1
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Jalboush SA, Wadsworth ID, Sethi K, Rogers LC, Hollis T, Hall AR. Improving the Performance of Selective Solid-State Nanopore Sensing Using a Polyhistidine-Tagged Monovalent Streptavidin. ACS Sens 2024; 9:1602-1610. [PMID: 38451864 PMCID: PMC11056946 DOI: 10.1021/acssensors.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Solid-state (SS-) nanopore sensing has gained tremendous attention in recent years, but it has been constrained by its intrinsic lack of selectivity. To address this, we previously established a novel SS-nanopore assay that produces translocation signals only when a target biotinylated nucleic acid fragment binds to monovalent streptavidin (MS), a protein variant with a single high-affinity biotin-binding domain. While this approach has enabled selective quantification of diverse nucleic acid biomarkers, sensitivity enhancements are needed to improve the detection of low-abundance translational targets. Because the translocation dynamics that determine assay efficacy are largely governed by constituent charge characteristics, we here incorporate a polyhistidine-tagged MS (hMS) to alter the component detectability. We investigate the effects of buffer pH, salt concentration, and SS-nanopore diameter on the performance with the alternate reagent, achieve significant improvements in measurement sensitivity and selectivity, and expand the range of device dimensions viable for the assay. We used this improvement to detect as little as 1 nM miRNA spiked into human plasma. Overall, our findings improve the potential for broader applications of SS-nanopores in the quantitative analyses of molecular biomarkers.
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Affiliation(s)
- Sara Abu Jalboush
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Ian D. Wadsworth
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - LeAnn C. Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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2
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Yang JE, Wright ER, Kawaoka Y, Kane RS. Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine. Nat Commun 2024; 15:1284. [PMID: 38346966 PMCID: PMC10861510 DOI: 10.1038/s41467-024-45495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protect female hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicit highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protects human ACE2-transgenic female hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Cryo-EM Research Center, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biochemistry, Midwest Center for Cryo-Electron Tomography, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA.
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, 162-8655, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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3
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Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Sci Rep 2024; 14:882. [PMID: 38195620 PMCID: PMC10776792 DOI: 10.1038/s41598-023-50827-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024] Open
Abstract
Molecular interactions are contingent upon the system's dimensionality. Notably, comprehending the impact of dimensionality on protein-protein interactions holds paramount importance in foreseeing protein behaviour across diverse scenarios, encompassing both solution and membrane environments. Here, we unravel interactions among membrane proteins across various dimensionalities by quantifying their binding rates through fluorescence recovery experiments. Our findings are presented through the examination of two protein systems: streptavidin-biotin and a protein complex constituting a bacterial efflux pump. We present here an original approach for gauging a two-dimensional binding constant between membrane proteins embedded in two opposite membranes. The quotient of protein binding rates in solution and on the membrane represents a metric denoting the exploration distance of the interacting sites-a novel interpretation.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Department of Infectious Diseases, Avicenne Hospital, AP-HP, Université Sorbonne Paris Nord, Bobigny, France.
- Université Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and Neuroscience of Paris (IPNP), Paris, France.
| | - Myriam Reffay
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS and Université de Paris Cité, 75205, Paris Cedex 13, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France
| | - Alice Verchère
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Laura Monlezun
- Université Paris Cité, CNRS, Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France
| | - Martin Picard
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 75005, Paris, France
| | - Arnaud Ducruix
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Isabelle Broutin
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Frédéric Pincet
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
| | - Wladimir Urbach
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France.
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4
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Platzer R, Hellmeier J, Göhring J, Perez ID, Schatzlmaier P, Bodner C, Focke‐Tejkl M, Schütz GJ, Sevcsik E, Stockinger H, Brameshuber M, Huppa JB. Monomeric agonist peptide/MHCII complexes activate T-cells in an autonomous fashion. EMBO Rep 2023; 24:e57842. [PMID: 37768718 PMCID: PMC10626418 DOI: 10.15252/embr.202357842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular crowding of agonist peptide/MHC class II complexes (pMHCIIs) with structurally similar, yet per se non-stimulatory endogenous pMHCIIs is postulated to sensitize T-cells for the recognition of single antigens on the surface of dendritic cells and B-cells. When testing this premise with the use of advanced live cell microscopy, we observe pMHCIIs as monomeric, randomly distributed entities diffusing rapidly after entering the APC surface. Synaptic TCR engagement of highly abundant endogenous pMHCIIs is low or non-existent and affects neither TCR engagement of rare agonist pMHCII in early and advanced synapses nor agonist-induced TCR-proximal signaling. Our findings highlight the capacity of single freely diffusing agonist pMHCIIs to elicit the full T-cell response in an autonomous and peptide-specific fashion with consequences for adaptive immunity and immunotherapeutic approaches.
