1
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Nonappa. Precision nanoengineering for functional self-assemblies across length scales. Chem Commun (Camb) 2023; 59:13800-13819. [PMID: 37902292 DOI: 10.1039/d3cc02205f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
As nanotechnology continues to push the boundaries across disciplines, there is an increasing need for engineering nanomaterials with atomic-level precision for self-assembly across length scales, i.e., from the nanoscale to the macroscale. Although molecular self-assembly allows atomic precision, extending it beyond certain length scales presents a challenge. Therefore, the attention has turned to size and shape-controlled metal nanoparticles as building blocks for multifunctional colloidal self-assemblies. However, traditionally, metal nanoparticles suffer from polydispersity, uncontrolled aggregation, and inhomogeneous ligand distribution, resulting in heterogeneous end products. In this feature article, I will discuss how virus capsids provide clues for designing subunit-based, precise, efficient, and error-free self-assembly of colloidal molecules. The atomically precise nanoscale proteinic subunits of capsids display rigidity (conformational and structural) and patchy distribution of interacting sites. Recent experimental evidence suggests that atomically precise noble metal nanoclusters display an anisotropic distribution of ligands and patchy ligand bundles. This enables symmetry breaking, consequently offering a facile route for two-dimensional colloidal crystals, bilayers, and elastic monolayer membranes. Furthermore, inter-nanocluster interactions mediated via the ligand functional groups are versatile, offering routes for discrete supracolloidal capsids, composite cages, toroids, and macroscopic hierarchically porous frameworks. Therefore, engineered nanoparticles with atomically precise structures have the potential to overcome the limitations of molecular self-assembly and large colloidal particles. Self-assembly allows the emergence of new optical properties, mechanical strength, photothermal stability, catalytic efficiency, quantum yield, and biological properties. The self-assembled structures allow reproducible optoelectronic properties, mechanical performance, and accurate sensing. More importantly, the intrinsic properties of individual nanoclusters are retained across length scales. The atomically precise nanoparticles offer enormous potential for next-generation functional materials, optoelectronics, precision sensors, and photonic devices.
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Affiliation(s)
- Nonappa
- Facutly of Engineering and Natural Sciences, Tampere University, FI-33720, Tampere, Finland.
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2
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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3
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Zheng M, Ye Q, Chen X, Zeng M, Song G, Zhang J, Yuan J. In situ generation and evolution of polymer toroids by liquid crystallization-assisted seeded dispersion polymerization. Chem Commun (Camb) 2022; 58:6922-6925. [PMID: 35635333 DOI: 10.1039/d1cc06709e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An effective method is presented for preparing high solid content azobenzene-containing triblock copolymer toroidal assemblies by liquid crystallization-assisted seeded dispersion polymerization. Vesicles are prepared via polymerization-induced self-assembly (PISA), and used as seeds for further chain extension. By introducing smectic liquid crystalline (LC) ordering into the core-forming block, toroids are formed in situ during the polymerization. The morphological transformation from toroids to barrels is observed under ultraviolet irradiation due to the photo-isomerization of the azobenzene mesogens. This strategy expands the scope of tunable anisotropic morphologies for potential functional nanomaterials based on a LC copolymer by seeded dispersion polymerization.
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Affiliation(s)
- Mingxin Zheng
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Qiquan Ye
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Xi Chen
- School of Materials Science and Engineering, Chang'an University, Xi'an 710061, P. R. China
| | - Min Zeng
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Guangjie Song
- CAS Key Laboratory of Engineering Plastics and CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Jun Zhang
- CAS Key Laboratory of Engineering Plastics and CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, P. R. China
| | - Jinying Yuan
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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4
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Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. NANOSCALE HORIZONS 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
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Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
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5
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Fan L, Jiang J, Sun Q, Hong K, Cornel EJ, Zhu Y, Du J. Fluorescent homopolypeptide toroids. Polym Chem 2022. [DOI: 10.1039/d1py01691a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Toroids are important ring-like nanostructures in living systems; intrinsically luminogenic toroids are promising in bioimaging but it is challenging to synthesize such nanoparticles. Herein, we report a fluorescent toroid that...
