1
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Harms M, Smith N, Han M, Groß R, von Maltitz P, Stürzel C, Ruiz-Blanco YB, Almeida-Hernández Y, Rodriguez-Alfonso A, Cathelin D, Caspar B, Tahar B, Sayettat S, Bekaddour N, Vanshylla K, Kleipass F, Wiese S, Ständker L, Klein F, Lagane B, Boonen A, Schols D, Benichou S, Sanchez-Garcia E, Herbeuval JP, Münch J. Spermine and spermidine bind CXCR4 and inhibit CXCR4- but not CCR5-tropic HIV-1 infection. Sci Adv 2023; 9:eadf8251. [PMID: 37406129 DOI: 10.1126/sciadv.adf8251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/01/2023] [Indexed: 07/07/2023]
Abstract
Semen is an important vector for sexual HIV-1 transmission. Although CXCR4-tropic (X4) HIV-1 may be present in semen, almost exclusively CCR5-tropic (R5) HIV-1 causes systemic infection after sexual intercourse. To identify factors that may limit sexual X4-HIV-1 transmission, we generated a seminal fluid-derived compound library and screened it for antiviral agents. We identified four adjacent fractions that blocked X4-HIV-1 but not R5-HIV-1 and found that they all contained spermine and spermidine, abundant polyamines in semen. We showed that spermine, which is present in semen at concentrations up to 14 mM, binds CXCR4 and selectively inhibits cell-free and cell-associated X4-HIV-1 infection of cell lines and primary target cells at micromolar concentrations. Our findings suggest that seminal spermine restricts sexual X4-HIV-1 transmission.
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Affiliation(s)
- Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Nikaïa Smith
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Mingyu Han
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Pascal von Maltitz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christina Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, Emil-Figge Str. 66., 44227 Dortmund, Germany
| | - Armando Rodriguez-Alfonso
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Dominique Cathelin
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Birgit Caspar
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Bouceba Tahar
- Sorbonne University, CNRS, Institut de Biologie Paris-Seine (IBPS), Protein Engineering Platform, Molecular Interaction Service, F-75252 Paris, France
| | - Sophie Sayettat
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Nassima Bekaddour
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Franziska Kleipass
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research (DZIF), Partner site Bonn-Cologne, 50937 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Bernard Lagane
- Infinity, Université de Toulouse, CNRS, INSERM, Toulouse, France
| | - Arnaud Boonen
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, P.O. Box 1030, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, P.O. Box 1030, 3000 Leuven, Belgium
| | - Serge Benichou
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris-Cité, 75014 Paris, France
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, Emil-Figge Str. 66., 44227 Dortmund, Germany
| | - Jean-Philippe Herbeuval
- CNRS UMR-8601, Université Paris Cité, 75006 Paris, France
- Chemistry and Biology, Modeling and Immunology for Therapy (CBMIT), Paris, France
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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2
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Romero-Molina S, Ruiz-Blanco YB, Mieres-Perez J, Harms M, Münch J, Ehrmann M, Sanchez-Garcia E. PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity. J Proteome Res 2022; 21:1829-1841. [PMID: 35654412 PMCID: PMC9361347 DOI: 10.1021/acs.jproteome.2c00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Virtual screening
of protein–protein and protein–peptide
interactions is a challenging task that directly impacts the processes
of hit identification and hit-to-lead optimization in drug design
projects involving peptide-based pharmaceuticals. Although several
screening tools designed to predict the binding affinity of protein–protein
complexes have been proposed, methods specifically developed to predict
protein–peptide binding affinity are comparatively scarce.
Frequently, predictors trained to score the affinity of small molecules
are used for peptides indistinctively, despite the larger complexity
and heterogeneity of interactions rendered by peptide binders. To
address this issue, we introduce PPI-Affinity, a tool that leverages
support vector machine (SVM) predictors of binding affinity to screen
datasets of protein–protein and protein–peptide complexes,
as well as to generate and rank mutants of a given structure. The
performance of the SVM models was assessed on four benchmark datasets,
which include protein–protein and protein–peptide binding
affinity data. In addition, we evaluated our model on a set of mutants
of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor
CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with
peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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3
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. Sci Adv 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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4
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Ingenbosch KN, Vieyto-Nuñez JC, Ruiz-Blanco YB, Mayer C, Hoffmann-Jacobsen K, Sanchez-Garcia E. Effect of Organic Solvents on the Structure and Activity of a Minimal Lipase. J Org Chem 2021; 87:1669-1678. [PMID: 34706196 DOI: 10.1021/acs.joc.1c01136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipases are ubiquitously used in chemo-enzymatic synthesis and industrial applications. Nevertheless, the modulation of the activity of lipases by organic solvents still is not fully understood at the molecular level. We systematically investigated the activity and structure of lipase A from Bacillus subtilis in binary water-organic solvent mixtures of dimethyl sulfoxide (DMSO), acetonitrile (ACN), and isopropyl alcohol (IPA) using activity assays, fluorescence spectroscopy, molecular dynamics (MD) simulations, and FRET/MD analysis. The enzymatic activity strongly depended on the type and amount of organic solvent in the reaction media. Whereas IPA and ACN reduced the activity of the enzyme, small concentrations of DMSO led to lipase activation via an uncompetitive mechanism. DMSO molecules did not directly interfere with the binding of the substrate in the active site, contrary to what is known for other solvents and enzymes. We propose that the His156-Asp133 interaction, the binding of organic molecules to the active site, and the water accessibility of the substrate are key factors modulating the catalytic activity. Furthermore, we rationalized the role of solvent descriptors on the regulation of enzymatic activity in mixtures with low concentrations of the organic molecule, with prospective implications for the optimization of biocatalytic processes via solvent tuning.
