1
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Siegel F, Schmidt H, Juneja M, Smith J, Herrmann P, Kobelt D, Sharma K, Fichtner I, Walther W, Dittmar G, Volkmer R, Rathjen FG, Schlag PM, Stein U. GIPC1 regulates MACC1-driven metastasis. Front Oncol 2023; 13:1280977. [PMID: 38144523 PMCID: PMC10748395 DOI: 10.3389/fonc.2023.1280977] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Background Identification of cancer metastasis-relevant molecular networks is desired to provide the basis for understanding and developing intervention strategies. Here we address the role of GIPC1 in the process of MACC1-driven metastasis. MACC1 is a prognostic indicator for patient metastasis formation and metastasis-free survival. MACC1 controls gene transcription, promotes motility, invasion and proliferation of colon cancer cells in vitro, and causes tumor growth and metastasis in mice. Methods By using yeast-two-hybrid assay, mass spectrometry, co-immunoprecipitation and peptide array we analyzed GIPC1 protein binding partners, by using the MACC1 gene promoter and chromatin immunoprecipitation and electrophoretic mobility shift assay we probed for GIPC1 as transcription factor. We employed GIPC1/MACC1-manipulated cell lines for in vitro and in vivo analyses, and we probed the GIPC1/MACC1 impact using human primary colorectal cancer (CRC) tissue. Results We identified MACC1 and its paralogue SH3BP4 as protein binding partners of the protein GIPC1, and we also demonstrated the binding of GIPC1 as transcription factor to the MACC1 promoter (TSS to -60 bp). GIPC1 knockdown reduced endogenous, but not CMV promoter-driven MACC1 expression, and diminished MACC1-induced cell migration and invasion. GIPC1 suppression reduced tumor growth and metastasis in mice intrasplenically transplanted with MACC1-overexpressing CRC cells. In human primary CRC specimens, GIPC1 correlates with MACC1 expression and is of prognostic value for metastasis formation and metastasis-free survival. Combination of MACC1 and GIPC1 expression improved patient survival prognosis, whereas SH3BP4 expression did not show any prognostic value. Conclusions We identified an important, dual function of GIPC1 - as protein interaction partner and as transcription factor of MACC1 - for tumor progression and cancer metastasis.
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Affiliation(s)
- Franziska Siegel
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Hannes Schmidt
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Manisha Juneja
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Janice Smith
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Pia Herrmann
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Dennis Kobelt
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Kamal Sharma
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology, GmbH, Berlin, Germany
| | - Wolfgang Walther
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department Mass Spectrometry, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Rudolf Volkmer
- Institute for Medicinal Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Fritz G. Rathjen
- Department Developmental Neurobiology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Ulrike Stein
- Department Translational Oncology of Solid Tumors, Experimental and Clinical Research Institute, Charité Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium, Heidelberg, Germany
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2
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Pfeil J, Simonetti M, Lauer U, Volkmer R, von Thülen B, Durek P, Krähmer R, Leenders F, Hamann A, Hoffmann U. Tolerogenic Immunomodulation by PEGylated Antigenic Peptides. Front Immunol 2020; 11:529035. [PMID: 33162973 PMCID: PMC7581722 DOI: 10.3389/fimmu.2020.529035] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/22/2020] [Indexed: 01/29/2023] Open
Abstract
Current treatments for autoimmune disorders rely on non-specific immunomodulatory and global immunosuppressive drugs, which show a variable degree of efficiency and are often accompanied by side effects. In contrast, strategies aiming at inducing antigen-specific tolerance promise an exclusive specificity of the immunomodulation. However, although successful in experimental models, peptide-based tolerogenic "inverse" vaccines have largely failed to show efficacy in clinical trials. Recent studies showed that repetitive T cell epitopes, coupling of peptides to autologous cells, or peptides coupled to nanoparticles can improve the tolerogenic efficacy of peptides, suggesting that size and biophysical properties of antigen constructs affect the induction of tolerance. As these materials bear hurdles with respect to preparation or regulatory aspects, we wondered whether conjugation of peptides to the well-established and clinically proven synthetic material polyethylene glycol (PEG) might also work. We here coupled the T cell epitope OVA323-339 to polyethylene glycols of different size and structure and tested the impact of these nano-sized constructs on regulatory (Treg) and effector T cells in the DO11.10 adoptive transfer mouse model. Systemic vaccination with PEGylated peptides resulted in highly increased frequencies of Foxp3+ Tregs and reduced frequencies of antigen-specific T cells producing pro-inflammatory TNF compared to vaccination with the native peptide. PEGylation was found to extend the bioavailability of the model peptide. Both tolerogenicity and bioavailability were dependent on PEG size and structure. In conclusion, PEGylation of antigenic peptides is an effective and feasible strategy to improve Treg-inducing, peptide-based vaccines with potential use for the treatment of autoimmune diseases, allergies, and transplant rejection.
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Affiliation(s)
- Jennifer Pfeil
- Experimental Rheumatology, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute (DRFZ), Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Mario Simonetti
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Uta Lauer
- Experimental Rheumatology, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute (DRFZ), Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Rudolf Volkmer
- Institute for Medical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | | | - Pawel Durek
- Experimental Rheumatology, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute (DRFZ), Berlin, Germany
| | | | | | - Alf Hamann
- Experimental Rheumatology, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute (DRFZ), Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Ute Hoffmann
- Experimental Rheumatology, Deutsches Rheuma-Forschungszentrum, a Leibniz Institute (DRFZ), Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin, Berlin, Germany
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3
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Czuban M, Srinivasan S, Yee NA, Agustin E, Koliszak A, Miller E, Khan I, Quinones I, Noory H, Motola C, Volkmer R, Di Luca M, Trampuz A, Royzen M, Mejia Oneto JM. Bio-Orthogonal Chemistry and Reloadable Biomaterial Enable Local Activation of Antibiotic Prodrugs and Enhance Treatments against Staphylococcus aureus Infections. ACS Cent Sci 2018; 4:1624-1632. [PMID: 30648146 PMCID: PMC6311693 DOI: 10.1021/acscentsci.8b00344] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 05/08/2023]
Abstract
Systemic administration of antibiotics can cause severe side-effects such as liver and kidney toxicity, destruction of healthy gut bacteria, as well as multidrug resistance. Here, we present a bio-orthogonal chemistry-based strategy toward local prodrug concentration and activation. The strategy is based on the inverse electron-demand Diels-Alder chemistry between trans-cyclooctene and tetrazine and involves a biomaterial that can concentrate and activate multiple doses of systemic antibiotic therapy prodrugs at a local site. We demonstrate that a biomaterial, consisting of alginate hydrogel modified with tetrazine, is efficient at activating multiple doses of prodrugs of vancomycin and daptomycin in vitro as well as in vivo. These results support a drug delivery process that is independent of endogenous environmental markers. This approach is expected to improve therapeutic efficacy with decreased side-effects of antibiotics against bacterial infections. The platform has a wide scope of possible applications such as wound healing, and cancer and immunotherapy.
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Affiliation(s)
- Magdalena Czuban
- Berlin-Brandenburg
Center for Regenerative Therapies and Berlin-Brandenburg School for
Regenerative Therapies, Charité Universitätsmedizin
Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität, Takustr. 3, 14195 Berlin, Germany
| | | | - Nathan A. Yee
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
| | - Edgar Agustin
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Anna Koliszak
- Berlin-Brandenburg
Center for Regenerative Therapies, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ethan Miller
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
| | - Irfan Khan
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Ilenis Quinones
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Hasina Noory
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher Motola
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Rudolf Volkmer
- Institute
for Medical Immunology and Leibniz-Institut für Molekulare
Pharmakologie, Charité Universitätsmedizin
Berlin, 10117 Berlin, Germany
| | - Mariagrazia Di Luca
- Berlin-Brandenburg
Center for Regenerative Therapies, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Andrej Trampuz
- Charité −
Universitätsmedizin Berlin, corporate member
of Freie Universität Berlin,
Humboldt-Universitat zu Berlin, and Berlin Institute of Health, Center
for Musculoskeletal Surgery, Charitéplatz 1, 10117 Berlin, Germany
| | - Maksim Royzen
- Department
of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Jose M. Mejia Oneto
- Shasqi
Inc., 665 Third Street, San Francisco, California 94107, United States
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4
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Mertens M, Hilsch M, Haralampiev I, Volkmer R, Wessig P, Müller P. Synthesis and Characterization of a New Bifunctionalized, Fluorescent, and Amphiphilic Molecule for Recruiting SH-Containing Molecules to Membranes. Chembiochem 2018; 19:1643-1647. [PMID: 29785742 DOI: 10.1002/cbic.201800268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 11/10/2022]
Abstract
This study describes the synthesis and characterization of an amphiphilic construct intended to recruit SH-containing molecules to membranes. The construct consists of 1) an aliphatic chain to enable anchoring within membranes, 2) a maleimide moiety to react with the sulfhydryl group of a soluble (bio)molecule, and 3) a fluorescence moiety to allow the construct to be followed by fluorescence spectroscopy and microscopy. It is shown that the construct can be incorporated into preformed membranes, thus allowing application of the approach with biological membranes. The close proximity between the fluorophore and the maleimide moiety within the construct causes fluorescence quenching. This allows monitoring of the reaction with SH-containing molecules by measurement of increases in fluorescence intensity and lifetime. Notably, the construct distributes into laterally ordered membrane domains of lipid vesicles, which is probably triggered by the length of its membrane anchor. The advantages of the new construct can be employed for several biological, biotechnological, and medicinal applications.