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6
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Álamo P, Parladé E, López-Laguna H, Voltà-Durán E, Unzueta U, Vazquez E, Mangues R, Villaverde A. Ion-dependent slow protein release from in vivo disintegrating micro-granules. Drug Deliv 2021; 28:2383-2391. [PMID: 34747685 PMCID: PMC8584089 DOI: 10.1080/10717544.2021.1998249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Through the controlled addition of divalent cations, polyhistidine-tagged proteins can be clustered in form of chemically pure and mechanically stable micron-scale particles. Under physiological conditions, these materials act as self-disintegrating protein depots for the progressive release of the forming polypeptide, with potential applications in protein drug delivery, diagnosis, or theragnosis. Here we have explored the in vivo disintegration pattern of a set of such depots, upon subcutaneous administration in mice. These microparticles were fabricated with cationic forms of either Zn, Ca, Mg, or Mn, which abound in the mammalian body. By using a CXCR4-targeted fluorescent protein as a reporter building block we categorized those cations regarding their ability to persist in the administration site and to sustain a slow release of functional protein. Ca2+ and specially Zn2+ have been observed as particularly good promoters of time-prolonged protein leakage. The released polypeptides result is available for selective molecular interactions, such as specific fluorescent labeling of tumor tissues, in which the protein reaches nearly steady levels.
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Affiliation(s)
- Patricia Álamo
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), Barcelona, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Eloi Parladé
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Hèctor López-Laguna
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Eric Voltà-Durán
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Ugutz Unzueta
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), Barcelona, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Esther Vazquez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Ramon Mangues
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain.,Josep Carreras Leukaemia Research Institute (IJC Campus Sant Pau), Barcelona, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
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7
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Skeene K, Khatri K, Soloviev Z, Lapthorn C. Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140697. [PMID: 34246790 DOI: 10.1016/j.bbapap.2021.140697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.
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Affiliation(s)
- Kirsty Skeene
- Biopharm Process Research, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Kshitij Khatri
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Collegeville, PA 19406, USA.
| | - Zoja Soloviev
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Cris Lapthorn
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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8
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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9
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Bolduc J, Koruza K, Luo T, Malo Pueyo J, Vo TN, Ezeriņa D, Messens J. Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities. Redox Biol 2021; 42:101959. [PMID: 33895094 PMCID: PMC8113037 DOI: 10.1016/j.redox.2021.101959] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/07/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.
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Affiliation(s)
- Jesalyn Bolduc
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Katarina Koruza
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Ting Luo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Julia Malo Pueyo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Trung Nghia Vo
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Daria Ezeriņa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium.
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10
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Ardini M, Bellelli A, Williams DL, Di Leandro L, Giansanti F, Cimini A, Ippoliti R, Angelucci F. Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology. Bioconjug Chem 2021; 32:43-62. [PMID: 33411522 PMCID: PMC8023583 DOI: 10.1021/acs.bioconjchem.0c00621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Morpheeins
are proteins that reversibly assemble into different
oligomers, whose architectures are governed by conformational changes
of the subunits. This property could be utilized in bionanotechnology
where the building of nanometric and new high-ordered structures is
required. By capitalizing on the adaptability of morpheeins to create
patterned structures and exploiting their inborn affinity toward inorganic
and living matter, “bottom-up” creation of nanostructures
could be achieved using a single protein building block, which may
be useful as such or as scaffolds for more complex materials. Peroxiredoxins
represent the paradigm of a morpheein that can be applied to bionanotechnology.
This review describes the structural and functional transitions that
peroxiredoxins undergo to form high-order oligomers, e.g., rings,
tubes, particles, and catenanes, and reports on the chemical and genetic
engineering approaches to employ them in the generation of responsive
nanostructures and nanodevices. The usefulness of the morpheeins’
behavior is emphasized, supporting their use in future applications.