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Affiliation(s)
- Kim N Ingenbosch
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany.,Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Julio Cesar Vieyto-Nuñez
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Christian Mayer
- Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kerstin Hoffmann-Jacobsen
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
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5
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Holch A, Bauer R, Olari LR, Rodriguez AA, Ständker L, Preising N, Karacan M, Wiese S, Walther P, Ruiz-Blanco YB, Sanchez-Garcia E, Schumann C, Münch J, Spellerberg B. Respiratory ß-2-Microglobulin exerts pH dependent antimicrobial activity. Virulence 2021; 11:1402-1414. [PMID: 33092477 PMCID: PMC7588194 DOI: 10.1080/21505594.2020.1831367] [Citation(s) in RCA: 4] [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] [Indexed: 12/13/2022] Open
Abstract
The respiratory tract is a major entry site for microbial pathogens. To combat bacterial infections, the immune system has various defense mechanisms at its disposal, including antimicrobial peptides (AMPs). To search for novel AMPs from the respiratory tract, a peptide library from human broncho-alveolar-lavage (BAL) fluid was screened for antimicrobial activity by radial diffusion assays allowing the efficient detection of antibacterial activity within a small sample size. After repeated testing-cycles and subsequent purification, we identified ß-2-microglobulin (B2M) in antibacterially active fractions. B2M belongs to the MHC-1 receptor complex present at the surface of nucleated cells. It is known to inhibit the growth of Listeria monocytogenes and Escherichia coli and to facilitate phagocytosis of Staphylococcus aureus. Using commercially available B2M we confirmed a dose-dependent inhibition of Pseudomonas aeruginosa and L. monocytogenes. To characterize AMP activity within the B2M sequence, peptide fragments of the molecule were tested for antimicrobial activity. Activity could be localized to the C-terminal part of B2M. Investigating pH dependency of the antimicrobial activity of B2M demonstrated an increased activity at pH values of 5.5 and below, a hallmark of infection and inflammation. Sytox green uptake into bacterial cells following the exposure to B2M was determined and revealed a pH-dependent loss of bacterial membrane integrity. TEM analysis showed areas of disrupted bacterial membranes in L. monocytogenes incubated with B2M and high amounts of lysed bacterial cells. In conclusion, B2M as part of a ubiquitous cell surface complex may represent a potent antimicrobial agent by interfering with bacterial membrane integrity.
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Affiliation(s)
- Armin Holch
- Institute of Medical Microbiology and Hygiene, University Hospital , Ulm, Germany
| | - Richard Bauer
- Institute of Medical Microbiology and Hygiene, University Hospital , Ulm, Germany
| | - Lia-Raluca Olari
- Institute of Molecular Virology, University Hospital , Ulm, Germany
| | - Armando A Rodriguez
- Core Facility Functional Peptidomics, Ulm University Medical Center , Ulm, Germany.,Core Unit Mass Spectrometry and Proteomics, Ulm University , Ulm, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center , Ulm, Germany
| | - Nico Preising
- Core Facility Functional Peptidomics, Ulm University Medical Center , Ulm, Germany
| | - Merve Karacan
- Core Facility Functional Peptidomics, Ulm University Medical Center , Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University , Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University Medical Center , Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen , Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen , Essen, Germany
| | - Christian Schumann
- Pneumology, Thoracic Oncology, Sleep and Respiratory Critical Care Medicine, Clinics Kempten-Allgäu, Kempten and Immenstadt , Germany
| | - Jan Münch
- Institute of Molecular Virology, University Hospital , Ulm, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center , Ulm, Germany
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, University Hospital , Ulm, Germany
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6
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Malishev R, Salinas N, Gibson J, Eden AB, Mieres-Perez J, Ruiz-Blanco YB, Malka O, Kolusheva S, Klärner FG, Schrader T, Sanchez-Garcia E, Wang C, Landau M, Bitan G, Jelinek R. Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
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Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nir Salinas
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Angela Bailey Eden
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
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7
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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8
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Schütz D, Ruiz-Blanco YB, Münch J, Kirchhoff F, Sanchez-Garcia E, Müller JA. Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020; 167:47-65. [PMID: 33189768 PMCID: PMC7665879 DOI: 10.1016/j.addr.2020.11.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [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: 10/07/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022]
Abstract
To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.