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Affiliation(s)
- Monique Mertens
- University of Potsdam, Department of Chemistry, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Malte Hilsch
- Humboldt Universität zu Berlin, Department of Biology, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Ivan Haralampiev
- Humboldt Universität zu Berlin, Department of Biology, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Rudolf Volkmer
- Institute for Medical Immunology, Charité, University Medicine Berlin, Hessische Strasse 3, 10115, Berlin, Germany
| | - Pablo Wessig
- University of Potsdam, Department of Chemistry, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Peter Müller
- Humboldt Universität zu Berlin, Department of Biology, Invalidenstrasse 42, 10115, Berlin, Germany
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5
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Arellano VJ, Martinell García P, Rodríguez Plaza JG, Lara Ortiz MT, Schreiber G, Volkmer R, Klipp E, Rio GD. An Antimicrobial Peptide Induces FIG1-Dependent Cell Death During Cell Cycle Arrest in Yeast. Front Microbiol 2018; 9:1240. [PMID: 29963019 PMCID: PMC6010521 DOI: 10.3389/fmicb.2018.01240] [Citation(s) in RCA: 4] [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: 11/02/2017] [Accepted: 05/23/2018] [Indexed: 12/30/2022] Open
Abstract
Although most antibiotics act on cells that are actively dividing and non-dividing cells such as in microbe sporulation or cancer stem cells represent a new paradigm for the control of disease. In addition to their relevance to health, such antibiotics may promote our understanding of the relationship between the cell cycle and cell death. No antibiotic specifically acting on microbial cells arrested in their cell cycle has been identified until the present time. In this study we used an antimicrobial peptide derived from α-pheromone, IP-1, targeted against MATa Saccharomyces cerevisiae cells in order to assess its dependence on cell cycle arrest to kill cells. Analysis by flow cytometry and fluorescence microscopy of various null mutations of genes involved in biological processes activated by the pheromone pathway (the mitogen-activated protein kinase pathway, cell cycle arrest, cell proliferation, autophagy, calcium influx) showed that IP-1 requires arrest in G0/G1 in order to kill yeast cells. Isolating cells in different cell cycle phases by elutriation provided further evidence that entry into cell cycle arrest, and not into G1 phase, is necessary if our peptide is to kill yeast cells. We also describe a variant of IP-1 that does not activate the pheromone pathway and consequently does not kill yeast cells that express the pheromone’s receptor; the use of this variant peptide in combination with different cell cycle inhibitors that induce cell cycle arrest independently of the pheromone pathway confirmed that it is cell cycle arrest that is required for the cell death induced by this peptide in yeast. We show that the cell death induced by IP-1 differs from that induced by α-pheromone and depends on FIG1 in a way independent of the cell cycle arrest induced by the pheromone. Thus, IP-1 is the first molecule described that specifically kills microbial cells during cell cycle arrest, a subject of interest beyond the process of mating in yeast cells. The experimental system described in this study should be useful in the study of the mechanisms at play in the communication between cell cycle arrest and cell death on other organisms, hence promoting the development of new antibiotics.
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Affiliation(s)
- Vladimir J Arellano
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Paula Martinell García
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Maria T Lara Ortiz
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Edda Klipp
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gabriel Del Rio
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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6
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Pulido D, Prats-Ejarque G, Villalba C, Albacar M, Moussaoui M, Andreu D, Volkmer R, Torrent M, Boix E. Positional scanning library applied to the human eosinophil cationic protein/RNase3 N-terminus reveals novel and potent anti-biofilm peptides. Eur J Med Chem 2018; 152:590-599. [DOI: 10.1016/j.ejmech.2018.05.012] [Citation(s) in RCA: 10] [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] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 05/07/2018] [Indexed: 01/14/2023]
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7
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Jiang K, Faltova L, Hua S, Capitani G, Prota AE, Landgraf C, Volkmer R, Kammerer RA, Steinmetz MO, Akhmanova A. Structural Basis of Formation of the Microtubule Minus-End-Regulating CAMSAP-Katanin Complex. Structure 2018; 26:375-382.e4. [DOI: 10.1016/j.str.2017.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/28/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022]
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8
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Su J, Thomas AS, Grabietz T, Landgraf C, Volkmer R, Marrink SJ, Williams C, Melo MN. The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission. Biochim Biophys Acta Biomembr 2018; 1860:1292-1300. [PMID: 29501607 DOI: 10.1016/j.bbamem.2018.02.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/07/2018] [Accepted: 02/27/2018] [Indexed: 10/17/2022]
Abstract
Pex11p plays a crucial role in peroxisome fission. Previously, it was shown that a conserved N-terminal amphipathic helix in Pex11p, termed Pex11-Amph, was necessary for peroxisomal fission in vivo while in vitro studies revealed that this region alone was sufficient to bring about tubulation of liposomes with a lipid consistency resembling the peroxisomal membrane. However, molecular details of how Pex11-Amph remodels the peroxisomal membrane remain unknown. Here we have combined in silico, in vitro and in vivo approaches to gain insights into the molecular mechanisms underlying Pex11-Amph activity. Using molecular dynamics simulations, we observe that Pex11-Amph peptides form linear aggregates on a model membrane. Furthermore, we identify mutations that disrupted this aggregation in silico, which also abolished the peptide's ability to remodel liposomes in vitro, establishing that Pex11p oligomerisation plays a direct role in membrane remodelling. In vivo studies revealed that these mutations resulted in a strong reduction in Pex11 protein levels, indicating that these residues are important for Pex11p function. Taken together, our data demonstrate the power of combining in silico techniques with experimental approaches to investigate the molecular mechanisms underlying Pex11p-dependent membrane remodelling.
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Affiliation(s)
- Juanjuan Su
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Ann S Thomas
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Tanja Grabietz
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Christiane Landgraf
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany; Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Manuel N Melo
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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9
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Eibl C, Riva I, Volkmer R, Carbone AL, Plested AJ. Control of AMPA Receptor Activity by the Extracellular Loops of Auxiliary Proteins. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2092] [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: 10/18/2022] Open
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10
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Riva I, Eibl C, Volkmer R, Carbone AL, Plested AJ. Control of AMPA receptor activity by the extracellular loops of auxiliary proteins. eLife 2017; 6:28680. [PMID: 28871958 PMCID: PMC5599240 DOI: 10.7554/elife.28680] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 05/16/2017] [Accepted: 08/28/2017] [Indexed: 11/13/2022] Open
Abstract
At synapses throughout the mammalian brain, AMPA receptors form complexes with auxiliary proteins, including TARPs. However, how TARPs modulate AMPA receptor gating remains poorly understood. We built structural models of TARP-AMPA receptor complexes for TARPs γ2 and γ8, combining recent structural studies and de novo structure predictions. These models, combined with peptide binding assays, provide evidence for multiple interactions between GluA2 and variable extracellular loops of TARPs. Substitutions and deletions of these loops had surprisingly rich effects on the kinetics of glutamate-activated currents, without any effect on assembly. Critically, by altering the two interacting loops of γ2 and γ8, we could entirely remove all allosteric modulation of GluA2, without affecting formation of AMPA receptor-TARP complexes. Likewise, substitutions in the linker domains of GluA2 completely removed any effect of γ2 on receptor kinetics, indicating a dominant role for this previously overlooked site proximal to the AMPA receptor channel gate.
