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Brodmerkel MN, Thiede L, De Santis E, Uetrecht C, Caleman C, Marklund EG. Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Phys Chem Chem Phys 2024; 26:13094-13105. [PMID: 38628116 DOI: 10.1039/d3cp06344e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the gas-phase unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation, together with CIU experiments. The dimers have highly similar structures, but their CIU reveals different stability that can be explained by the different dynamics that arises in response to the activation seen in the simulations, including a part of the sequence with previously observed strain-specific dynamics in solution. Our findings show how similar protein variants can be examined using mass spectrometric techniques in conjunction with atomistic molecular dynamics simulations to reveal differences in stability as well as differences in how and where unfolding takes place upon activation.
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Affiliation(s)
- Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
| | - Lars Thiede
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Charlotte Uetrecht
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Leibniz Institute of Virology (LIV), Notkestrasse 85, 22607 Hamburg, Germany
- Institute of Chemistry and Metabolomics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, 75123 Uppsala, Sweden.
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2
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Kierspel T, Kadek A, Barran P, Bellina B, Bijedic A, Brodmerkel MN, Commandeur J, Caleman C, Damjanović T, Dawod I, De Santis E, Lekkas A, Lorenzen K, Morillo LL, Mandl T, Marklund EG, Papanastasiou D, Ramakers LAI, Schweikhard L, Simke F, Sinelnikova A, Smyrnakis A, Timneanu N, Uetrecht C. Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC. Anal Bioanal Chem 2023:10.1007/s00216-023-04658-y. [PMID: 37014373 PMCID: PMC10329076 DOI: 10.1007/s00216-023-04658-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm-1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.
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Affiliation(s)
- Thomas Kierspel
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany.
| | - Alan Kadek
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany
- Institute of Microbiology of the Czech Academy of Sciences - BIOCEV, Průmyslová 595, Vestec, 252 50, Czech Republic
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Perdita Barran
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Bruno Bellina
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Adi Bijedic
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Maxim N Brodmerkel
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Jan Commandeur
- MS Vision, Televisieweg 40, 1322 AM, Almere, Netherlands
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
- Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, E22607, Hamburg, Germany
| | - Tomislav Damjanović
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Faculty V: School of Life Sciences, University of Siegen, Adolf-Reichwein-Str. 2a, 57076, Siegen, Germany
| | - Ibrahim Dawod
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Alexandros Lekkas
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | | | | | - Thomas Mandl
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
- University of Applied Sciences Technikum Wien, Höchstädtpl. 6, 1200, Vienna, Austria
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Dimitris Papanastasiou
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | - Lennart A I Ramakers
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Lutz Schweikhard
- Institut Für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489, Greifswald, Germany
| | - Florian Simke
- Institut Für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489, Greifswald, Germany
| | - Anna Sinelnikova
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Athanasios Smyrnakis
- Fasmatech, Technological and Scientific Park of Attica Lefkippos, NCSR DEMOKRITOS Patr, Gregoriou E' 27, Neapoleos Str. 153 41, Agia Paraskevi, Attica, Greece
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, 75120, Uppsala, Sweden
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251, Hamburg, Germany.
- Faculty V: School of Life Sciences, University of Siegen, Adolf-Reichwein-Str. 2a, 57076, Siegen, Germany.