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Affiliation(s)
- Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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9
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Ruiz-Blanco YB, Ávila-Barrientos LP, Hernández-García E, Antunes A, Agüero-Chapin G, García-Hernández E. Engineering protein fragments via evolutionary and protein-protein interaction algorithms: de novo design of peptide inhibitors for F O F 1 -ATP synthase. FEBS Lett 2020; 595:183-194. [PMID: 33151544 DOI: 10.1002/1873-3468.13988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 11/08/2022]
Abstract
Enzyme subunit interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution-driven strategy for the de novo design of peptide inhibitors targeting interfaces of the Escherichia coli FoF1-ATP synthase as a case study. The evolutionary algorithm ROSE was applied to generate diversity-oriented peptide libraries by engineering peptide fragments from ATP synthase interfaces. The resulting peptides were scored with PPI-Detect, a sequence-based predictor of protein-protein interactions. Two selected peptides were confirmed by in vitro inhibition and binding tests. The proposed methodology can be widely applied to design peptides targeting relevant interfaces of enzymatic complexes.
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Affiliation(s)
| | | | | | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
| | - Guillermin Agüero-Chapin
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal
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10
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Weil T, Groß R, Röcker A, Bravo-Rodriguez K, Heid C, Sowislok A, Le MH, Erwin N, Dwivedi M, Bart SM, Bates P, Wettstein L, Müller JA, Harms M, Sparrer K, Ruiz-Blanco YB, Stürzel CM, von Einem J, Lippold S, Read C, Walther P, Hebel M, Kreppel F, Klärner FG, Bitan G, Ehrmann M, Weil T, Winter R, Schrader T, Shorter J, Sanchez-Garcia E, Münch J. Supramolecular Mechanism of Viral Envelope Disruption by Molecular Tweezers. J Am Chem Soc 2020; 142:17024-17038. [PMID: 32926779 PMCID: PMC7523239 DOI: 10.1021/jacs.0c06400] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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] [Indexed: 12/14/2022]
Abstract
![]()
Broad-spectrum
antivirals are powerful weapons against dangerous
viruses where no specific therapy exists, as in the case of the ongoing
SARS-CoV-2 pandemic. We discovered that a lysine- and arginine-specific
supramolecular ligand (CLR01) destroys enveloped viruses, including
HIV, Ebola, and Zika virus, and remodels amyloid fibrils in semen
that promote viral infection. Yet, it is unknown how CLR01 exerts
these two distinct therapeutic activities. Here, we delineate a novel
mechanism of antiviral activity by studying the activity of tweezer
variants: the “phosphate tweezer” CLR01, a “carboxylate
tweezer” CLR05, and a “phosphate clip” PC. Lysine
complexation inside the tweezer cavity is needed to antagonize amyloidogenesis
and is only achieved by CLR01. Importantly, CLR01 and CLR05 but not
PC form closed inclusion complexes with lipid head groups of viral
membranes, thereby altering lipid orientation and increasing surface
tension. This process disrupts viral envelopes and diminishes infectivity
but leaves cellular membranes intact. Consequently, CLR01 and CLR05
display broad antiviral activity against all enveloped viruses tested,
including herpesviruses, Measles virus, influenza, and SARS-CoV-2.
Based on our mechanistic insights, we potentiated the antiviral, membrane-disrupting
activity of CLR01 by introducing aliphatic ester arms into each phosphate
group to act as lipid anchors that promote membrane targeting. The
most potent ester modifications harbored unbranched C4 units, which
engendered tweezers that were approximately one order of magnitude
more effective than CLR01 and nontoxic. Thus, we establish the mechanistic
basis of viral envelope disruption by specific tweezers and establish
a new class of potential broad-spectrum antivirals with enhanced activity.