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Affiliation(s)
- René Platzer
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Joschka Hellmeier
- TU Wien, Institute of Applied PhysicsViennaAustria
- Present address:
Max Planck Institute of Biochemistry, Molecular Imaging and BionanotechnologyMartinsriedGermany
| | - Janett Göhring
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Iago Doel Perez
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
- Present address:
Takeda Manufacturing Austria AGViennaAustria
| | - Philipp Schatzlmaier
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | - Clara Bodner
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Margarete Focke‐Tejkl
- Center for Pathophysiology, Infectiology, Immunology, Institute for Pathophysiology and Allergy ResearchMedical University of ViennaViennaAustria
| | | | - Eva Sevcsik
- TU Wien, Institute of Applied PhysicsViennaAustria
| | - Hannes Stockinger
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
| | | | - Johannes B Huppa
- Center for Pathophysiology, Infectiology, Immunology, Institute for Hygiene and Applied ImmunologyMedical University of ViennaViennaAustria
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5
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Halfmann PJ, Loeffler K, Duffy A, Kuroda M, Kawaoka Y, Kane RS. Broad Protection Against Clade 1 Sarbecoviruses After a Single Immunization with Cocktail Spike-Protein-Nanoparticle Vaccine. RESEARCH SQUARE 2023:rs.3.rs-3088907. [PMID: 37461652 PMCID: PMC10350183 DOI: 10.21203/rs.3.rs-3088907/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations such as Pfizer-BioNTech's bivalent vaccine are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protected hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicited highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protected human ACE2-transgenic hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
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Affiliation(s)
- Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Augustine Duffy
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Ravi S. Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
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6
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Frey SJ, Carreño JM, Bielak D, Arsiwala A, Altomare CG, Varner C, Rosen-Cheriyan T, Bajic G, Krammer F, Kane RS. Nanovaccines Displaying the Influenza Virus Hemagglutinin in an Inverted Orientation Elicit an Enhanced Stalk-Directed Antibody Response. Adv Healthc Mater 2023; 12:e2202729. [PMID: 36689343 PMCID: PMC10386890 DOI: 10.1002/adhm.202202729] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/18/2023] [Indexed: 01/24/2023]
Abstract
Despite the availability of licensed vaccines, influenza causes considerable morbidity and mortality worldwide. Current influenza vaccines elicit an immune response that primarily targets the head domain of the viral glycoprotein hemagglutinin (HA). Influenza viruses, however, readily evade this response by acquiring mutations in the head domain. While vaccines that target the more conserved HA stalk may circumvent this problem, low levels of antistalk antibodies are elicited by vaccination, possibly due to the poor accessibility of the stalk domain to B cell receptors. In this work, it is demonstrated that nanoparticles presenting HA in an inverted orientation generate tenfold higher antistalk antibody titers after a prime immunization and fivefold higher antistalk titers after a boost than nanoparticles displaying HA in its regular orientation. Moreover, nanoparticles presenting HA in an inverted orientation elicit a broader antistalk response that reduces mouse weight loss and improves survival after challenge to a greater extent than nanoparticles displaying HA in a regular orientation. Refocusing the antibody response toward conserved epitopes by controlling antigen orientation may enable the design of broadly protective nanovaccines targeting influenza viruses and other pathogens with pandemic potential.