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3
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Faizuloev E, Gracheva A, Korchevaya E, Smirnova D, Samoilikov R, Pankratov A, Trunova G, Khokhlova V, Ammour Y, Petrusha O, Poromov A, Leneva I, Svitich O, Zverev V. Cold-adapted SARS-CoV-2 variants with different temperature sensitivity exhibit an attenuated phenotype and confer protective immunity. Vaccine 2023; 41:892-902. [PMID: 36528447 PMCID: PMC9744683 DOI: 10.1016/j.vaccine.2022.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
As novel SARS-CoV-2 Variants of Concern emerge, the efficacy of existing vaccines against COVID-19 is declining. A possible solution to this problem lies in the development of a live attenuated vaccine potentially able of providing cross-protective activity against a wide range of SARS-CoV-2 antigenic variants. Cold-adapted (ca) SARS-CoV-2 variants, Dubrovka-ca-B4 (D-B4) and Dubrovka-ca-D2 (D-D2), were obtained after long-term passaging of the Dubrovka (D) strain in Vero cells at reduced temperatures. Virulence, immunogenicity, and protective activity of SARS-CoV-2 variants were evaluated in experiments on intranasal infection of Syrian golden hamsters (Mesocricetus auratus). In animal model infecting with ca variants, the absence of body weight loss, the significantly lower viral titer and viral RNA concentration in animal tissues, the less pronounced inflammatory lesions in animal lungs as compared with the D strain indicated the reduced virulence of the virus variant. Single intranasal immunization with D-B4 and D-D2 variants induced the production of neutralizing antibodies in hamsters and protected them from infection with the D strain and the development of severe pneumonia. It was shown that for ca SARS-CoV-2 variants, the temperature-sensitive (ts) phenotype was not obligate for virulence reduction. Indeed, the D-B4 variant, which did not possess the ts phenotype but had lost the ability to infect human lung cells Calu-3, exhibited reduced virulence in hamsters. Consequently, the potential phenotypic markers of attenuation of ca SARS-CoV-2 variants are the ca phenotype, the ts phenotype, and the change in species specificity of the virus. This study demonstrates the great potential of SARS-CoV-2 cold adaptation as a strategy to develop a live attenuated COVID-19 vaccine.
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Affiliation(s)
- Evgeny Faizuloev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia; Russian Medical Academy of Continuous Professional Education, Moscow, Russia.
| | | | | | - Daria Smirnova
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Roman Samoilikov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Andrey Pankratov
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Galina Trunova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Varvara Khokhlova
- FSBI NMRRC of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow Oncology Research Institute, Moscow, Russia
| | - Yulia Ammour
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Olga Petrusha
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Artem Poromov
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,Peoples' Friendship University of Russia, Department of Biochemistry, Moscow, Russia
| | - Irina Leneva
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines and Sera, Moscow, Russia,I.M. Sechenov First Moscow State Medical University (Sechenov University), F.F. Erisman Institute of Public Health, Moscow, Russia
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4
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Çakır U, Gabed N, Brunet M, Roucou X, Kryvoruchko I. Mosaic translation hypothesis: chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability. FEBS J 2023; 290:370-378. [PMID: 34743413 DOI: 10.1111/febs.16269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/03/2021] [Accepted: 11/05/2021] [Indexed: 02/05/2023]
Abstract
How many different proteins can be produced from a single spliced transcript? Genome annotation projects overlook the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins, have been shown to carry out important functions in various organisms. AltORFs overlapping refORFs or other altORFs in a different reading frame may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. Specialized ribosomes acting as sensors probably played a central role in this process. Importantly, mosaic translation may be the main source of protein diversity in genomes that lack alternative splicing. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is challenging. Should mosaic translation occur, we would currently highly underestimate the complexity of translation mechanisms and thus the proteome.