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Affiliation(s)
- Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Annika Röcker
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Kenny Bravo-Rodriguez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christian Heid
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Andrea Sowislok
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - My-Hue Le
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Nelli Erwin
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Mridula Dwivedi
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Stephen M Bart
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Konstantin Sparrer
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Sina Lippold
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Clarissa Read
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany.,Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Marco Hebel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Florian Kreppel
- Center for Biomedical Education and Research, University of Witten/Herdecke, Stockumer Strasse 10, 58453 Witten, Germany
| | | | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Michael Ehrmann
- Microbiology II, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - James Shorter
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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11
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Romero-Molina S, Ruiz-Blanco YB, Green JR, Sanchez-Garcia E. ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. Protein Sci 2020; 28:1734-1743. [PMID: 31271472 DOI: 10.1002/pro.3673] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 04/11/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/24/2022]
Abstract
Computational tools for the analysis of protein data and the prediction of biological properties are essential in life sciences and biomedical research. Here, we introduce ProtDCal-Suite, a web server comprising a set of machine learning-based methods for studying proteins. The main module of ProtDCal-Suite is the ProtDCal software. ProtDCal translates the structural information of proteins into numerical descriptors that serve as input to machine-learning techniques. The ProtDCal-Suite server also incorporates a post-processing optional stage that allows ranking and filtering the obtained descriptors by computing their Shannon entropy values across the input set of proteins. ProtDCal's codification was used in the development of models for the prediction of specific protein properties. Thus, the other modules of ProtDCal-Suite are protein analysis tools implemented using ProtDCal's descriptors. Among them are PPI-Detect, for predicting the interaction likelihood of protein-protein and protein-peptide pairs, Enzyme Identifier, for identifying enzymes from amino acid sequences or 3D structures, and Pred-NGlyco, for predicting N-glycosylation sites. ProtDCal-Suite is freely accessible at https://protdcal.zmb.uni-due.de.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - James R Green
- Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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12
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Groß R, Bauer R, Krüger F, Rücker-Braun E, Olari LR, Ständker L, Preising N, Rodríguez AA, Conzelmann C, Gerbl F, Sauter D, Kirchhoff F, Hagemann B, Gačanin J, Weil T, Ruiz-Blanco YB, Sanchez-Garcia E, Forssmann WG, Mankertz A, Santibanez S, Stenger S, Walther P, Wiese S, Spellerberg B, Münch J. A Placenta Derived C-Terminal Fragment of β-Hemoglobin With Combined Antibacterial and Antiviral Activity. Front Microbiol 2020; 11:508. [PMID: 32328038 PMCID: PMC7153485 DOI: 10.3389/fmicb.2020.00508] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 11/14/2019] [Accepted: 03/09/2020] [Indexed: 01/08/2023] Open
Abstract
The placenta acts as physical and immunological barrier against the transmission of viruses and bacteria from mother to fetus. However, the specific mechanisms by which the placenta protects the developing fetus from viral and bacterial pathogens are poorly understood. To identify placental peptides and small proteins protecting from viral and bacterial infections, we generated a peptide library from 10 kg placenta by chromatographic means. Screening the resulting 250 fractions against Herpes-Simplex-Virus 2 (HSV-2), which is rarely transmitted through the placenta, in a cell-based system identified two adjacent fractions with significant antiviral activity. Further rounds of chromatographic purification and anti-HSV-2 testing allowed to purify the bioactive peptide. Mass spectrometry revealed the presence of a 36-mer derived from the C-terminal region of the hemoglobin β subunit. The purified and corresponding chemically synthesized peptide, termed HBB(112–147), inhibited HSV-2 infection in a dose-dependent manner, with a mean IC50 in the median μg/ml range. Full-length hemoglobin tetramer had no antiviral activity. HBB(112–147) did not impair infectivity by direct targeting of the virions but prevented HSV-2 infection at the cell entry level. The peptide was inactive against Human Immunodeficiency Virus Type 1, Rubella and Zika virus infection, suggesting a specific anti-HSV-2 mechanism. Notably, HBB(112–147) has previously been identified as broad-spectrum antibacterial agent. It is abundant in placenta, reaching concentrations between 280 and 740 μg/ml, that are well sufficient to inhibit HSV-2 and prototype Gram-positive and -negative bacteria. We here additionally show, that HBB(112–147) also acts potently against Pseudomonas aeruginosa strains (including a multi-drug resistant strain) in a dose dependent manner, while full-length hemoglobin is inactive. Interestingly, the antibacterial activity of HBB(112–147) was increased under acidic conditions, a hallmark of infection and inflammatory conditions. Indeed, we found that HBB(112–147) is released from the hemoglobin precursor by Cathepsin D and Napsin A, acidic proteases highly expressed in placental and other tissues. We propose that upon viral or bacterial infection, the abundant hemoglobin precursor is proteolytically processed to release HBB(112–147), a broadly active antimicrobial innate immune defense peptide.