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Affiliation(s)
- Steven J Frey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dominika Bielak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ammar Arsiwala
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chad Varner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tania Rosen-Cheriyan
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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7
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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8
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Batugal T, Pendyala G, Tomasovic L, Varner C, Caplin JD, Page AM, Davis M, Satola SW, García AJ, Kane RS. Engineering active lysostaphin variants that incorporate noncanonical amino acids and characterizing the effects of site-specific PEGylation. Biotechnol Bioeng 2023; 120:1694-1701. [PMID: 36810983 DOI: 10.1002/bit.28360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/11/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
We describe a facile strategy to identify sites for the incorporation of noncanonical amino acids into lysostaphin-an enzyme that degrades the cell wall of Staphylococcus aureus-while retaining stapholytic activity. We used this strategy to generate active variants of lysostaphin incorporating para-azidophenylalanine. The incorporation of this "reactive handle" enabled the orthogonal site-specific modification of the enzyme variants with polyethylene glycol (PEG) using copper-free click cycloaddition. PEGylated lysostaphin variants could retain their stapholytic activity, with the extent of retention depending on the site of modification and the PEG molecular weight. The site-specific modification of lysostaphin could be useful not only for PEGylation to improve biocompatibility but also for the incorporation of the enzyme into hydrogels and other biomaterials and for studies of protein structure and dynamics. Moreover, the approach described herein could be readily applied to identify suitable sites for the incorporation of reactive handles into other proteins of interest.
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Affiliation(s)
- Troy Batugal
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Geetanjali Pendyala
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke Tomasovic
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chad Varner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jeremy D Caplin
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.,Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Alexander M Page
- Department of Medicine, Division of Infectious Diseases and Emory Investigational Clinical Microbiology Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michelle Davis
- Department of Medicine, Division of Infectious Diseases and Emory Investigational Clinical Microbiology Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sarah W Satola
- Department of Medicine, Division of Infectious Diseases and Emory Investigational Clinical Microbiology Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrés J García
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA.,Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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9
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Hellmeier J, Platzer R, Huppa JB, Sevcsik E. A DNA Origami-Based Biointerface to Interrogate the Spatial Requirements for Sensitized T-Cell Antigen Recognition. Methods Mol Biol 2023; 2654:277-302. [PMID: 37106189 DOI: 10.1007/978-1-0716-3135-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
When T cells scan the surface of antigen-presenting cells (APCs), they can detect the presence of just a few antigenic peptide/MHC complexes (pMHCs), in some cases even a single agonist pMHC. These are typically vastly outnumbered by structurally similar yet non-stimulatory endogenous pMHCs. How T cells achieve this enormous sensitivity and selectivity is still not clear, in particular in view of the rather moderate (1-100 μM) affinity that T-cell receptors (TCRs) typically exert for antigenic pMHCs. Experimental approaches that enable the control and quantification of physical input parameters within the context of the immunological synapse to precisely interrogate the molecular consequences of TCR-engagement, appear highly advantageous when searching for better answers.We here describe the implementation of a biointerface that allows to experimentally define molecular distances between T-cell ligands as a means to correlate them with molecular dynamics of antigen engagement, downstream signaling, and the overall T-cell response. The basis of this biointerface is DNA origami nanostructures, which are (i) rigid and highly versatile platforms that can (ii) be embedded as laterally mobile entities within supported lipid bilayers and functionalized (iii) in a site-specific and orthogonal manner with (iv) one or more proteins of choice.
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Affiliation(s)
- Joschka Hellmeier
- Institute of Applied Physics, TU Wien, Vienna, Austria
- Max Planck Institute of Biochemistry, Planegg, Germany
| | - René Platzer
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Johannes B Huppa
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria.
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10
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Wehrum S, Siukstaite L, Williamson DJ, Branson TR, Sych T, Madl J, Wildsmith GC, Dai W, Kempmann E, Ross JF, Thomsen M, Webb ME, Römer W, Turnbull WB. Membrane Fusion Mediated by Non-covalent Binding of Re-engineered Cholera Toxin Assemblies to Glycolipids. ACS Synth Biol 2022; 11:3929-3938. [PMID: 36367814 PMCID: PMC9764410 DOI: 10.1021/acssynbio.2c00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Membrane fusion is essential for the transport of macromolecules and viruses across membranes. While glycan-binding proteins (lectins) often initiate cellular adhesion, subsequent fusion events require additional protein machinery. No mechanism for membrane fusion arising from simply a protein binding to membrane glycolipids has been described thus far. Herein, we report that a biotinylated protein derived from cholera toxin becomes a fusogenic lectin upon cross-linking with streptavidin. This novel reengineered protein brings about hemifusion and fusion of vesicles as demonstrated by mixing of fluorescently labeled lipids between vesicles as well as content mixing of liposomes filled with fluorescently labeled dextran. Exclusion of the complex at vesicle-vesicle interfaces could also be observed, indicating the formation of hemifusion diaphragms. Discovery of this fusogenic lectin complex demonstrates that new emergent properties can arise from simple changes in protein architecture and provides insights into new mechanisms of lipid-driven fusion.
