46. J Mol Biol 2013; 425:1340-62. [PMID: 23376096 DOI: 10.1016/j.jmb.2013.01.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 01/09/2013] [Accepted: 01/23/2013] [Indexed: 11/18/2022]
Abstract
The protein disulfide isomerase (PDI) family member ERp46/endoPDI/thioredoxin domain-containing protein 5 is preferentially expressed in a limited number of tissues, where it may function as a survival factor for nitrosative stress in vivo. It is involved in insulin production as well as in adiponectin signaling and interacts specifically with the redox-regulatory endoplasmic reticulum proteins endoplasmic oxidoreductin 1α (Ero1α) and peroxiredoxin-4. Here, we show that ERp46, although lacking a PDI-like redox-inactive b'-thioredoxin domain with its hydrophobic substrate binding site, is able to bind to a large pool of peptides containing aromatic and basic residues via all three of its catalytic domains (a(0), a and a'), though the a(0) domain may contain the primary binding site. ERp46, which shows relatively higher activity as a disulfide-reductase than as an oxidase/isomerase in vitro compared to PDI and ERp57, possesses chaperone activity in vivo, a property also shared by the C-terminal a' domain. A crystal structure of the a' domain is also presented, offering a view of possible substrate binding sites within catalytic domains of PDI proteins.
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Affiliation(s)
- Andreas Funkner
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle (Saale), Germany
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Simon C, Schaepe S, Breunig K, Lilie H. PRODUCTION OF POLYOMAVIRUS-LIKE PARTICLES IN AKlgal80KNOCKOUT STRAIN OF THE YEASTKluyveromyces lactis. Prep Biochem Biotechnol 2013; 43:217-35. [DOI: 10.1080/10826068.2012.750613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Buschmann J, Moritz B, Jeske M, Lilie H, Schierhorn A, Wahle E. Identification of Drosophila and human 7-methyl GMP-specific nucleotidases. J Biol Chem 2012; 288:2441-51. [PMID: 23223233 DOI: 10.1074/jbc.m112.426700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Turnover of mRNA releases, in addition to the four regular nucleoside monophosphates, the methylated cap nucleotide in the form of 7-methylguanosine monophosphate (m(7)GMP) or diphosphate (m(7)GDP). The existence of pathways to eliminate the modified nucleotide seems likely, as its incorporation into nucleic acids is undesirable. Here we describe a novel 5' nucleotidase from Drosophila that cleaves m(7)GMP to 7-methylguanosine and inorganic phosphate. The enzyme, encoded by the predicted gene CG3362, also efficiently dephosphorylates CMP, although with lower apparent affinity; UMP and the purine nucleotides are poor substrates. The enzyme is inhibited by elevated concentrations of AMP and also cleaves m(7)GDP to the nucleoside and two inorganic phosphates, albeit less efficiently. CG3362 has equivalent sequence similarity to two human enzymes, cytosolic nucleotidase III (cNIII) and the previously uncharacterized cytosolic nucleotidase III-like (cNIII-like). We show that cNIII-like also displays 5' nucleotidase activity with a high affinity for m(7)GMP. CMP is a slightly better substrate but again with a higher K(m). The activity of cNIII-like is stimulated by phosphate. In contrast to cNIII-like, cNIII and human cytosolic nucleotidase II do not accept m(7)GMP as a substrate. We suggest that the m(7)G-specific nucleotidases protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids.
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Affiliation(s)
- Juliane Buschmann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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Hüttl S, Fiebig J, Kutter S, Hause G, Lilie H, Spinka M, König S. Catalytically active filaments - pyruvate decarboxylase from Neurospora crassa. pH-controlled oligomer structure and catalytic function. FEBS J 2011; 279:275-84. [PMID: 22077835 DOI: 10.1111/j.1742-4658.2011.08421.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pyruvate decarboxylase is a key enzyme in organisms whose energy metabolism is based on alcoholic fermentation. The enzyme catalyses the nonoxidative decarboxylation of 2-oxo acids in the presence of the cofactors thiamine diphosphate and magnesium ions. Pyruvate decarboxylase species from yeasts and plant seeds studied to date are allosterically activated by their substrate pyruvate. However, detailed kinetic studies on the enzyme from Neurospora crassa demonstrate for the first time the lack of substrate activation for a yeast pyruvate decarboxylase species. The quaternary structure of this enzyme species is also peculiar because it forms filamentous structures. The complex enzyme structure was analysed using a number of methods, including small-angle X-ray solution scattering, transmission electron microscopy, analytical ultracentrifugation and size-exclusion chromatography. These measurements were complemented by detailed kinetic studies in dependence on the pH.