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Affiliation(s)
- Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Richard Bauer
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Franziska Krüger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elke Rücker-Braun
- Department of Medicine I, University Hospital of Dresden, Dresden, Germany
| | - Lia-Raluca Olari
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Nico Preising
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Armando A Rodríguez
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany.,Core Unit of Mass Spectrometry and Proteomics, Ulm University, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Gerbl
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Benjamin Hagemann
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Jasmina Gačanin
- Max Planck Institute for Polymer Research, Mainz, Germany.,Institute of Inorganic Chemistry I, University of Ulm, Ulm, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Mainz, Germany.,Institute of Inorganic Chemistry I, University of Ulm, Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Annette Mankertz
- WHO Measles/Rubella European RRL and NRC Measles, Mumps, Rubella, Robert Koch-Institute, Berlin, Germany
| | - Sabine Santibanez
- WHO Measles/Rubella European RRL and NRC Measles, Mumps, Rubella, Robert Koch-Institute, Berlin, Germany
| | - Steffen Stenger
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Core Unit of Mass Spectrometry and Proteomics, Ulm University, Ulm, Germany
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
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13
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Affiliation(s)
- Yasser B. Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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14
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Kuusk A, Neves JF, Bravo-Rodriguez K, Gunnarsson A, Ruiz-Blanco YB, Ehrmann M, Chen H, Landrieu I, Sanchez-Garcia E, Boyd H, Ottmann C, Doveston RG. Adoption of a Turn Conformation Drives the Binding Affinity of p53 C-Terminal Domain Peptides to 14-3-3σ. ACS Chem Biol 2020; 15:262-271. [PMID: 31742997 DOI: 10.1021/acschembio.9b00893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between the adapter protein 14-3-3σ and transcription factor p53 is important for preserving the tumor-suppressor functions of p53 in the cell. A phosphorylated motif within the C-terminal domain (CTD) of p53 is key for binding to the amphipathic groove of 14-3-3. This motif is unique among 14-3-3 binding partners, and the precise dynamics of the interaction is not yet fully understood. Here, we investigate this interaction at the molecular level by analyzing the binding of different length p53 CTD peptides to 14-3-3σ using ITC, SPR, NMR, and MD simulations. We observed that the propensity of the p53 peptide to adopt turn-like conformation plays an important role in the binding to the 14-3-3σ protein. Our study contributes to elucidate the molecular mechanism of the 14-3-3-p53 binding and provides useful insight into how conformation properties of a ligand influence protein binding.
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Affiliation(s)
- Ave Kuusk
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | | | | | | | | | - Hongming Chen
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, Sweden
- Chemistry and Chemical Biology Centre, Guangzhou Regenerative Medicine and Health-Guangdong Laboratory, Guangzhou, China
| | | | | | - Helen Boyd
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, U.K
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Richard G. Doveston
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
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15
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Bartsch L, Bartel M, Gigante A, Iglesias-Fernández J, Ruiz-Blanco YB, Beuck C, Briels J, Toetsch N, Bayer P, Sanchez-Garcia E, Ottmann C, Schmuck C. Multivalent Ligands with Tailor-Made Anion Binding Motif as Stabilizers of Protein-Protein Interactions. Chembiochem 2019; 20:2921-2926. [PMID: 31168888 DOI: 10.1002/cbic.201900288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Indexed: 12/23/2022]
Abstract
Modulation of protein-protein interactions (PPIs) is essential for understanding and tuning biologically relevant processes. Although inhibitors for PPIs are widely used, the field still lacks the targeted design of stabilizers. Here, we report unnatural stabilizers based on the combination of multivalency effects and the artificial building block guanidiniocarbonylpyrrol (GCP), an arginine mimetic. Unlike other GCP-based ligands that modulate PPIs in different protein targets, only a tetrameric design shows potent activity as stabilizer of the 14-3-3ζ/C-Raf and 14-3-3ζ/Tau complexes in the low-micromolar range. This evidences the role of multivalency for achieving higher specificity in the modulation of PPIs.