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Affiliation(s)
- Irene Riva
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Clarissa Eibl
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Rudolf Volkmer
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Anna L Carbone
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Andrew Jr Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
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11
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Kathage B, Gehlert S, Ulbricht A, Lüdecke L, Tapia VE, Orfanos Z, Wenzel D, Bloch W, Volkmer R, Fleischmann BK, Fürst DO, Höhfeld J. The cochaperone BAG3 coordinates protein synthesis and autophagy under mechanical strain through spatial regulation of mTORC1. Biochim Biophys Acta Mol Cell Res 2016; 1864:62-75. [PMID: 27756573 DOI: 10.1016/j.bbamcr.2016.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022]
Abstract
The cochaperone BAG3 is a central protein homeostasis factor in mechanically strained mammalian cells. It mediates the degradation of unfolded and damaged forms of the actin-crosslinker filamin through chaperone-assisted selective autophagy (CASA). In addition, BAG3 stimulates filamin transcription in order to compensate autophagic disposal and to maintain the actin cytoskeleton under strain. Here we demonstrate that BAG3 coordinates protein synthesis and autophagy through spatial regulation of the mammalian target of rapamycin complex 1 (mTORC1). The cochaperone utilizes its WW domain to contact a proline-rich motif in the tuberous sclerosis protein TSC1 that functions as an mTORC1 inhibitor in association with TSC2. Interaction with BAG3 results in a recruitment of TSC complexes to actin stress fibers, where the complexes act on a subpopulation of mTOR-positive vesicles associated with the cytoskeleton. Local inhibition of mTORC1 is essential to initiate autophagy at sites of filamin unfolding and damage. At the same time, BAG3-mediated sequestration of TSC1/TSC2 relieves mTORC1 inhibition in the remaining cytoplasm, which stimulates protein translation. In human muscle, an exercise-induced association of TSC1 with the cytoskeleton coincides with mTORC1 activation in the cytoplasm. The spatial regulation of mTORC1 exerted by BAG3 apparently provides the basis for a simultaneous induction of autophagy and protein synthesis to maintain the proteome under mechanical strain.
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Affiliation(s)
- Barbara Kathage
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Sebastian Gehlert
- German Sport University Cologne, Department of Molecular and Cellular Sport Medicine, Am Sportpark Müngersdorf 6, 50933 Cologne, Germany
| | - Anna Ulbricht
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Laura Lüdecke
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Victor E Tapia
- Department of Medicinal Immunology, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Zacharias Orfanos
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Daniela Wenzel
- Institute of Physiology I, Life & Brain Center, University Clinic Bonn, Sigmund Freud Str. 25, 53105 Bonn, Germany
| | - Wilhelm Bloch
- German Sport University Cologne, Department of Molecular and Cellular Sport Medicine, Am Sportpark Müngersdorf 6, 50933 Cologne, Germany
| | - Rudolf Volkmer
- Department of Medicinal Immunology, Charité - University Medicine Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Bernd K Fleischmann
- Institute of Physiology I, Life & Brain Center, University Clinic Bonn, Sigmund Freud Str. 25, 53105 Bonn, Germany
| | - Dieter O Fürst
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
| | - Jörg Höhfeld
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany.
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12
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Manatschal C, Farcas AM, Degen MS, Bayer M, Kumar A, Landgraf C, Volkmer R, Barral Y, Steinmetz MO. Molecular basis of Kar9-Bim1 complex function during mating and spindle positioning. Mol Biol Cell 2016; 27:mbc.E16-07-0552. [PMID: 27682587 PMCID: PMC5170556 DOI: 10.1091/mbc.e16-07-0552] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/17/2022] Open
Abstract
The Kar9 pathway promotes nuclear fusion during mating and spindle alignment during metaphase in budding yeast. How Kar9 supports the different outcome of these two divergent processes is an open question. Here, we show that three sites in the C-terminal disordered domain of Kar9 mediate tight Kar9 interaction with the C-terminal dimerization domain of Bim1 (EB1 orthologue). Site1 and Site2 contain SxIP motifs; however, Site3 defines a novel type of EB1-binding site. Whereas Site2 and Site3 mediate Kar9 recruitment to microtubule tips, nuclear movement and karyogamy, solely Site2 functions in spindle positioning during metaphase. Site1 in turn plays an inhibitory role during mating. Additionally, the Kar9-Bim1 complex is involved in microtubule-independent activities during mating. Together, our data reveal how multiple and partially redundant EB1-binding sites provide a microtubule-associated protein with the means to modulate its biochemical properties to promote different molecular processes during cell proliferation and differentiation.
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Affiliation(s)
- Cristina Manatschal
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Ana-Maria Farcas
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Miriam Steiner Degen
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Mathias Bayer
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Anil Kumar
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
| | - Christiane Landgraf
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yves Barral
- Institute of Biochemistry, Biology Department, ETH Zürich, Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen PSI, Switzerland
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13
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Memczak H, Lauster D, Kar P, Di Lella S, Volkmer R, Knecht V, Herrmann A, Ehrentreich-Förster E, Bier FF, Stöcklein WFM. Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding. PLoS One 2016; 11:e0159074. [PMID: 27415624 PMCID: PMC4944999 DOI: 10.1371/journal.pone.0159074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 03/01/2016] [Accepted: 06/27/2016] [Indexed: 12/23/2022] Open
Abstract
Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/Mute Swan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing.
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Affiliation(s)
- Henry Memczak
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel Lauster
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Parimal Kar
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Santiago Di Lella
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Volker Knecht
- Department of Theory and Bio-Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Andreas Herrmann
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Eva Ehrentreich-Förster
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
| | - Walter F. M. Stöcklein
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses, Potsdam, Germany
- * E-mail:
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14
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Tapia Mancilla VE, Volkmer R. Erratum To: Peptide Arrays on Planar Supports. Methods Mol Biol 2016; 1352:E1. [PMID: 27215402 DOI: 10.1007/978-1-4939-3037-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin zu Berlin, Hessische Str. 3-4, Berlin, 10115, Germany
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15
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Abstract
On a past volume of this monograph we have reviewed general aspects of the varied technologies available to generate peptide arrays. Hallmarks in the development of the technology and a main sketch of preparative steps and applications in binding assays were used to walk the reader through details of peptide arrays. In this occasion, we resume from that work and bring in some considerations on quantitative evaluation of measurements as well as on selected reports applying the technology.
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Affiliation(s)
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin zu Berlin, Hessische Str. 3-4, Berlin, 10115, Germany
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16
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Mikut R, Ruden S, Reischl M, Breitling F, Volkmer R, Hilpert K. Improving short antimicrobial peptides despite elusive rules for activity. Biochim Biophys Acta 2015; 1858:1024-33. [PMID: 26687790 DOI: 10.1016/j.bbamem.2015.12.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/25/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Antimicrobial peptides (AMPs) can effectively kill a broad range of life threatening multidrug-resistant bacteria, a serious threat to public health worldwide. However, despite great hopes novel drugs based on AMPs are still rare. To accelerate drug development we studied different approaches to improve the antibacterial activity of short antimicrobial peptides. Short antimicrobial peptides seem to be ideal drug candidates since they can be synthesized quickly and easily, modified and optimized. In addition, manufacturing a short peptide drug will be more cost efficient than long and structured ones. In contrast to longer and structured peptides short AMPs seem hard to design and predict. Here, we designed, synthesized and screened five different peptide libraries, each consisting of 600 9-mer peptides, against Pseudomonas aeruginosa. Each library is presenting a different approach to investigate effectiveness of an optimization strategy. The data for the 3000 peptides were analyzed using models based on fuzzy logic bioinformatics and plausible descriptors. The rate of active or superior active peptides was improved from 31.0% in a semi-random library from a previous study to 97.8% in the best new designed library. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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Affiliation(s)
- Ralf Mikut
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Serge Ruden
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces and Institute of Biological Interfaces 2, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Markus Reischl
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Frank Breitling
- Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Rudolf Volkmer
- Institute of Medical Immunology, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Schumannstr. 20-21, 10117 Berlin, Germany
| | - Kai Hilpert
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces and Institute of Biological Interfaces 2, P.O. Box 3640, 76021 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology, P.O. Box 3640, 76021 Karlsruhe, Germany; Institute of Infection and Immunity, St. George's University of London, Cranmer Terrace, London, SW17 0RE, United Kingdom.