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Affiliation(s)
- Stefanie Hüttl
- Division of Enzymology, Institute of Biochemistry & Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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Winter J, Gleiter S, Klappa P, Lilie H. Protein disulfide isomerase isomerizes non-native disulfide bonds in human proinsulin independent of its peptide-binding activity. Protein Sci 2011; 20:588-96. [PMID: 21308844 DOI: 10.1002/pro.592] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein disulfide isomerase (PDI) supports proinsulin folding as chaperone and isomerase. Here, we focus on how the two PDI functions influence individual steps in the complex folding process of proinsulin. We generated a PDI mutant (PDI-aba'c) where the b' domain was partially deleted, thus abolishing peptide binding but maintaining a PDI-like redox potential. PDI-aba'c catalyzes the folding of human proinsulin by increasing the rate of formation and the final yield of native proinsulin. Importantly, PDI-aba'c isomerizes non-native disulfide bonds in completely oxidized folding intermediates, thereby accelerating the formation of native disulfide bonds. We conclude that peptide binding to PDI is not essential for disulfide isomerization in fully oxidized proinsulin folding intermediates.
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Affiliation(s)
- Jeannette Winter
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, 85747 Garching, Germany.
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Koch D, Chan ACK, Murphy MEP, Lilie H, Grass G, Nies DH. Characterization of a dipartite iron uptake system from uropathogenic Escherichia coli strain F11. J Biol Chem 2011; 286:25317-30. [PMID: 21596746 DOI: 10.1074/jbc.m111.222745] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the uropathogenic Escherichia coli strain F11, in silico genome analysis revealed the dicistronic iron uptake operon fetMP, which is under iron-regulated control mediated by the Fur regulator. The expression of fetMP in a mutant strain lacking known iron uptake systems improved growth under iron depletion and increased cellular iron accumulation. FetM is a member of the iron/lead transporter superfamily and is essential for iron uptake by the Fet system. FetP is a periplasmic protein that enhanced iron uptake by FetM. Recombinant FetP bound Cu(II) and the iron analog Mn(II) at distinct sites. The crystal structure of the FetP dimer reveals a copper site in each FetP subunit that adopts two conformations: CuA with a tetrahedral geometry composed of His(44), Met(90), His(97), and His(127), and CuB, a second degenerate octahedral geometry with the addition of Glu(46). The copper ions of each site occupy distinct positions and are separated by ∼1.3 Å. Nearby, a putative additional Cu(I) binding site is proposed as an electron source that may function with CuA/CuB displacement to reduce Fe(III) for transport by FetM. Together, these data indicate that FetMP is an additional iron uptake system composed of a putative iron permease and an iron-scavenging and potentially iron-reducing periplasmic protein.