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Affiliation(s)
- Lina Bartsch
- Department of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141, Essen, Germany
| | - Maria Bartel
- Department of Biomedical Engineering, Eindhoven University of Technology, P. O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Alba Gigante
- Department of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141, Essen, Germany
| | | | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstrasse 2, 45117, Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätstrasse 1-5, 45141, Essen, Germany
| | - Jeroen Briels
- Department of Biomedical Engineering, Eindhoven University of Technology, P. O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Niklas Toetsch
- Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstrasse 2, 45117, Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätstrasse 1-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Theory, Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany.,Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University Duisburg-Essen, Universitätsstrasse 2, 45117, Essen, Germany
| | - Christian Ottmann
- Department of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141, Essen, Germany.,Department of Biomedical Engineering, Eindhoven University of Technology, P. O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Carsten Schmuck
- Department of Organic Chemistry, University of Duisburg-Essen, Universitätstrasse 7, 45141, Essen, Germany
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16
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Smith N, Rodero MP, Bekaddour N, Bondet V, Ruiz-Blanco YB, Harms M, Mayer B, Bader-Meunier B, Quartier P, Bodemer C, Baudouin V, Dieudonné Y, Kirchhoff F, Sanchez Garcia E, Charbit B, Leboulanger N, Jahrsdörfer B, Richard Y, Korganow AS, Münch J, Nisole S, Duffy D, Herbeuval JP. Control of TLR7-mediated type I IFN signaling in pDCs through CXCR4 engagement-A new target for lupus treatment. Sci Adv 2019; 5:eaav9019. [PMID: 31309143 PMCID: PMC6620093 DOI: 10.1126/sciadv.aav9019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
Type I interferons are highly potent cytokines essential for self-protection against tumors and infections. Deregulations of type I interferon signaling are associated with multiple diseases that require novel therapeutic options. Here, we identified the small molecule, IT1t, a previously described CXCR4 ligand, as a highly potent inhibitor of Toll-like receptor 7 (TLR7)-mediated inflammation. IT1t inhibits chemical (R848) and natural (HIV) TLR7-mediated inflammation in purified human plasmacytoid dendritic cells from blood and human tonsils. In a TLR7-dependent lupus-like model, in vivo treatment of mice with IT1t drives drastic reduction of both systemic inflammation and anti-double-stranded DNA autoantibodies and prevents glomerulonephritis. Furthermore, IT1t controls inflammation, including interferon α secretion, in resting and stimulated cells from patients with systemic lupus erythematosus. Our findings highlight a groundbreaking immunoregulatory property of CXCR4 signaling that opens new therapeutic perspectives in inflammatory settings and autoimmune diseases.
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Affiliation(s)
- Nikaïa Smith
- CNRS UMR-8601, CICB, 45 rue des Saints-Pères, 75006 Paris, France
- Team Chemistry & Biology, Modeling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Mathieu P. Rodero
- CNRS UMR-8601, CICB, 45 rue des Saints-Pères, 75006 Paris, France
- Team Chemistry & Biology, Modeling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nassima Bekaddour
- CNRS UMR-8601, CICB, 45 rue des Saints-Pères, 75006 Paris, France
- Team Chemistry & Biology, Modeling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Vincent Bondet
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
| | - Yasser B. Ruiz-Blanco
- Computational Biochemistry and Center of Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Benjamin Mayer
- Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Brigitte Bader-Meunier
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Imagine Institute, Paris, France
- Paediatric Haematology-Immunology and Rheumatology Department, Hôpital Universitaire Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM UMR 1163, Laboratory of Immunogenetics of Paediatric Autoimmunity, Paris, France
| | - Pierre Quartier
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Imagine Institute, Paris, France
- Paediatric Haematology-Immunology and Rheumatology Department, Hôpital Universitaire Necker, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Christine Bodemer
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Imagine Institute, Paris, France
- Department of Paediatric Dermatology, Reference Centre for Rare Skin Disorders (MAGEC), Hôpital Universitaire Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Véronique Baudouin
- Hôpital Universitaire Robert Debré, Néphrologie pédiatrique, Paris, France
| | - Yannick Dieudonné
- CNRS UPR 3572 “Immunopathology and Therapeutic Chemistry”/Laboratory of Excellence Médalis, Institute of Molecular and Cellular Biology (IBMC), Strasbourg, France
- Department of Clinical Immunology and Internal Medicine, National Reference Center for Rare Autoimmune Diseases, University Hospital, Strasbourg, France
- UFR Medicine, University of Strasbourg, Strasbourg, France
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Elsa Sanchez Garcia
- Computational Biochemistry and Center of Medical Biotechnology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Bruno Charbit
- Centre for Translational Research, Institut Pasteur, Paris, France
| | - Nicolas Leboulanger
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Pediatric Otolaryngology Department, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Bernd Jahrsdörfer
- Institute of Transfusion Medicine and Immunogenetics (IKT) Ulm, Helmholtzstr. 10, 89081 Ulm, Germany
| | - Yolande Richard
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- INSERM U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
| | - Anne-Sophie Korganow
- CNRS UPR 3572 “Immunopathology and Therapeutic Chemistry”/Laboratory of Excellence Médalis, Institute of Molecular and Cellular Biology (IBMC), Strasbourg, France
- Department of Clinical Immunology and Internal Medicine, National Reference Center for Rare Autoimmune Diseases, University Hospital, Strasbourg, France