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Affiliation(s)
- Umut Çakır
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
| | - Noujoud Gabed
- Cellular and Molecular Biology Department, Oran High School of Biological Sciences (ESSBO), Oran, Algeria
| | - Marie Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, QC, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada
| | - Xavier Roucou
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), QC, Canada.,Department of Biochemistry and Functional Genomics, Université de Sherbrooke, QC, Canada
| | - Igor Kryvoruchko
- Molecular Biology and Genetics Department, Faculty of Arts and Sciences, Boğaziçi University, Istanbul, Turkey
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5
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Laureano RS, Sprooten J, Vanmeerbeerk I, Borras DM, Govaerts J, Naulaerts S, Berneman ZN, Beuselinck B, Bol KF, Borst J, Coosemans A, Datsi A, Fučíková J, Kinget L, Neyns B, Schreibelt G, Smits E, Sorg RV, Spisek R, Thielemans K, Tuyaerts S, De Vleeschouwer S, de Vries IJM, Xiao Y, Garg AD. Trial watch: Dendritic cell (DC)-based immunotherapy for cancer. Oncoimmunology 2022; 11:2096363. [PMID: 35800158 PMCID: PMC9255073 DOI: 10.1080/2162402x.2022.2096363] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dendritic cell (DC)-based vaccination for cancer treatment has seen considerable development over recent decades. However, this field is currently in a state of flux toward niche-applications, owing to recent paradigm-shifts in immuno-oncology mobilized by T cell-targeting immunotherapies. DC vaccines are typically generated using autologous (patient-derived) DCs exposed to tumor-associated or -specific antigens (TAAs or TSAs), in the presence of immunostimulatory molecules to induce DC maturation, followed by reinfusion into patients. Accordingly, DC vaccines can induce TAA/TSA-specific CD8+/CD4+ T cell responses. Yet, DC vaccination still shows suboptimal anti-tumor efficacy in the clinic. Extensive efforts are ongoing to improve the immunogenicity and efficacy of DC vaccines, often by employing combinatorial chemo-immunotherapy regimens. In this Trial Watch, we summarize the recent preclinical and clinical developments in this field and discuss the ongoing trends and future perspectives of DC-based immunotherapy for oncological indications.
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Affiliation(s)
- Raquel S Laureano
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Isaure Vanmeerbeerk
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Daniel M Borras
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stefan Naulaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Zwi N Berneman
- Department of Haematology, Antwerp University Hospital, Edegem, Belgium
- Vaccine and Infectious Disease Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium
| | | | - Kalijn F Bol
- Department of Tumour Immunology, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jannie Borst
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - an Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, ImmunOvar Research Group, Ku Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Angeliki Datsi
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine University, Düsseldorf, Germany
| | - Jitka Fučíková
- Sotio Biotech, Prague, Czech Republic
- Department of Immunology, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Lisa Kinget
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Bart Neyns
- Department of Medical Oncology, UZ Brussel, Brussels, Belgium
| | - Gerty Schreibelt
- Department of Tumour Immunology, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Smits
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium
- Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium
| | - Rüdiger V Sorg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine University, Düsseldorf, Germany
| | - Radek Spisek
- Sotio Biotech, Prague, Czech Republic
- Department of Immunology, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Kris Thielemans
- Laboratory of Molecular and Cellular Therapy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sandra Tuyaerts
- Department of Medical Oncology, UZ Brussel, Brussels, Belgium
- Laboratory of Medical and Molecular Oncology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Steven De Vleeschouwer
- Research Group Experimental Neurosurgery and Neuroanatomy, KU Leuven, Leuven, Belgium
- Department of Neurosurgery, UZ Leuven, Leuven, Belgium
| | - I Jolanda M de Vries
- Department of Tumour Immunology, Radboud Institute for Molecular Life Sciences; Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yanling Xiao
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Abhishek D Garg
- Laboratory of Cell Stress & Immunity, Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
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Abstract
Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of their mass-to-charge ratio (m/z) and charge. Masses are determined for thousands of individual ions, and then the results are binned to give a mass spectrum. Using this approach, accurate mass distributions can be measured for heterogeneous and high-molecular-weight samples that are usually not amenable to analysis by conventional mass spectrometry. Recent applications include heavily glycosylated proteins, protein complexes, protein aggregates such as amyloid fibers, infectious viruses, gene therapies, vaccines, and vesicles such as exosomes.