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Affiliation(s)
- Doreen Koch
- Molecular Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
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Schröder T, Lilie H, Lange C. The myristoylation of guanylate cyclase-activating protein-2 causes an increase in thermodynamic stability in the presence but not in the absence of Ca²⁺. Protein Sci 2011; 20:1155-65. [PMID: 21520322 DOI: 10.1002/pro.643] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 04/08/2011] [Accepted: 04/11/2011] [Indexed: 11/07/2022]
Abstract
Guanylate cyclase activating protein-2 (GCAP-2) is a Ca²⁺-binding protein of the neuronal calcium sensor (NCS) family. Ca²⁺-free GCAP-2 activates the retinal rod outer segment guanylate cyclases ROS-GC1 and 2. Native GCAP-2 is N-terminally myristoylated. Detailed structural information on the Ca²⁺-dependent conformational switch of GCAP-2 is missing so far, as no atomic resolution structures of the Ca²⁺-free state have been determined. The role of the myristoyl moiety remains poorly understood. Available functional data is incompatible with a Ca²⁺-myristoyl switch as observed in the prototype NCS protein, recoverin. For the homologous GCAP-1, a Ca²⁺-independent sequestration of the myristoyl moiety inside the proteins structure has been proposed. In this article, we compare the thermodynamic stabilities of myristoylated and non-myristoylated GCAP-2 in their Ca²⁺-bound and Ca²⁺-free forms, respectively, to gain information on the nature of the Ca²⁺-dependent conformational switch of the protein and shed some light on the role of its myristoyl group. In the absence of Ca²⁺, the stability of the myristoylated and non-myristoylated forms was indistinguishable. Ca²⁺ exerted a stabilizing effect on both forms of the protein, which was significantly stronger for myr GCAP-2. The stability data were corroborated by dye binding experiments performed to probe the solvent-accessible hydrophobic surface of the protein. Our results strongly suggest that the myristoyl moiety is permanently solvent-exposed in Ca²⁺-free GCAP-2, whereas it interacts with a hydrophobic part of the protein's structure in the Ca²⁺-bound state.
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Affiliation(s)
- Thomas Schröder
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle 06120, Germany
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Arnold U, Leich F, Neumann P, Lilie H, Ulbrich-Hofmann R. Crystal structure of RNase A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor. FEBS J 2010; 278:331-40. [PMID: 21134128 DOI: 10.1111/j.1742-4658.2010.07957.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because of their ability to degrade RNA, RNases are potent cytotoxins. The cytotoxic activity of most members of the RNase A superfamily, however, is abolished by the cytosolic ribonuclease inhibitor (RI). RNase A tandem enzymes, in which two RNase A molecules are artificially connected by a peptide linker, and thus have a pseudodimeric structure, exhibit remarkable cytotoxic activity. In vitro, however, these enzymes are still inhibited by RI. Here, we present the crystal structures of three tandem enzymes with the linker sequences GPPG, SGSGSG, and SGRSGRSG, which allowed us to analyze the mode of binding of RI to the RNase A tandem enzymes. Modeling studies with the crystal structures of the RI-RNase A complex and the SGRSGRSG-RNase A tandem enzyme as templates suggested a 1 : 1 binding stoichiometry for the RI-RNase A tandem enzyme complex, with binding of the RI molecule to the N-terminal RNase A entity. These results were experimentally verified by analytical ultracentrifugation, quantitative electrophoresis, and proteolysis studies with trypsin. As other dimeric RNases, which are comparably cytotoxic, either evade RI binding or potentially even bind two RI molecules, inactivation by RI cannot be the crucial limitation to the cytotoxicity of dimeric RNases.
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Affiliation(s)
- Ulrich Arnold
- Department of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle, Germany.
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Tischer A, Lilie H, Rudolph R, Lange C. L-arginine hydrochloride increases the solubility of folded and unfolded recombinant plasminogen activator rPA. Protein Sci 2010; 19:1783-95. [PMID: 20665695 PMCID: PMC2975141 DOI: 10.1002/pro.465] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 07/07/2010] [Accepted: 07/07/2010] [Indexed: 11/06/2022]
Abstract
L-arginine hydrochloride (L-ArgHCl) was found to be an effective enhancer for in vitro protein refolding more than two decades ago. A detailed understanding of the mechanism of action, by which L-ArgHCl as co-solvent is capable to effectively suppress protein aggregation, while protein stability is preserved, has remained elusive. Concepts for the effects of co-solvents, which have been established over the last decades, were found to be insufficient to completely explain the effects of L-ArgHCl on protein refolding. In this article, we present data, which clearly establish that L-ArgHCl acts on the equilibrium solubility of the native model protein recombinant plasminogen activator (rPA), while for S-carboxymethylated rPA (IAA-rPA) that served as a model protein for denatured protein states, equilibrium solubilities could not be obtained. Solid to solute free transfer energies for native rPA were lowered by up to 14 kJ mol(-1) under the tested conditions. This finding is in marked contrast to a previously proposed model in which L-ArgHCl acts as a neutral crowder which exclusively has an influence on the stability of the transition state of aggregation. The effects on the apparent solubility of IAA-rPA, as well as on the aggregation kinetics of all studied protein species, that were observed in the present work could tentatively be explained within the framework of a nucleation-aggregation scheme, in which L-ArgHCl exerts a strong effect on the pre-equilibria leading to formation of the aggregation seed.