- UFR Medicine, University of Strasbourg, Strasbourg, France
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Sébastien Nisole
- IRIM, Université de Montpellier, CNRS UMR, 9004 Montpellier, France
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- INSERM U1223, Paris, France
- Centre for Translational Research, Institut Pasteur, Paris, France
| | - Jean-Philippe Herbeuval
- CNRS UMR-8601, CICB, 45 rue des Saints-Pères, 75006 Paris, France
- Team Chemistry & Biology, Modeling & Immunology for Therapy, CBMIT, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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17
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Romero-Molina S, Ruiz-Blanco YB, Harms M, Münch J, Sanchez-Garcia E. PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions. J Comput Chem 2019; 40:1233-1242. [PMID: 30768790 DOI: 10.1002/jcc.25780] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 09/24/2018] [Revised: 11/29/2018] [Accepted: 12/29/2018] [Indexed: 12/18/2022]
Abstract
The prediction of peptide-protein or protein-protein interactions (PPI) is a challenging task, especially if amino acid sequences are the only information available. Machine learning methods allow us to exploit the information content in PPI datasets. However, the numerical codification of these datasets often influences the performance of data mining approaches. Here, we introduce a procedure for the general-purpose numerical codification of polypeptides. This procedure transforms pairs of amino acid sequences into a machine learning-friendly vector, whose elements represent numerical descriptors of residues in proteins. We used this numerical encoding procedure for the development of a support vector machine model (PPI-Detect), which allows predicting whether two proteins will interact or not. PPI-Detect (https://ppi-detect.zmb.uni-due.de/) outperforms state of the art sequence-based predictors of PPI. We employed PPI-Detect for the analysis of derivatives of EPI-X4, an endogenous peptide inhibitor of CXCR4, a G-protein-coupled receptor. There, we identified with high accuracy those peptides which bind better than EPI-X4 to the receptor. Also using PPI-Detect, we designed a novel peptide and then experimentally established its anti-CXCR4 activity. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandra Romero-Molina
- Center of Medical Biotechnology, University of Duisburg-Essen, Duisburg, Germany
| | - Yasser B Ruiz-Blanco
- Center of Medical Biotechnology, University of Duisburg-Essen, Duisburg, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Elsa Sanchez-Garcia
- Center of Medical Biotechnology, University of Duisburg-Essen, Duisburg, Germany
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18
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Yilmaz E, Bier D, Guillory X, Briels J, Ruiz-Blanco YB, Sanchez-Garcia E, Ottmann C, Kaiser M. Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry 2018; 24:13807-13814. [PMID: 29924885 DOI: 10.1002/chem.201801074] [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: 03/02/2018] [Revised: 06/15/2018] [Indexed: 12/26/2022]
Abstract
Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling complexation of the amino group by the ether oxygen residues. The resulting biochemical binding affinity and thus biological relevance of this supramolecular interaction however remains unclear so far. Here, we report that OEG-containing phosphophenol ether inhibitors of 14-3-3 proteins also display such a "lysine-wrapping" binding mode. For better investigating the biochemical relevance of this binding mode, we made use of the dimeric nature of 14-3-3 proteins and designed as well as synthesized a set of bivalent 14-3-3 inhibitors for biochemical and X-ray crystallography-based structural studies. We found that all synthesized derivatives adapted the "lysine-wrapping" binding mode in the crystal structures; in solution, a different binding mode is however observed, most probably as the "lysine-wrapping" binding mode turned out to be a rather weak interaction. Accordingly, our studies demonstrate that structural studies of OEG-lysine interactions are difficult to interpret and their presence in structural studies may not automatically be correlated with a relevant interaction also in solution but requires further biochemical studies.
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Affiliation(s)
- Elvan Yilmaz
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - David Bier
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Xavier Guillory
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen Briels
- Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christian Ottmann
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Markus Kaiser
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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19
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Ruiz-Blanco YB, Agüero-Chapin G, García-Hernández E, Álvarez O, Antunes A, Green J. Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. BMC Bioinformatics 2017; 18:349. [PMID: 28732462 PMCID: PMC5521120 DOI: 10.1186/s12859-017-1758-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/13/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Yasser B Ruiz-Blanco
- Facultad de Química y Farmacia, Universidad Central "Marta Abreu" de Las Villas, 54830, Santa Clara, Cuba.,Theoretical Chemistry, Max Planck Institute für Kohlenforschung, 45470, Mulheim an der Ruhr, Germany
| | - Guillermin Agüero-Chapin
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal. .,Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México (UNAM), 04360, D.F, México, Mexico
| | - Orlando Álvarez
- Centro de Bioactivos Químicos (CBQ), Universidad Central ¨Marta Abreu¨ de Las Villas (UCLV), 54830, Santa Clara, Cuba
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - James Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada
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20
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García Y, Ruiz-Blanco YB, Marrero-Ponce Y, Sotomayor-Torres CM. Orthotropic Piezoelectricity in 2D Nanocellulose. Sci Rep 2016; 6:34616. [PMID: 27708364 PMCID: PMC5052617 DOI: 10.1038/srep34616] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 04/04/2016] [Accepted: 09/02/2016] [Indexed: 11/08/2022] Open
Abstract
The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V-1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.