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Affiliation(s)
- Matteo Ardini
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Roma "Sapienza", Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - David L Williams
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Luana Di Leandro
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Francesco Giansanti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Annamaria Cimini
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health, and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
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11
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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12
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Wu H, Zhang R, Zhang W, Hong J, Xiang Y, Xu W. Rapid 3-dimensional shape determination of globular proteins by mobility capillary electrophoresis and native mass spectrometry. Chem Sci 2020; 11:4758-4765. [PMID: 34122932 PMCID: PMC8159243 DOI: 10.1039/d0sc01965h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Established high-throughput proteomics methods provide limited information on the stereostructures of proteins. Traditional technologies for protein structure determination typically require laborious steps and cannot be performed in a high-throughput fashion. Here, we report a new medium throughput method by combining mobility capillary electrophoresis (MCE) and native mass spectrometry (MS) for the 3-dimensional (3D) shape determination of globular proteins in the liquid phase, which provides both the geometric structure and molecular mass information of proteins. A theory was established to correlate the ion hydrodynamic radius and charge state distribution in the native mass spectrum with protein geometrical parameters, through which a low-resolution structure (shape) of the protein could be determined. Our test data of 11 different globular proteins showed that this approach allows us to determine the shapes of individual proteins, protein complexes and proteins in a mixture, and to monitor protein conformational changes. Besides providing complementary protein structure information and having mixture analysis capability, this MCE and native MS based method is fast in speed and low in sample consumption, making it potentially applicable in top–down proteomics and structural biology for intact globular protein or protein complex analysis. Using native mass spectrometry and mobility capillary electrophoresis, the ellipsoid dimensions of globular proteins or protein complexes could be measured efficiently.![]()
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Affiliation(s)
- Haimei Wu
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Rongkai Zhang
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Wenjing Zhang
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
| | - Ye Xiang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University Beijng China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology No. 5 South Zhongguancun Street, Haidian Dist Beijing China
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13
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Wang H, Lee M. Switching between Stacked Toroids and Helical Supramolecular Polymers in Aqueous Nanotubules. Macromol Rapid Commun 2020; 41:e2000138. [PMID: 32307804 DOI: 10.1002/marc.202000138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022]
Abstract
Although significant advances have been made in supramolecular tubules, reversible polymerization in the tubular walls while maintaining their intact structure remains a great challenge. Here, reversible helical supramolecular polymerization of stacked toroids is reported, while maintaining tubular structures in aqueous solution. At room temperature, the tubules consist of discrete toroid stackings with hydrophobic interior. Upon heating, the tubules based on toroid stackings undergo a reversible helical supramolecular polymerization to transform into helical tubules by interconnecting between spirally open toroids. The helical polymerization arises from a tilting transition of the closed toroids that transform into spirally open toroids driven by the thermal dehydration of a hydrophilic oligoether dendron surrounding the toroid frameworks.
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Affiliation(s)
- Huaxin Wang
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Myongsoo Lee
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China.,Department of Chemistry, Fudan University, Shanghai, 200438, China
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14
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Shirzadeh M, Poltash ML, Laganowsky A, Russell DH. Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin. Biochemistry 2020; 59:1013-1022. [PMID: 32101399 PMCID: PMC7171973 DOI: 10.1021/acs.biochem.0c00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.
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Affiliation(s)
- Mehdi Shirzadeh
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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15
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Li H, Doruker P, Hu G, Bahar I. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophys J 2020; 118:1782-1794. [PMID: 32130874 DOI: 10.1016/j.bpj.2020.01.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/05/2020] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.
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Affiliation(s)
- Hongchun Li
- Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Research Center for Computer-Aided Drug Discovery, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Guang Hu
- Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China.
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
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16
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Li C, Attanayake K, Valentine SJ, Li P. Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization. Anal Chem 2020; 92:2492-2502. [PMID: 31940176 PMCID: PMC7318871 DOI: 10.1021/acs.analchem.9b03983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.
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Affiliation(s)
- Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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18
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Abstract
Protein nanotechnology research is at the intersection of protein biology and nanotechnology. Protein molecules are repurposed as nanostructures and nanoscaffolds, and nanoscale tools are used to investigate protein assembly and function. In this chapter, a select review is given of some of the recent examples of protein nanostructures, covering both those directly borrowed from biology and those designed for use in nanotechnology. It updates the introductory chapter to Edition 2 of this volume to reflect significant progress in this field. Some strategies to incorporate protein structures into devices are also covered, with the successes and challenges of this interdisciplinary field identified. This provides an overarching framework for the rest of the volume, which details the case studies of some of the protein building blocks that have been designed and produced, along with tips and tools for their incorporation into devices and making functional measurements.