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17
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Kenngott EE, Cole S, Hein WR, Hoffmann U, Lauer U, Maass D, Moore L, Pfeil J, Rosanowski S, Shoemaker CB, Umair S, Volkmer R, Hamann A, Pernthaner A. Identification of Targeting Peptides for Mucosal Delivery in Sheep and Mice. Mol Pharm 2015; 13:202-10. [DOI: 10.1021/acs.molpharmaceut.5b00635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Sally Cole
- AgResearch Ltd., Hamilton 3240, New Zealand
| | | | - Ute Hoffmann
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany
| | - Uta Lauer
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany
| | - David Maass
- AgResearch Ltd., Hamilton 3240, New Zealand
- Charité Universitätsmedizin, 10117 Berlin, Germany
| | | | - Jennifer Pfeil
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany
| | | | | | | | | | - Alf Hamann
- Deutsches Rheuma-Forschungszentrum, 10117 Berlin, Germany
- Charité Universitätsmedizin, 10117 Berlin, Germany
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18
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Rouka E, Simister PC, Janning M, Kumbrink J, Konstantinou T, Muniz JRC, Joshi D, O'Reilly N, Volkmer R, Ritter B, Knapp S, von Delft F, Kirsch KH, Feller SM. Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3). J Biol Chem 2015; 290:25275-92. [PMID: 26296892 DOI: 10.1074/jbc.m115.637207] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 11/06/2022] Open
Abstract
CD2AP is an adaptor protein involved in membrane trafficking, with essential roles in maintaining podocyte function within the kidney glomerulus. CD2AP contains three Src homology 3 (SH3) domains that mediate multiple protein-protein interactions. However, a detailed comparison of the molecular binding preferences of each SH3 remained unexplored, as well as the discovery of novel interactors. Thus, we studied the binding properties of each SH3 domain to the known interactor Casitas B-lineage lymphoma protein (c-CBL), conducted a peptide array screen based on the recognition motif PxPxPR and identified 40 known or novel candidate binding proteins, such as RIN3, a RAB5-activating guanine nucleotide exchange factor. CD2AP SH3 domains 1 and 2 generally bound with similar characteristics and specificities, whereas the SH3-3 domain bound more weakly to most peptide ligands tested yet recognized an unusually extended sequence in ALG-2-interacting protein X (ALIX). RIN3 peptide scanning arrays revealed two CD2AP binding sites, recognized by all three SH3 domains, but SH3-3 appeared non-functional in precipitation experiments. RIN3 recruited CD2AP to RAB5a-positive early endosomes via these interaction sites. Permutation arrays and isothermal titration calorimetry data showed that the preferred binding motif is Px(P/A)xPR. Two high-resolution crystal structures (1.65 and 1.11 Å) of CD2AP SH3-1 and SH3-2 solved in complex with RIN3 epitopes 1 and 2, respectively, indicated that another extended motif is relevant in epitope 2. In conclusion, we have discovered novel interaction candidates for CD2AP and characterized subtle yet significant differences in the recognition preferences of its three SH3 domains for c-CBL, ALIX, and RIN3.
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Affiliation(s)
- Evgenia Rouka
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Philip C Simister
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Melanie Janning
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Joerg Kumbrink
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Tassos Konstantinou
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - João R C Muniz
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Dhira Joshi
- the Peptide Chemistry Laboratory, London Research Institute Cancer Research UK, London WC2A 3LY, United Kingdom
| | - Nicola O'Reilly
- the Peptide Chemistry Laboratory, London Research Institute Cancer Research UK, London WC2A 3LY, United Kingdom
| | - Rudolf Volkmer
- the Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
| | - Brigitte Ritter
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Stefan Knapp
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom, the Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and the Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Kathrin H Kirsch
- the Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Stephan M Feller
- From the Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, United Kingdom, the Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany,
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19
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Verschueren E, Spiess M, Gkourtsa A, Avula T, Landgraf C, Mancilla VT, Huber A, Volkmer R, Winsor B, Serrano L, Hochstenbach F, Distel B. Evolution of the SH3 Domain Specificity Landscape in Yeasts. PLoS One 2015; 10:e0129229. [PMID: 26068101 PMCID: PMC4466140 DOI: 10.1371/journal.pone.0129229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/06/2015] [Indexed: 11/18/2022] Open
Abstract
To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida albicans, and Schizosaccharomyces pombe, encompassing 400 million years of evolution. We first aligned and catalogued the families of SH3-containing proteins in these four species to determine the relationships between homologous domains. Then, we tagged and purified all soluble SH3 domains (82 in total) to perform a quantitative peptide assay (SPOT) for each SH3 domain. All SPOT readouts were hierarchically clustered and we observed that the organization of the SH3 specificity landscape in three distinct profile classes remains conserved across these four yeast species. We also produced a specificity profile for each SH3 domain from manually aligned top SPOT hits and compared the within-family binding motif consensus. This analysis revealed a striking example of binding motif divergence in a C. albicans Rvs167 paralog, which cannot be explained by overall SH3 sequence or interface residue divergence, and we validated this specificity change with a yeast two-hybrid (Y2H) assay. In addition, we show that position-weighted matrices (PWM) compiled from SPOT assays can be used for binding motif screening in potential binding partners and present cases where motifs are either conserved or lost among homologous SH3 interacting proteins. Finally, by comparing pairwise SH3 sequence identity to binding profile correlation we show that for ~75% of all analyzed families the SH3 specificity profile was remarkably conserved over a large evolutionary distance. Thus, a high sequence identity within an SH3 domain family predicts conserved binding specificity, whereas divergence in sequence identity often coincided with a change in binding specificity within this family. As such, our results are important for future studies aimed at unraveling complex specificity networks of peptide recognition domains in higher eukaryotes, including mammals.
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Affiliation(s)
- Erik Verschueren
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation-CRG, Barcelona, Spain
| | - Matthias Spiess
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Areti Gkourtsa
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Teja Avula
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Christiane Landgraf
- Institut für Medizinische Immunologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor Tapia Mancilla
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
- Institut für Medizinische Immunologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Aline Huber
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Barbara Winsor
- Department of Molecular and Cellular Genetics, UMR7156, Université de Strasbourg and CNRS, Strasbourg, France
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation-CRG, Barcelona, Spain
| | - Frans Hochstenbach
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Distel
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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20
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Henning LM, Bhatia S, Bertazzon M, Marczynke M, Seitz O, Volkmer R, Haag R, Freund C. Exploring monovalent and multivalent peptides for the inhibition of FBP21-tWW. Beilstein J Org Chem 2015; 11:701-706. [PMID: 26124874 PMCID: PMC4464085 DOI: 10.3762/bjoc.11.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 02/28/2015] [Accepted: 04/29/2015] [Indexed: 12/03/2022] Open
Abstract
The coupling of peptides to polyglycerol carriers represents an important route towards the multivalent display of protein ligands. In particular, the inhibition of low affinity intracellular protein–protein interactions can be addressed by this design. We have applied this strategy to develop binding partners for FBP21, a protein which is important for the splicing of pre-mRNA in the nucleus of eukaryotic cells. Firstly, by using phage display the optimized sequence WPPPPRVPR was derived which binds with KDs of 80 μM and 150 µM to the individual WW domains and with a KD of 150 μM to the tandem-WW1–WW2 construct. Secondly, this sequence was coupled to a hyperbranched polyglycerol (hPG) that allowed for the multivalent display on the surface of the dendritic polymer. This novel multifunctional hPG-peptide conjugate displayed a KD of 17.6 µM which demonstrates that the new carrier provides a venue for the future inhibition of proline-rich sequence recognition by FBP21 during assembly of the spliceosome.
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Affiliation(s)
- Lisa Maria Henning
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
| | - Sumati Bhatia
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Miriam Bertazzon
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michaela Marczynke
- Institute for Chemistry, Humboldt-Universität Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Oliver Seitz
- Institute for Chemistry, Humboldt-Universität Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Rudolf Volkmer
- Leibniz Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str.10, 13125 Berlin, Germany.,Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Haag
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Thielallee 63, Freie Universität Berlin, 14195 Berlin, Germany
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21
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Lauster D, Pawolski D, Storm J, Ludwig K, Volkmer R, Memczak H, Herrmann A, Bhatia S. Potential of acylated peptides to target the influenza A virus. Beilstein J Org Chem 2015; 11:589-95. [PMID: 26124860 PMCID: PMC4464269 DOI: 10.3762/bjoc.11.65] [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: 03/03/2015] [Accepted: 04/24/2015] [Indexed: 01/15/2023] Open
Abstract
For antiviral drug design, especially in the field of influenza virus research, potent multivalent inhibitors raise high expectations for combating epidemics and pandemics. Among a large variety of covalent and non-covalent scaffold systems for a multivalent display of inhibitors, we created a simple supramolecular platform to enhance the antiviral effect of our recently developed antiviral Peptide B (PeB(GF)), preventing binding of influenza virus to the host cell. By conjugating the peptide with stearic acid to create a higher-order structure with a multivalent display, we could significantly enhance the inhibitory effect against the serotypes of both human pathogenic influenza virus A/Aichi/2/1968 H3N2, and avian pathogenic A/FPV/Rostock/34 H7N1 in the hemagglutination inhibition assay. Further, the inhibitory potential of stearylated PeB(GF) (C18-PeB(GF)) was investigated by infection inhibition assays, in which we achieved low micromolar inhibition constants against both viral strains. In addition, we compared C18-PeB(GF) to other published amphiphilic peptide inhibitors, such as the stearylated sugar receptor mimicking peptide (Matsubara et al. 2010), and the "Entry Blocker" (EB) (Jones et al. 2006), with respect to their antiviral activity against infection by Influenza A Virus (IAV) H3N2. However, while this strategy seems at a first glance promising, the native situation is quite different from our experimental model settings. First, we found a strong potential of those peptides to form large amyloid-like supramolecular assemblies. Second, in vivo, the large excess of cell surface membranes provides an unspecific target for the stearylated peptides. We show that acylated peptides insert into the lipid phase of such membranes. Eventually, our study reveals serious limitations of this type of self-assembling IAV inhibitors.