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Affiliation(s)
- Y. García
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Yasser B. Ruiz-Blanco
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatics Research (CAMD-BIR Unit), Facultad de Química y Farmacia. Universidad Central “Marta Abreu” de Las Villas, 54830 Santa Clara, Cuba
| | - Yovani Marrero-Ponce
- Unit of Computer-Aided Molecular “Biosilico” Discovery and Bioinformatics Research (CAMD-BIR Unit), Facultad de Química y Farmacia. Universidad Central “Marta Abreu” de Las Villas, 54830 Santa Clara, Cuba
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Hospital de los Valles, Av. Interoceánica Km 12 —Cumbayá, e Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Ecuador
| | - C. M. Sotomayor-Torres
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- ICREA—Institució Catalana de Recerca i Estudis Avançats, E-08010 Barcelona, Spain
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21
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Ruiz-Blanco YB, Paz W, Green J, Marrero-Ponce Y. ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. BMC Bioinformatics 2015; 16:162. [PMID: 25982853 PMCID: PMC4432771 DOI: 10.1186/s12859-015-0586-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 01/15/2015] [Accepted: 04/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now make it possible to apply well-established data mining and pattern recognition techniques to these data to learn models that effectively relate structure and function. However, extracting meaningful numerical descriptors of protein sequence and structure is a key issue that requires an efficient and widely available solution. RESULTS We here introduce ProtDCal, a new computational software suite capable of generating tens of thousands of features considering both sequence-based and 3D-structural descriptors. We demonstrate, by means of principle component analysis and Shannon entropy tests, how ProtDCal's sequence-based descriptors provide new and more relevant information not encoded by currently available servers for sequence-based protein feature generation. The wide diversity of the 3D-structure-based features generated by ProtDCal is shown to provide additional complementary information and effectively completes its general protein encoding capability. As demonstration of the utility of ProtDCal's features, prediction models of N-linked glycosylation sites are trained and evaluated. Classification performance compares favourably with that of contemporary predictors of N-linked glycosylation sites, in spite of not using domain-specific features as input information. CONCLUSIONS ProtDCal provides a friendly and cross-platform graphical user interface, developed in the Java programming language and is freely available at: http://bioinf.sce.carleton.ca/ProtDCal/ . ProtDCal introduces local and group-based encoding which enhances the diversity of the information captured by the computed features. Furthermore, we have shown that adding structure-based descriptors contributes non-redundant additional information to the features-based characterization of polypeptide systems. This software is intended to provide a useful tool for general-purpose encoding of protein sequences and structures for applications is protein classification, similarity analyses and function prediction.
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Affiliation(s)
- Yasser B Ruiz-Blanco
- Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research (CAMD-BIR Unit), Facultad de Química y Farmacia, Universidad Central "Marta Abreu" de Las Villas, Road to Camajuani km 5 ½, Santa Clara, CP: 54830, Villa Clara, Cuba. .,Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada.
| | - Waldo Paz
- Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research (CAMD-BIR Unit), Facultad de Química y Farmacia, Universidad Central "Marta Abreu" de Las Villas, Road to Camajuani km 5 ½, Santa Clara, CP: 54830, Villa Clara, Cuba. .,Centre of Informatics Studies (CEI), Universidad Central "Marta Abreu" de Las Villas, Road to Camajuani km 5 ½, Santa Clara, CP:54830, Villa Clara, Cuba.
| | - James Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada.
| | - Yovani Marrero-Ponce
- Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research (CAMD-BIR Unit), Facultad de Química y Farmacia, Universidad Central "Marta Abreu" de Las Villas, Road to Camajuani km 5 ½, Santa Clara, CP: 54830, Villa Clara, Cuba. .,Grupo de Investigación Microbiología y Ambiente (GIMA). Programa de Bacteriología, Facultad Ciencias de la Salud, Universidad de San Buenaventura, Calle Real de Ternera, Cartagena (Bolivar), Colombia.
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22
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Ruiz-Blanco YB, Marrero-Ponce Y, Prieto PJ, Salgado J, García Y, Sotomayor-Torres CM. A Hooke׳s law-based approach to protein folding rate. J Theor Biol 2015; 364:407-17. [DOI: 10.1016/j.jtbi.2014.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/28/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
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23
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Ruiz-Blanco YB, Marrero-Ponce Y, García Y, Puris A, Bello R, Green J, Sotomayor-Torres CM. A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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