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Affiliation(s)
| | | | | | - Christian Lange
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-WittenbergKurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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Kirstein J, Hoffmann A, Lilie H, Schmidt R, Rübsamen-Waigmann H, Brötz-Oesterhelt H, Mogk A, Turgay K. The antibiotic ADEP reprogrammes ClpP, switching it from a regulated to an uncontrolled protease. EMBO Mol Med 2010; 1:37-49. [PMID: 20049702 PMCID: PMC3378108 DOI: 10.1002/emmm.200900002] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel class of antibiotic acyldepsipeptides (designated ADEPs) exerts its unique antibacterial activity by targeting the peptidase caseinolytic protease P (ClpP). ClpP forms proteolytic complexes with heat shock proteins (Hsp100) that select and process substrate proteins for ClpP-mediated degradation. Here, we analyse the molecular mechanism of ADEP action and demonstrate that ADEPs abrogate ClpP interaction with cooperating Hsp100 adenosine triphosphatases (ATPases). Consequently, ADEP treated bacteria are affected in ClpP-dependent general and regulatory proteolysis. At the same time, ADEPs also activate ClpP by converting it from a tightly regulated peptidase, which can only degrade short peptides, into a proteolytic machinery that recognizes and degrades unfolded polypeptides. In vivo nascent polypeptide chains represent the putative primary target of ADEP-activated ClpP, providing a rationale for the antibacterial activity of the ADEPs. Thus, ADEPs cause a complete functional reprogramming of the Clp–protease complex.
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Affiliation(s)
- Janine Kirstein
- Institut für Biologie-Mikrobiologie, FU Berlin, Berlin, Germany
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Reich S, Golbik RP, Geissler R, Lilie H, Behrens SE. Mechanisms of activity and inhibition of the hepatitis C virus RNA-dependent RNA polymerase. J Biol Chem 2010; 285:13685-93. [PMID: 20194503 DOI: 10.1074/jbc.m109.082206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The RNA-dependent RNA polymerase NS5B is a key enzyme of the replication of hepatitis C virus (HCV) and a major therapeutic target. Applying a novel continuous assay with highly purified protein and a fluorescent RNA-template we provide for the first time a comprehensive mechanistic description of the enzymatic reaction. Using fluorescence spectroscopy, the kinetics of NS5B was confirmed to consist of two half-reactions, namely substrate binding and turnover. Determining the binding constants of the substrates and the rate constants of individual reaction steps, NS5B was shown to bind the template single-stranded RNA with high affinity (nanomolar range) and in a stepwise process that reflects the substrate positioning. As demonstrated by CD, NTP(s) binding caused a tertiary structural change of the enzyme into an active conformation. The second half-reaction was dissected into a sequential polymerization and a subsequent, rate-limiting product release reaction. Taking advantage of these tools, we analyzed the mechanism of action of the NS5B inhibitor HCV-796, which was shown to interfere with the formation of double-stranded RNA by blocking the second half-reaction.