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Affiliation(s)
- Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47404, United States
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Mustopa AZ, Meilina L, Irawan S, Ekawati N, Fathurahman AT, Triratna L, Kusumawati A, Prastyowati A, Nurfatwa M, Hertati A, Harmoko R. Construction, expression, and in vitro assembly of virus-like particles of L1 protein of human papillomavirus type 52 in Escherichia coli BL21 DE3. J Genet Eng Biotechnol 2022; 20:19. [PMID: 35132511 PMCID: PMC8821762 DOI: 10.1186/s43141-021-00281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022]
Abstract
Abstract
Background
A major discovery in human etiology recognized that cervical cancer is a consequence of an infection caused by some mucosatropic types of human papillomavirus (HPV). Since L1 protein of HPV is able to induce the formation of neutralizing antibodies, it becomes a protein target to develop HPV vaccines. Therefore, this study aims to obtain and analyze the expression of HPV subunit recombinant protein, namely L1 HPV 52 in E. coli BL21 DE3. The raw material used was L1 HPV 52 protein, while the synthetic gene, which is measured at 1473 bp in pD451-MR plasmid, was codon-optimized (ATUM) and successfully integrated into 5643 base pairs (bps) of pETSUMO. Bioinformatic studies were also conducted to analyze B cell epitope, T cell epitope, and immunogenicity prediction for L1HPV52 protein.
Results
The pETSUMO-L1HPV52 construct was successfully obtained in a correct ligation size when it was cut with EcoRI. Digestion by EcoRI revealed a size of 5953 and 1160 bps for both TA cloning petSUMO vector and gene of interest, respectively. Furthermore, the right direction of construct pETSUMO-L1HPV52 was proven by PCR techniques using specific primer pairs then followed by sequencing, which shows 147 base pairs. Characterization of L1 HPV 52 by SDS-PAGE analysis confirms the presence of a protein band at a size of ~55 kDa with 6.12 mg/L of total protein concentration. Observation under by transmission electron microscope demonstrates the formation of VLP-L1 at a size between 30 and 40 nm in assembly buffer under the condition of pH 5.4. Based on bioinformatics studies, we found that there are three B cell epitopes (GFPDTSFYNPET, DYLQMASEPY, KEKFSADLDQFP) and four T cell epitopes (YLQMASEPY, PYGDSLFFF, DSLFFFLRR, MFVRHFFNR). Moreover, an immunogenicity study shows that among all the T cell epitopes, the one that has the highest affinity value is DSLFFFLRR for Indonesian HLAs.
Conclusion
Regarding the achievement on successful formation of L1 HPV52-VLPs, followed by some possibilities found from bioinformatics studies, this study suggests promising results for future development of L1 HPV type 52 vaccine in Indonesia.
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Staudt RE, Carlson RD, Snook AE. Targeting gastrointestinal cancers with chimeric antigen receptor (CAR)-T cell therapy. Cancer Biol Ther 2022; 23:127-133. [PMID: 35129050 PMCID: PMC8820794 DOI: 10.1080/15384047.2022.2033057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The immune system is capable of remarkably potent and specific efficacy against infectious diseases. For decades, investigators sought to leverage those characteristics to create immune-based therapies (immunotherapy) that might be far more effective and less toxic than conventional chemotherapy and radiation therapy for cancer. Those studies revealed many factors and mechanisms underlying the success or failure of cancer immunotherapy, leading to synthetic biology approaches, including CAR-T cell therapy. In this approach, patient T cells are genetically modified to express a chimeric antigen receptor (CAR) that converts T cells of any specificity into tumor-specific T cells that can be expanded to large numbers and readministered to the patient to eliminate cancer cells, including bulky metastatic disease. This approach has been most successful against hematologic cancers, resulting in five FDA approvals to date. Here, we discuss some of the most promising attempts to apply this technology to cancers of the gastrointestinal tract.