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19
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Abstract
Peroxiredoxins are ubiquitous antioxidant proteins that exhibit a striking variety of quaternary structures, making them appealing building blocks with which nanoscale architectures are created for applications in nanotechnology. The solution environment of the protein, as well as protein sequence, influences the presentation of a particular structure, thereby enabling mesoscopic manipulations that affect arrangments at the nanoscale. This chapter will equip us with the knowledge necessary to not only produce and manipulate peroxiredoxin proteins into desired structures but also to characterize the different structures using dynamic light scattering, analytical centrifugation, and negative stain transmission electron microscopy, thereby setting the stage for us to use these proteins for applications in nanotechnology.
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Affiliation(s)
- Frankie Conroy
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - N Amy Yewdall
- Bio-Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
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20
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Zhang W, Wu H, Zhang R, Fang X, Xu W. Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method. Chem Sci 2019; 10:7779-7787. [PMID: 31588326 PMCID: PMC6761862 DOI: 10.1039/c9sc02039j] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Measuring the conformations and effective charges of proteins in solution is critical for investigating protein bioactivity, but their rapid analysis remains a challenging problem. Here we report a mobility capillary electrophoresis (MCE) based method for the rapid analysis of protein stereo-structures and effective charges in different solution environments. With the capability of mixture separation, MCE measures the hydrodynamic radius of a protein through Taylor dispersion analysis and its effective charge through ion mobility analysis. The experimental results acquired from MCE are then utilized to restrain molecular dynamics simulations, so that the most probable conformation of that protein can be obtained. As proof-of-concept demonstrations, the charge states and structures of five proteins were analyzed under close to native environments. The conformation transitions and charge state variations of bovine serum albumin and lysozyme under different pH conditions were also investigated. This method is promising for high-throughput protein analysis, which could potentially be coupled with mass spectrometry for investigating protein stereo-structures and functions in top-down proteomics.
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Affiliation(s)
- Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
| | - Xiang Fang
- National Institute of Metrology , No. 18, Bei San Huan Dong Lu, Chaoyang Dist , Beijing , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , No. 5 South Zhongguancun Street, Haidian Dist , Beijing , China .
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21
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Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen TH, Capua AD, Bell CE, Ahmer BMM, Lindert S, Wysocki VH, Gopalan V. Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase. J Mol Biol 2019; 431:4497-4513. [PMID: 31493410 DOI: 10.1016/j.jmb.2019.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023]
Abstract
Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including the terminal FraB deglycase. Salmonella mutants lacking FraB are highly attenuated in mouse models of inflammation due to the toxic build-up of the substrate 6-phosphofructose-aspartate (6-P-F-Asp). This toxicity makes Salmonella FraB an appealing drug target, but there is currently little experimental information about its catalytic mechanism. Therefore, we sought to test our postulated mechanism for the FraB-catalyzed deglycation of 6-P-F-Asp (via an enaminol intermediate) to glucose-6-phosphate and aspartate. A FraB homodimer model generated by RosettaCM was used to build substrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putative active site. Five candidate active-site residues-including three expected to participate in substrate binding-were mutated individually and characterized. Native mass spectrometry and ion mobility were used to assess collision cross sections and confirm that the quaternary structure of the mutants mirrored the wild type, and that there are two active sites/homodimer. Our biochemical studies revealed that FraB Glu214Ala, Glu214Asp, and His230Ala were inactive in vitro, consistent with deprotonated-Glu214 and protonated-His230 serving as a general base and a general acid, respectively. Glu214Ala or His230Ala introduced into the Salmonella chromosome by CRISPR/Cas9-mediated genome editing abolished growth on F-Asn. Results from our computational and experimental approaches shed light on the catalytic mechanism of Salmonella FraB and of phosphosugar deglycases in general.