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Affiliation(s)
- Stefan Reich
- Department of Microbial Biotechnology, Institute of Biochemistry and Biotechnology, Faculty of Life Sciences, Martin-Luther-University Halle-Wittenberg, D-06120 Halle/Saale, Germany
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Falke DÃ, Schulz K, Doberenz C, Beyer L, Lilie H, Thiemer B, Sawers RG. Unexpected oligomeric structure of the FocA formate channel ofEscherichia coli: a paradigm for the formateânitrite transporter family of integral membrane proteins. FEMS Microbiol Lett 2010; 303:69-75. [DOI: 10.1111/j.1574-6968.2009.01862.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Thoms S, Max KE, Wunderlich M, Jacso T, Lilie H, Reif B, Heinemann U, Schmid FX. Dimer Formation of a Stabilized Gβ1 Variant: A Structural and Energetic Analysis. J Mol Biol 2009; 391:918-32. [DOI: 10.1016/j.jmb.2009.06.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/09/2009] [Accepted: 06/10/2009] [Indexed: 11/25/2022]
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Abstract
Monoclonal antibodies (mAbs) have been developed over the past years as promising anticancer therapeutics. The conjugation of tumor specific mAbs with cytotoxic molecules has been shown to improve their efficacy dramatically. These bifunctional immunotoxins, consisting of covalently linked antibodies and protein toxins, possess considerable potential in cancer therapy. Many of them are under investigation in clinical trials. As a result of general interest in new toxic components, we describe here the suitability of the bacterial protein Listeriolysin O (LLO) as cytotoxic component of an immunotoxin. Unique characteristics of LLO, such as its acidic pH optimum and the possibility to regulate the cytolytic activity by cysteine-oxidation, make LLO an interesting toxophore. Oxidized LLO shows a substantially decreased cytolytic activity when compared with the reduced protein as analyzed by hemolysis. Both oxidized and reduced LLO exhibit a cell-type-unspecific toxicity in cell culture with a significantly higher toxicity of reduced LLO. For cell-type-specific targeting of LLO to tumor cells, LLO was coupled to the dsFv fragment of the monoclonal antibody B3, which recognizes the tumor-antigen Lewis Y. The coupling of LLO to dsFv-B3 was performed via cysteine-containing polyionic fusion peptides that act as a specific heterodimerization motif. The novel immunotoxin B3-LLO could be shown to specifically eliminate antigen positive MCF7 cells with an EC(50) value of 2.3 nM, whereas antigen negative cell lines were 80- to 250-fold less sensitive towards B3-LLO.
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Affiliation(s)
- Sabine Bergelt
- Institute of Biotechnology, Martin-Luther-University, Halle-Wittenberg, Kurt-Mothes Strasse 3, Halle, Saale, Germany
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Temme C, Weissbach R, Lilie H, Wilson C, Meinhart A, Meyer S, Golbik R, Schierhorn A, Wahle E. The Drosophila melanogaster Gene cg4930 Encodes a High Affinity Inhibitor for Endonuclease G. J Biol Chem 2009; 284:8337-48. [PMID: 19129189 DOI: 10.1074/jbc.m808319200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endonuclease G (EndoG) is a mitochondrial enzyme believed to be released during apoptosis to participate in the degradation of nuclear DNA. This paper describes a Drosophila protein, EndoGI, which inhibits EndoG specifically. EndoG and EndoGI associate with subpicomolar affinity, forming a 2:1 complex in which dimeric EndoG is bound by two tandemly repeated homologous domains of monomeric EndoGI. Binding appears to involve the active site of EndoG. EndoGI is present in the cell nucleus at micromolar concentrations. Upon induction of apoptosis, levels of the inhibitor appear to be reduced, and it is relocalized to the cytoplasm. EndoGI, encoded by the predicted open reading frame cg4930, is expressed throughout Drosophila development. Flies homozygous for a hypomorphic EndoGI mutation have a strongly reduced viability, which is modulated by genetic background and diet. We propose that EndoGI protects the cell against low levels of EndoG outside mitochondria.
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Affiliation(s)
- Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle, Germany
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Giese C, Lepthien S, Metzner L, Brandsch M, Budisa N, Lilie H. Cover Picture: Intracellular uptake and inhibitory activity of aromatic fluorinated amino acids in human breast cancer cells (ChemMedChem 9/2008). ChemMedChem 2008. [DOI: 10.1002/cmdc.200890034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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