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Affiliation(s)
- Daniel Lauster
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Damian Pawolski
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Julian Storm
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Kai Ludwig
- Freie Universität Berlin, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Rudolf Volkmer
- Charité Universitätsmedizin Berlin, Institute of Immunology, Charitéplatz 1, 10117 Berlin, Germany
| | - Henry Memczak
- Fraunhofer Institute for Cell Therapy and Immunology, Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin, Institute of Biology, Invalidenstr. 42, 10115 Berlin, Germany
| | - Sumati Bhatia
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 3, 14195 Berlin, Germany
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22
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Haralampiev I, Mertens M, Schwarzer R, Herrmann A, Volkmer R, Wessig P, Müller P. Rekrutierung Sulfhydryl‐haltiger Peptide an Lipid‐ und biologische Membranen durch eine Maleimid‐funktionalisierte Palmitinsäure. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ivan Haralampiev
- Institut für Biologie, Humboldt‐Universität zu Berlin, Invalidenstraße 42, 10115‐Berlin (Deutschland)
| | - Monique Mertens
- Institut für Chemie, Universität Potsdam, Karl‐Liebknecht‐Straße 24‐25, 14476 Potsdam (Deutschland)
| | - Roland Schwarzer
- Institut für Biologie, Humboldt‐Universität zu Berlin, Invalidenstraße 42, 10115‐Berlin (Deutschland)
| | - Andreas Herrmann
- Institut für Biologie, Humboldt‐Universität zu Berlin, Invalidenstraße 42, 10115‐Berlin (Deutschland)
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité, Universitätsmedizin Berlin, Hessische Straße 3, 10115 Berlin (Deutschland)
| | - Pablo Wessig
- Institut für Chemie, Universität Potsdam, Karl‐Liebknecht‐Straße 24‐25, 14476 Potsdam (Deutschland)
| | - Peter Müller
- Institut für Biologie, Humboldt‐Universität zu Berlin, Invalidenstraße 42, 10115‐Berlin (Deutschland)
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23
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Haralampiev I, Mertens M, Schwarzer R, Herrmann A, Volkmer R, Wessig P, Müller P. Recruitment of SH‐Containing Peptides to Lipid and Biological Membranes through the Use of a Palmitic Acid Functionalized with a Maleimide Group. Angew Chem Int Ed Engl 2014; 54:323-6. [DOI: 10.1002/anie.201408089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/17/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Ivan Haralampiev
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin (Germany)
| | - Monique Mertens
- Department of Chemistry, University Potsdam, Karl‐Liebknecht‐Strasse 24–25, 14476 Potsdam (Germany)
| | - Roland Schwarzer
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin (Germany)
| | - Andreas Herrmann
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin (Germany)
| | - Rudolf Volkmer
- Institute for Medical Immunology, Charité, University Medicine Berlin, Hessische Strasse 3, 10115 Berlin (Germany)
| | - Pablo Wessig
- Department of Chemistry, University Potsdam, Karl‐Liebknecht‐Strasse 24–25, 14476 Potsdam (Germany)
| | - Peter Müller
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin (Germany)
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24
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Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G. Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. J Biol Chem 2014; 289:14448-57. [PMID: 24706763 DOI: 10.1074/jbc.m113.515023] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 11/06/2022] Open
Abstract
Cell penetrating peptides (CPP) and cationic antibacterial peptides (CAP) have similar physicochemical properties and yet it is not understood how such similar peptides display different activities. To address this question, we used Iztli peptide 1 (IP-1) because it has both CPP and CAP activities. Combining experimental and computational modeling of the internalization of IP-1, we show it is not internalized by receptor-mediated endocytosis, yet it permeates into many different cell types, including fungi and human cells. We also show that IP-1 makes pores in the presence of high electrical potential at the membrane, such as those found in bacteria and mitochondria. These results provide the basis to understand the functional redundancy of CPPs and CAPs.
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Affiliation(s)
- Jonathan G Rodriguez Plaza
- From the Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, 04510 México D.F., México
| | - Rosmarbel Morales-Nava
- Materials science and biophysics department, Instituto de Ciencias Fisicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, Col. Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Christian Diener
- From the Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, 04510 México D.F., México
| | - Gabriele Schreiber
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Colonia Miraval, Cuernavaca, Morelos, México 62250
| | - Zyanya D Gonzalez
- From the Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, 04510 México D.F., México
| | - Maria Teresa Lara Ortiz
- From the Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, 04510 México D.F., México
| | - Ivan Ortega Blake
- Materials science and biophysics department, Instituto de Ciencias Fisicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, Col. Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Omar Pantoja
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Colonia Miraval, Cuernavaca, Morelos, México 62250
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10117 Berlin and Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle Strasse 10, 13125 Berlin, Germany, and
| | - Edda Klipp
- Theoretische und Molekulare Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Andreas Herrmann
- Theoretische und Molekulare Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Gabriel Del Rio
- From the Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N Ciudad Universitaria, 04510 México D.F., México,
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25
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Hovestädt M, Kuckelkorn U, Niewienda A, Keller C, Goede A, Ay B, Günther S, Janek K, Volkmer R, Holzhütter HG. Rapid degradation of solid-phase bound peptides by the 20S proteasome. J Pept Sci 2013; 19:588-97. [DOI: 10.1002/psc.2536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Marc Hovestädt
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Ulrike Kuckelkorn
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Agathe Niewienda
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Christin Keller
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Andrean Goede
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Bernhard Ay
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics Group, Institute of Pharmaceutical Sciences; Albert-Ludwigs-University Freiburg; Freiburg Germany
| | - Katharina Janek
- Proteolysis Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Rudolf Volkmer
- Institute of Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - Hermann-Georg Holzhütter
- Mathematical Systems Biochemistry Group, Institute of Biochemistry; Charité - Universitätsmedizin Berlin; Berlin Germany
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26
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Eulitz S, Sauer F, Pelissier MC, Boisguerin P, Molt S, Schuld J, Orfanos Z, Kley RA, Volkmer R, Wilmanns M, Kirfel G, van der Ven PFM, Fürst DO. Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling. Mol Biol Cell 2013; 24:3215-26. [PMID: 23985323 PMCID: PMC3810769 DOI: 10.1091/mbc.e13-04-0202] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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: 01/12/2023] Open
Abstract
The striated muscle–specific actin-binding proteins Xin and Xirp2 are identified as novel ligands of the SH3 domains of the thin filament ruler nebulin and nebulette. The interaction is spatially restricted to structures associated with myofibril development or remodeling, indicating a role for these proteins in myofibril assembly and repair. The Xin actin-binding repeat–containing proteins Xin and XIRP2 are exclusively expressed in striated muscle cells, where they are believed to play an important role in development. In adult muscle, both proteins are concentrated at attachment sites of myofibrils to the membrane. In contrast, during development they are localized to immature myofibrils together with their binding partner, filamin C, indicating an involvement of both proteins in myofibril assembly. We identify the SH3 domains of nebulin and nebulette as novel ligands of proline-rich regions of Xin and XIRP2. Precise binding motifs are mapped and shown to bind both SH3 domains with micromolar affinity. Cocrystallization of the nebulette SH3 domain with the interacting XIRP2 peptide PPPTLPKPKLPKH reveals selective interactions that conform to class II SH3 domain–binding peptides. Bimolecular fluorescence complementation experiments in cultured muscle cells indicate a temporally restricted interaction of Xin-repeat proteins with nebulin/nebulette during early stages of myofibril development that is lost upon further maturation. In mature myofibrils, this interaction is limited to longitudinally oriented structures associated with myofibril development and remodeling. These data provide new insights into the role of Xin actin-binding repeat–containing proteins (together with their interaction partners) in myofibril assembly and after muscle damage.