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Affiliation(s)
- Ross E Staudt
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Robert D Carlson
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Adam E Snook
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Microbiology & Immunology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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9
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Norovirus-glycan interactions - how strong are they really? Biochem Soc Trans 2021; 50:347-359. [PMID: 34940787 PMCID: PMC9022987 DOI: 10.1042/bst20210526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022]
Abstract
Infection with human noroviruses requires attachment to histo blood group antigens (HBGAs) via the major capsid protein VP1 as a primary step. Several crystal structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being most widely used. However, reported binding affinities are inconsistent. At the extreme, for the same system MS detects binding whereas NMR spectroscopy does not, suggesting a fundamental source of error. In this short essay, we will explain the reason for the observed differences and compile reliable and reproducible binding affinities. We will then highlight how a combination of MS techniques and NMR experiments affords unique insights into the process of HBGA binding by norovirus capsid proteins.
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Zoratto S, Weiss VU, van der Horst J, Commandeur J, Buengener C, Foettinger‐Vacha A, Pletzenauer R, Graninger M, Allmaier G. Molecular weight determination of adeno-associate virus serotype 8 virus-like particle either carrying or lacking genome via native nES gas-phase electrophoretic molecular mobility analysis and nESI QRTOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4786. [PMID: 34608711 PMCID: PMC9285973 DOI: 10.1002/jms.4786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Virus-like particles (VLPs) are proteinaceous shells derived from viruses lacking any viral genomic material. Adeno-associated virus (AAV) is a non-enveloped icosahedral virus used as VLP delivery system in gene therapy (GT). Its success as vehicle for GT is due to its selective tropism, high level of transduction, and low immunogenicity. In this study, two preparations of AAV serotype 8 (AAV8) VLPs either carrying or lacking completely genomic cargo (i.e., non-viral ssDNA) have been investigated by means of a native nano-electrospray gas-phase electrophoretic mobility molecular analyzer (GEMMA) (native nES GEMMA) and native nano-electrospray ionization quadrupole reflectron time-of-flight mass spectrometry (MS) (native nESI QRTOF MS). nES GEMMA is based on electrophoretic mobility principles: single-charge nanoparticles (NPs), that is, AAV8 particle, are separated in a laminar sheath flow of dry, particle-free air and a tunable orthogonal electric field. Thus, the electrophoretic mobility diameter (EMD) of a bio-NP (i.e., diameter of globular nano-objects) is obtained at atmospheric pressure, which can be converted into its MW based on a correlation. First is the native nESI QRTOF. MS's goal is to keep the native biological conformation of an analyte during the passage into the vacuum. Subsequently, highly accurate MW values are obtained from multiple-charged species after deconvolution. However, once applied to the analysis of megadalton species, native MS is challenging and requires customized instrumental modifications not readily available on standard devices. Hence, the analysis of AAV8 VLPs via native MS in our hands did not produce a defined charge state assignment, that is, charge deconvolution for exact MW determination was not possible. Nonetheless, the method we present is capable to estimate the MW of VLPs by combining the results from native nES GEMMA and native ESI QRTOF MS. In detail, our findings show a MW of 3.7 and 5.0 MDa for AAV8 VLPs either lacking or carrying an engineered genome, respectively.
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Affiliation(s)
- Samuele Zoratto
- Institute of Chemical Technologies and AnalyticsTU Wien (Vienna University of Technology)ViennaAustria
| | - Victor U. Weiss
- Institute of Chemical Technologies and AnalyticsTU Wien (Vienna University of Technology)ViennaAustria
| | | | | | - Carsten Buengener
- Pharmaceutical SciencesBaxalta Innovations (part of Takeda)ViennaAustria
| | | | - Robert Pletzenauer
- Pharmaceutical SciencesBaxalta Innovations (part of Takeda)ViennaAustria
| | - Michael Graninger
- Pharmaceutical SciencesBaxalta Innovations (part of Takeda)ViennaAustria
| | - Guenter Allmaier
- Institute of Chemical Technologies and AnalyticsTU Wien (Vienna University of Technology)ViennaAustria
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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