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Affiliation(s)
- Anindita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Nicholas Thomsen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Tien-Hao Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Angela Di Capua
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E Bell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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22
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Steinhaus A, Chakroun R, Müllner M, Nghiem TL, Hildebrandt M, Gröschel AH. Confinement Assembly of ABC Triblock Terpolymers for the High-Yield Synthesis of Janus Nanorings. ACS NANO 2019; 13:6269-6278. [PMID: 31082201 DOI: 10.1021/acsnano.8b09546] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Block copolymers are versatile building blocks for the self-assembly of functional nanostructures in bulk and solution. While spheres, cylinders, and bilayer sheets are thermodynamically preferred shapes and frequently observed, ring-shaped nanoparticles are more challenging to realize due to energetic penalties that originate from their anisotropic curvature. Today, a handful of concepts exist that produce core-shell nanorings, while more complex ( e. g., patchy) nanorings are currently out of reach and have only been predicted theoretically. Here, we demonstrate that confinement assembly of properly designed ABC triblock terpolymers is a general route to synthesize Janus nanorings in high purity. The triblock terpolymer self-assembles in the spherical confinement of nanoemulsion droplets into prolate ellipsoidal microparticles with an axially stacked lamellar-ring ( lr)-morphology. We clarified and visualized this complex, yet well-ordered, morphology with transmission electron tomography. Blocks A and C formed stacks of lamellae with the B microdomain sandwiched in-between as nanorings. Cross-linking of the B-rings allowed disassembly of the microparticles into Janus nanorings carrying two strictly separated polymer brushes of A and C on the top and bottom. Decreasing the B volume leads to Janus spheres and rods, while an increase of B results in perforated and filled Janus disks. The confinement assembly of ABC triblock terpolymers is a general process that can be extended to other block chemistries and will allow to synthesize a large variety of complex micro- and nanoparticles that inspire studies in self-assembly, interfacial stabilization, colloidal packing, and nanomedicine.
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Affiliation(s)
- Andrea Steinhaus
- Physical Chemistry , University of Duisburg-Essen , 47057 Duisburg , Germany
| | - Ramzi Chakroun
- Physical Chemistry , University of Duisburg-Essen , 47057 Duisburg , Germany
| | - Markus Müllner
- Key Center for Polymers and Colloids, School of Chemistry and The University of Sydney Nano Institute (Sydney Nano) , The University of Sydney , Sydney 2006 , New South Wales , Australia
| | - Tai-Lam Nghiem
- Physical Chemistry , University of Duisburg-Essen , 47057 Duisburg , Germany
| | - Marcus Hildebrandt
- Physical Chemistry , University of Duisburg-Essen , 47057 Duisburg , Germany
| | - André H Gröschel
- Physical Chemistry , University of Duisburg-Essen , 47057 Duisburg , Germany
- Center for Nanointegration Duisburg-Essen (CENIDE) , University of Duisburg-Essen , 45127 Essen , Germany
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23
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Conroy F, Rossi T, Ashmead H, Crowther JM, Mitra AK, Gerrard JA. Engineering peroxiredoxin 3 to facilitate control over self-assembly. Biochem Biophys Res Commun 2019; 512:263-268. [PMID: 30885432 DOI: 10.1016/j.bbrc.2019.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Oligomeric proteins are abundant in nature and are useful for a range of nanotechnological applications; however, a key requirement in using these proteins is controlling when and how they form oligomeric assemblies. Often, protein oligomerisation is triggered by various cellular signals, allowing for controllable oligomerisation. An example of this is human peroxiredoxin 3 (Prx), a stable protein that natively forms dimers, dodecameric rings, stacks, and tubes in response to a range of environmental stimuli. Although we know the key environmental stimuli for switching between different oligomeric states of Prx, we still have limited molecular knowledge and control over the formation and size of the protein's stacks and tubes. Here, we have generated a range of Prx mutants with either a decreased or knocked out ability to stack, and used both imaging and solution studies to show that Prx stacks through electrostatic interactions that are stabilised by a hydrogen bonding network. Furthermore, we show that altering the length of the polyhistidine tag will alter the length of the Prx stacks, with longer polyhistidine tags giving longer stacks. Finally, we have analysed the effect a variety of heavy metals have on the oligomeric state of Prx, wherein small transition metals like nickel enhances Prx stacking, while larger positively charged metals like tungstate ions can prevent Prx stacking. This work provides further structural characterisation of Prx, to enhance its use as a platform from which to build protein nanostructures for a variety of applications.
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Affiliation(s)
- Frankie Conroy
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand.
| | - Tatiana Rossi
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Helen Ashmead
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand; Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Jennifer M Crowther
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand.
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24
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Recent advances in metal-organic frameworks for separation and enrichment in proteomics analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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