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Affiliation(s)
- Stefan Eulitz
- Institute for Cell Biology, University of Bonn, D-53121 Bonn, Germany European Molecular Biology Laboratory-Hamburg/Deutsches Elektronen-Synchrotron, D-22603 Hamburg, Germany Department of Medicinal Immunology, Charité-University Medicine Berlin, D-13353 Berlin, Germany Department of Neurology, Neuromuscular Center Ruhrgebiet, University Hospital Bergmannsheil, Ruhr-University Bochum, D-44789 Bochum, Germany
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27
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Zhang X, Tretjakov A, Hovestaedt M, Sun G, Syritski V, Reut J, Volkmer R, Hinrichs K, Rappich J. Electrochemical functionalization of gold and silicon surfaces by a maleimide group as a biosensor for immunological application. Acta Biomater 2013; 9:5838-44. [PMID: 23117146 DOI: 10.1016/j.actbio.2012.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/11/2012] [Accepted: 10/18/2012] [Indexed: 11/25/2022]
Abstract
In the present study we investigated the preparation of biofunctionalized surfaces using the direct electrochemical grafting of maleimidophenyl molecules with subsequent covalent immobilization of specific peptide to detect target antibody, thereby extending the application of the biosensing systems towards immunodiagnostics. Para-maleimidophenyl (p-MP) functional groups were electrochemically grafted on gold and silicon surfaces from solutions of the corresponding diazonium salt. A specially synthesized peptide modified with cysteine (Cys-peptide) was then immobilized on the p-MP grafted substrates by cross-linking between the maleimide groups and the sulfhydryl group of the cysteine residues. Accordingly, the Cys-peptide worked as an antigen that was able to bind specifically the target antibody (anti-GST antibody), while it was non-sensitive to a negative contrast antibody (i.e. anti-Flag β). The immobilization of both specific and non-specific antibodies on the Cys-peptide-modified surfaces was monitored by infrared spectroscopic ellipsometry, a quartz crystal microbalance integrated in flow injection analysis system and potentiometric response. The results obtained clearly demonstrated that the direct modification of a surface with maleimidophenyl provides a very simple and reliable way of preparing biofunctionalized surfaces suitable for the construction of immunological biosensors.
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28
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Ulbricht A, Eppler FJ, Tapia VE, van der Ven PFM, Hampe N, Hersch N, Vakeel P, Stadel D, Haas A, Saftig P, Behrends C, Fürst DO, Volkmer R, Hoffmann B, Kolanus W, Höhfeld J. Cellular mechanotransduction relies on tension-induced and chaperone-assisted autophagy. Curr Biol 2013; 23:430-5. [PMID: 23434281 DOI: 10.1016/j.cub.2013.01.064] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 12/06/2012] [Accepted: 01/29/2013] [Indexed: 11/25/2022]
Abstract
Mechanical tension is an ever-present physiological stimulus essential for the development and homeostasis of locomotory, cardiovascular, respiratory, and urogenital systems. Tension sensing contributes to stem cell differentiation, immune cell recruitment, and tumorigenesis. Yet, how mechanical signals are transduced inside cells remains poorly understood. Here, we identify chaperone-assisted selective autophagy (CASA) as a tension-induced autophagy pathway essential for mechanotransduction in muscle and immune cells. The CASA complex, comprised of the molecular chaperones Hsc70 and HspB8 and the cochaperone BAG3, senses the mechanical unfolding of the actin-crosslinking protein filamin. Together with the chaperone-associated ubiquitin ligase CHIP, the complex initiates the ubiquitin-dependent autophagic sorting of damaged filamin to lysosomes for degradation. Autophagosome formation during CASA depends on an interaction of BAG3 with synaptopodin-2 (SYNPO2). This interaction is mediated by the BAG3 WW domain and facilitates cooperation with an autophagosome membrane fusion complex. BAG3 also utilizes its WW domain to engage in YAP/TAZ signaling. Via this pathway, BAG3 stimulates filamin transcription to maintain actin anchoring and crosslinking under mechanical tension. By integrating tension sensing, autophagosome formation, and transcription regulation during mechanotransduction, the CASA machinery ensures tissue homeostasis and regulates fundamental cellular processes such as adhesion, migration, and proliferation.
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Affiliation(s)
- Anna Ulbricht
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121 Bonn, Germany
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29
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Jaeger IS, Kretzschmar I, Körner J, Weiser AA, Mahrenholz CC, Potty A, Kourentzi K, Willson RC, Volkmer R, Preissner R. Mapping discontinuous protein-binding sites via structure-based peptide libraries: combiningin silicoandin vitroapproaches. J Mol Recognit 2012; 26:23-31. [DOI: 10.1002/jmr.2237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Ines S. Jaeger
- Institute for Physiology, Structural Bioinformatics Group; Charité-Universitätsmedizin Berlin; Lindenberger Weg 80; 13125; Berlin; Germany
| | - Ines Kretzschmar
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | - Jana Körner
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP); R.-Rössle-Strasse 10; 13125; Berlin; Germany
| | | | - Carsten C. Mahrenholz
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | | | - Katerina Kourentzi
- University of Houston; Department of Chemical and Biomolecular Engineering; Houston; TX; 77204-4004; USA
| | - Richard C. Willson
- University of Houston; Department of Chemical and Biomolecular Engineering; Houston; TX; 77204-4004; USA
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | - Robert Preissner
- Institute for Physiology, Structural Bioinformatics Group; Charité-Universitätsmedizin Berlin; Lindenberger Weg 80; 13125; Berlin; Germany
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30
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Buey RM, Sen I, Kortt O, Mohan R, Gfeller D, Veprintsev D, Kretzschmar I, Scheuermann J, Neri D, Zoete V, Michielin O, de Pereda JM, Akhmanova A, Volkmer R, Steinmetz MO. Sequence determinants of a microtubule tip localization signal (MtLS). J Biol Chem 2012; 287:28227-42. [PMID: 22696216 DOI: 10.1074/jbc.m112.373928] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [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
Microtubule plus-end-tracking proteins (+TIPs) specifically localize to the growing plus-ends of microtubules to regulate microtubule dynamics and functions. A large group of +TIPs contain a short linear motif, SXIP, which is essential for them to bind to end-binding proteins (EBs) and target microtubule ends. The SXIP sequence site thus acts as a widespread microtubule tip localization signal (MtLS). Here we have analyzed the sequence-function relationship of a canonical MtLS. Using synthetic peptide arrays on membrane supports, we identified the residue preferences at each amino acid position of the SXIP motif and its surrounding sequence with respect to EB binding. We further developed an assay based on fluorescence polarization to assess the mechanism of the EB-SXIP interaction and to correlate EB binding and microtubule tip tracking of MtLS sequences from different +TIPs. Finally, we investigated the role of phosphorylation in regulating the EB-SXIP interaction. Together, our results define the sequence determinants of a canonical MtLS and provide the experimental data for bioinformatics approaches to carry out genome-wide predictions of novel +TIPs in multiple organisms.
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Affiliation(s)
- Rubén M Buey
- Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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31
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Volkmer R, Tapia V, Landgraf C. Synthetic peptide arrays for investigating protein interaction domains. FEBS Lett 2012; 586:2780-6. [PMID: 22576123 DOI: 10.1016/j.febslet.2012.04.028] [Citation(s) in RCA: 30] [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] [Received: 03/22/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/28/2022]
Abstract
Synthetic peptide array technology was first developed in the early 1990s by Ronald Frank. Since then the technique has become a powerful tool for high throughput approaches in biology and biochemistry. Here, we focus on peptide arrays applied to investigate the binding specificity of protein interaction domains such as WW, SH3, and PDZ domains. We describe array-based methods used to reveal domain networks in yeast, and briefly review rules as well as ideas about the synthesis and application of peptide arrays. We also provide initial results of a study designed to investigate the nature and evolution of SH3 domain interaction networks in eukaryotes.
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Affiliation(s)
- Rudolf Volkmer
- Institut für Medizinische Immunologie Berlin, Molecular Libraries and Recognition Group, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany.
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32
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Rezaei Araghi R, Mahrenholz CC, Volkmer R, Koksch B. Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique. Beilstein J Org Chem 2012; 8:640-9. [PMID: 22563362 PMCID: PMC3343290 DOI: 10.3762/bjoc.8.71] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/03/2012] [Indexed: 12/01/2022] Open
Abstract
We screened a randomized library and identified natural peptides that bound selectively to a chimeric peptide containing α-, β- and γ-amino acids. The SPOT arrays provide a means for the systematic study of the possible interaction space accessible to the αβγ-chimera. The mutational analysis reveals the dependence of the binding affinities of α-peptides to the αβγ-chimera, on the hydrophobicity and bulkiness of the side chains at the corresponding hydrophobic interface. The stability of the resulting heteroassemblies was further confirmed in solution by CD and thermal denaturation.
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Affiliation(s)
- Raheleh Rezaei Araghi
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Carsten C Mahrenholz
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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33
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Volkmer R, Kretzschmar I, Tapia V. Mapping receptor–ligand interactions with synthetic peptide arrays: Exploring the structure and function of membrane receptors. Eur J Cell Biol 2012; 91:349-56. [DOI: 10.1016/j.ejcb.2011.03.004] [Citation(s) in RCA: 6] [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] [Received: 12/27/2010] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 11/25/2022] Open
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Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Müller S, Pawson T, Gingras AC, Arrowsmith C, Knapp S. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 2012; 149:214-31. [PMID: 22464331 PMCID: PMC3326523 DOI: 10.1016/j.cell.2012.02.013] [Citation(s) in RCA: 1177] [Impact Index Per Article: 98.1] [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: 07/05/2011] [Revised: 10/16/2011] [Accepted: 01/13/2012] [Indexed: 12/18/2022]
Abstract
Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.
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Affiliation(s)
- Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tracy Keates
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ildiko Felletar
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Tony Pawson
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Biochemistry and Molecular Biology, George Washington University, School of Medicine and Health Sciences, 2300 Eye Street, NW, Suite 530, Washington, DC, 20037, USA
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35
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Müller J, Triebus J, Kretzschmar I, Volkmer R, Boisguerin P. The agony of choice: how to find a suitable CPP for cargo delivery. J Pept Sci 2012; 18:293-301. [DOI: 10.1002/psc.2396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 12/20/2011] [Accepted: 12/21/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Judith Müller
- Institute of Medical Immunology; Charité, Universitätsmedizin Berlin; Augustenburger Platz 1; 13353; Berlin; Germany
| | - Julia Triebus
- Institute of Medical Immunology; Charité, Universitätsmedizin Berlin; Augustenburger Platz 1; 13353; Berlin; Germany
| | - Ines Kretzschmar
- Institute of Medical Immunology; Charité, Universitätsmedizin Berlin; Augustenburger Platz 1; 13353; Berlin; Germany
| | - Rudolf Volkmer
- Institute of Medical Immunology; Charité, Universitätsmedizin Berlin; Augustenburger Platz 1; 13353; Berlin; Germany
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36
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Weski J, Meltzer M, Spaan L, Mönig T, Oeljeklaus J, Hauske P, Vouilleme L, Volkmer R, Boisguerin P, Boyd D, Huber R, Kaiser M, Ehrmann M. Chemical Biology Approaches Reveal Conserved Features of a C-Terminal Processing PDZ Protease. Chembiochem 2012; 13:402-8. [DOI: 10.1002/cbic.201100643] [Citation(s) in RCA: 9] [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: 10/14/2011] [Indexed: 12/21/2022]
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Schiefner A, Chatwell L, Körner J, Neumaier I, Colby DW, Volkmer R, Wittrup KD, Skerra A. A disulfide-free single-domain V(L) intrabody with blocking activity towards huntingtin reveals a novel mode of epitope recognition. J Mol Biol 2011; 414:337-55. [PMID: 21968397 DOI: 10.1016/j.jmb.2011.09.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 10/17/2022]
Abstract
We present the crystal structure and biophysical characterization of a human V(L) [variable domain immunoglobulin (Ig) light chain] single-domain intrabody that binds to the huntingtin (Htt) protein and has been engineered for antigen recognition in the absence of its intradomain disulfide bond, otherwise conserved in the Ig fold. Analytical ultracentrifugation demonstrated that the αHtt-V(L) 12.3 domain is a stable monomer under physiological conditions even at concentrations >20 μM. Using peptide SPOT arrays, we identified the minimal binding epitope to be EKLMKAFESLKSFQ, comprising the N-terminal residues 5-18 of Htt and including the first residue of the poly-Gln stretch. X-ray structural analysis of αHtt-V(L) both as apo protein and in the presence of the epitope peptide revealed several interesting insights: first, the role of mutations acquired during the combinatorial selection process of the αHtt-V(L) 12.3 domain-initially starting from a single-chain Fv fragment-that are responsible for its stability as an individually soluble Ig domain, also lacking the disulfide bridge, and second, a previously unknown mode of antigen recognition, revealing a novel paratope. The Htt epitope peptide adopts a purely α-helical structure in the complex with αHtt-V(L) and is bound at the base of the complementarity-determining regions (CDRs) at the concave β-sheet that normally gives rise to the interface between the V(L) domain and its paired V(H) (variable domain Ig heavy chain) domain, while only few interactions with CDR-L1 and CDR-L3 are formed. Notably, this noncanonical mode of antigen binding may occur more widely in the area of in vitro selected antibody fragments, including other Ig-like scaffolds, possibly even if a V(H) domain is present.
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Affiliation(s)
- André Schiefner
- Munich Center for Integrated Protein Science and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany
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Fidan Z, Younis A, Schmieder P, Volkmer R. Chemical synthesis of the third WW domain of TCERG 1 by native chemical ligation. J Pept Sci 2011; 17:644-9. [DOI: 10.1002/psc.1383] [Citation(s) in RCA: 6] [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] [Received: 03/07/2011] [Revised: 04/20/2011] [Accepted: 04/20/2011] [Indexed: 12/30/2022]
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Mahrenholz CC, Abfalter IG, Bodenhofer U, Volkmer R, Hochreiter S. Complex networks govern coiled-coil oligomerization--predicting and profiling by means of a machine learning approach. Mol Cell Proteomics 2011; 10:M110.004994. [PMID: 21311038 PMCID: PMC3098589 DOI: 10.1074/mcp.m110.004994] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 01/18/2011] [Indexed: 11/23/2022] Open
Abstract
Understanding the relationship between protein sequence and structure is one of the great challenges in biology. In the case of the ubiquitous coiled-coil motif, structure and occurrence have been described in extensive detail, but there is a lack of insight into the rules that govern oligomerization, i.e. how many α-helices form a given coiled coil. To shed new light on the formation of two- and three-stranded coiled coils, we developed a machine learning approach to identify rules in the form of weighted amino acid patterns. These rules form the basis of our classification tool, PrOCoil, which also visualizes the contribution of each individual amino acid to the overall oligomeric tendency of a given coiled-coil sequence. We discovered that sequence positions previously thought irrelevant to direct coiled-coil interaction have an undeniable impact on stoichiometry. Our rules also demystify the oligomerization behavior of the yeast transcription factor GCN4, which can now be described as a hybrid--part dimer and part trimer--with both theoretical and experimental justification.
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Affiliation(s)
- Carsten C. Mahrenholz
- From the ‡Institute of Medical Immunology, Charité Medical School, Hessische Str. 3-4, 10117 Berlin, Germany
| | - Ingrid G. Abfalter
- §Institute of Bioinformatics, Johannes Kepler University, Altenberger Str. 69, 4040 Linz, Austria
| | - Ulrich Bodenhofer
- §Institute of Bioinformatics, Johannes Kepler University, Altenberger Str. 69, 4040 Linz, Austria
| | - Rudolf Volkmer
- From the ‡Institute of Medical Immunology, Charité Medical School, Hessische Str. 3-4, 10117 Berlin, Germany
| | - Sepp Hochreiter
- §Institute of Bioinformatics, Johannes Kepler University, Altenberger Str. 69, 4040 Linz, Austria
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Vouilleme L, Cushing PR, Volkmer R, Madden DR, Boisguerin P. Engineering peptide inhibitors to overcome PDZ binding promiscuity. Angew Chem Int Ed Engl 2011; 49:9912-6. [PMID: 21105032 DOI: 10.1002/anie.201005575] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lars Vouilleme
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
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42
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Zhou X, Keller R, Volkmer R, Krauss N, Scheerer P, Hunke S. Structural basis for two-component system inhibition and pilus sensing by the auxiliary CpxP protein. J Biol Chem 2011; 286:9805-14. [PMID: 21239493 PMCID: PMC3059015 DOI: 10.1074/jbc.m110.194092] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [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: 10/17/2010] [Revised: 01/12/2011] [Indexed: 11/06/2022] Open
Abstract
Bacteria are equipped with two-component systems to cope with environmental changes, and auxiliary proteins provide response to additional stimuli. The Cpx two-component system is the global modulator of cell envelope stress in gram-negative bacteria that integrates very different signals and consists of the kinase CpxA, the regulator CpxR, and the dual function auxiliary protein CpxP. CpxP both inhibits activation of CpxA and is indispensable for the quality control system of P pili that are crucial for uropathogenic Escherichia coli during kidney colonization. How these two essential biological functions of CpxP are linked is not known. Here, we report the crystal structure of CpxP at 1.45 Å resolution with two monomers being interdigitated like "left hands" forming a cap-shaped dimer. Our combined structural and functional studies suggest that CpxP inhibits the kinase CpxA through direct interaction between its concave polar surface and the negatively charged sensor domain on CpxA. Moreover, an extended hydrophobic cleft on the convex surface suggests a potent substrate recognition site for misfolded pilus subunits. Altogether, the structural details of CpxP provide a first insight how a periplasmic two-component system inhibitor blocks its cognate kinase and is released from it.
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Affiliation(s)
- Xiaohui Zhou
- From the Institut für Biologie, Physiologie der Mikroorganismen, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany
| | - Rebecca Keller
- From the Institut für Biologie, Physiologie der Mikroorganismen, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany
| | - Rudolf Volkmer
- the Institut für Medizinische Immunologie, Charité – Universitätsmedizin Berlin, Hessische Strasse 3-4, Berlin D-10115, Germany
| | - Norbert Krauss
- the School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom, and
| | - Patrick Scheerer
- the Institut für Medizinische Physik und Biophysik (CC2), Charité – Universitätsmedizin Berlin, Ziegelstrasse 5-9, Berlin D-10117, Germany
| | - Sabine Hunke
- From the Institut für Biologie, Physiologie der Mikroorganismen, Humboldt Universität zu Berlin, Chausseestrasse 117, Berlin D-10115, Germany
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Vouilleme L, Cushing PR, Volkmer R, Madden DR, Boisguerin P. Engineering Peptide Inhibitors To Overcome PDZ Binding Promiscuity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nikolaus J, Scolari S, Bayraktarov E, Jungnick N, Engel S, Pia Plazzo A, Stöckl M, Volkmer R, Veit M, Herrmann A. Hemagglutinin of influenza virus partitions into the nonraft domain of model membranes. Biophys J 2010; 99:489-98. [PMID: 20643067 DOI: 10.1016/j.bpj.2010.04.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/07/2010] [Accepted: 04/12/2010] [Indexed: 11/16/2022] Open
Abstract
The HA of influenza virus is a paradigm for a transmembrane protein thought to be associated with membrane-rafts, liquid-ordered like nanodomains of the plasma membrane enriched in cholesterol, glycosphingolipids, and saturated phospholipids. Due to their submicron size in cells, rafts can not be visualized directly and raft-association of HA was hitherto analyzed by indirect methods. In this study, we have used GUVs and GPMVs, showing liquid disordered and liquid ordered domains, to directly visualize partition of HA by fluorescence microscopy. We show that HA is exclusively (GUVs) or predominantly (GPMVs) present in the liquid disordered domain, regardless of whether authentic HA or domains containing its raft targeting signals were reconstituted into model membranes. The preferential partition of HA into ld domains and the difference between lo partition in GUV and GPMV are discussed with respect to differences in packaging of lipids in membranes of model systems and living cells suggesting that physical properties of lipid domains in biological membranes are tightly regulated by protein-lipid interactions.
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Affiliation(s)
- Jörg Nikolaus
- Department of Biology, Molecular Biophysics, Humboldt University Berlin, Berlin, Germany
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Sun G, Hovestädt M, Zhang X, Hinrichs K, Rosu DM, Lauermann I, Zielke C, Vollmer A, Löchel H, Ay B, Holzhütter HG, Schade U, Esser N, Volkmer R, Rappich J. Infrared spectroscopic ellipsometry (IRSE) and X-ray photoelectron spectroscopy (XPS) monitoring the preparation of maleimide-functionalized surfaces: from Au towards Si (111). SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3699] [Citation(s) in RCA: 15] [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] [Indexed: 11/07/2022]
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Nikolaus J, Stöckl M, Langosch D, Volkmer R, Herrmann A. Direct visualization of large and protein-free hemifusion diaphragms. Biophys J 2010; 98:1192-9. [PMID: 20371318 DOI: 10.1016/j.bpj.2009.11.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/12/2009] [Accepted: 11/12/2009] [Indexed: 10/19/2022] Open
Abstract
Fusion of cellular membranes is a ubiquitous biological process requiring remodeling of two phospholipid bilayers. We believe it is very likely that merging of membranes proceeds via similar sequential intermediates. Contacting membranes form a stalk between the proximal leaflets that expands radially into an hemifusion diaphragm (HD) and subsequently open to a fusion pore. Although considered to be a key intermediate in fusion, direct experimental verification of this structure is difficult due to its transient nature. Using confocal fluorescence microscopy we have investigated the fusion of giant unilamellar vesicles (GUVs) containing phosphatidylserine and fluorescent virus derived transmembrane peptides or membrane proteins in the presence of divalent cations. Time-resolved imaging revealed that fusion was preceded by displacement of peptides and fluorescent lipid analogs from the GUV-GUV adhesion region. A detailed analysis of this area being several mum in size revealed that peptides were completely sequestered as expected for an HD. Lateral distribution of lipid analogs was consistent with formation of an HD but not with the presence of two adherent bilayers. Formation and size of the HD were dependent on lipid composition and peptide concentration.
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Affiliation(s)
- Jörg Nikolaus
- Institute of Biology, Faculty of Mathematics and Natural Sciences, Humboldt-University Berlin, Berlin, Germany
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Sereda MJ, Hartmann S, Büttner DW, Volkmer R, Hovestädt M, Brattig N, Lucius R. Characterization of the allergen filarial tropomyosin with an invertebrate specific monoclonal antibody. Acta Trop 2010; 116:61-7. [PMID: 20525500 DOI: 10.1016/j.actatropica.2010.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 05/25/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
Abstract
Tropomyosins of invertebrates are pan-allergens responsible for wide spread allergic reactions against seafood and arthropods. As invertebrate tropomyosins are highly conserved, helminth tropomyosins are likely to show properties similar to these medically important allergens. Studies with a monoclonal antibody, NR1, raised against tropomyosin of the rodent filarial nematode Acanthocheilonema viteae revealed a B cell epitope common to helminths and marine mollusks, which does not occur in vertebrate tropomyosin. This antibody detected tropomyosin of A. viteae, other filariids, nematodes, trematodes and a cestode, and recognized as well tropomyosin of oyster, squid and octopus, but not of arthropods and vertebrates. Immunohistological analyses of A. viteae, Onchocerca volvulus and other nematodes using NR1 showed that tropomyosin is located in the fibrillar part of the body wall muscles and the uterus, and is also conspicuous in muscles of the pharynx, the vagina and other organs of the nematodes. The abundance of a pan-allergen like tropomyosin in parasitic worms and the counterintuitive, but well documented protection against allergic reactivity by some chronic helminth infections is discussed.
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Zhang X, Sun G, Hovestädt M, Syritski V, Esser N, Volkmer R, Janietz S, Rappich J, Hinrichs K. A new strategy for the preparation of maleimide-functionalised gold surfaces. Electrochem commun 2010. [DOI: 10.1016/j.elecom.2010.07.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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49
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50
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Mahrenholz CC, Tapia V, Stigler RD, Volkmer R. A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid level. J Pept Sci 2010; 16:297-302. [PMID: 20474041 DOI: 10.1002/psc.1237] [Citation(s) in RCA: 8] [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: 11/11/2022]
Abstract
The growing demand for binding assays to study protein-protein interaction can be addressed by peptide array-based methods. The SPOT technique is a widespread peptide-array technology, which is able to distinguish semi-quantitatively the binding affinities of peptides to defined protein targets within one array. The quality of an assay system used for probing peptide arrays depends on the well-balanced combination of screening and read-out methods. The former address the steady-state of analyte capture, whereas the latter provide the means to detect captured analyte. In all cases, however, false-positive results can occur when challenging a peptide array with analyte or detecting captured analyte with label conjugates. Little is known about the cross-reactivity of peptides with the detection agents. Here, we describe at the amino acid level the potential of (i) 5-(and 6)-carboxytetramethylrhodamine (5(6)-TAMRA), (ii) fluoresceinisothiocyanate in form of the peptide-bound fluorescein-substituted thiourea derivative (FITC), and (iii) biotin/streptavidin-POD to cross-react with individual amino acids in a peptide sequence.
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Affiliation(s)
- Carsten C Mahrenholz
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
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