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Affiliation(s)
- Sarah Wehrum
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany
| | - Lina Siukstaite
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany
| | - Daniel J. Williamson
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Thomas R. Branson
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Taras Sych
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany,Freiburg
Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany,Science
for Life Laboratory, Department of Women’s and Children’s
Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Josef Madl
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany,Freiburg
Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Gemma C. Wildsmith
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Wenyue Dai
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Erik Kempmann
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany
| | - James F. Ross
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Maren Thomsen
- School of
Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Michael E. Webb
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..
| | - Winfried Römer
- Faculty
of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany,Bioss-Centre
for Biological Signalling Studies, Albert-Ludwigs-University
Freiburg, Schänzlestraße
18, 79104 Freiburg, Germany,Freiburg
Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany,
| | - W. Bruce Turnbull
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT Leeds, U.K..,
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11
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Halfmann PJ, Frey SJ, Loeffler K, Kuroda M, Maemura T, Armbrust T, Yang JE, Hou YJ, Baric R, Wright ER, Kawaoka Y, Kane RS. Multivalent S2-based vaccines provide broad protection against SARS-CoV-2 variants of concern and pangolin coronaviruses. EBioMedicine 2022; 86:104341. [PMID: 36375316 PMCID: PMC9651965 DOI: 10.1016/j.ebiom.2022.104341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic continues to cause morbidity and mortality worldwide. Most approved COVID-19 vaccines generate a neutralizing antibody response that primarily targets the highly variable receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein. SARS-CoV-2 "variants of concern" have acquired mutations in this domain allowing them to evade vaccine-induced humoral immunity. Recent approaches to improve the breadth of protection beyond SARS-CoV-2 have required the use of mixtures of RBD antigens from different sarbecoviruses. It may therefore be beneficial to develop a vaccine in which the protective immune response targets a more conserved region of the S protein. METHODS Here we have developed a vaccine based on the conserved S2 subunit of the S protein and optimized the adjuvant and immunization regimen in Syrian hamsters and BALB/c mice. We have characterized the efficacy of the vaccine against SARS-CoV-2 variants and other coronaviruses. FINDINGS Immunization with S2-based constructs elicited a broadly cross-reactive IgG antibody response that recognized the spike proteins of not only SARS-CoV-2 variants, but also SARS-CoV-1, and the four endemic human coronaviruses. Importantly, immunization reduced virus titers in respiratory tissues in vaccinated animals challenged with SARS-CoV-2 variants B.1.351 (beta), B.1.617.2 (delta), and BA.1 (omicron) as well as a pangolin coronavirus. INTERPRETATION These results suggest that S2-based constructs can elicit a broadly cross-reactive antibody response resulting in limited virus replication, thus providing a framework for designing vaccines that elicit broad protection against coronaviruses. FUNDING NIH, Japan Agency for Medical Research and Development, Garry Betty/ V Foundation Chair Fund, and NSF.
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Affiliation(s)
- Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Steven J Frey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Tammy Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53711, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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12
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Li H, Liu T, Yang H. Amplifying Intermolecular Events by Streptavidin-Induced Proximity. J Am Chem Soc 2022; 144:11377-11385. [PMID: 35715211 DOI: 10.1021/jacs.2c03666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Weak interactions between biomolecules play important roles in many cellular functions. Structural and kinetic analyses of these interactions, however, have been hindered by the transient nature of such events. Here, we pointed out a general approach to overcome this obstacle─anchoring the molecular partners to streptavidin hosts─and achieved constrained proximity and stoichiometry for the sought-after molecular coupling. We elaborated this idea through a series of DNA hybridization reactions and quantitatively characterized them using single-molecule experiments. Compared to a nominally 1 μM solution, for example, the streptavidin-induced proximity (SIP) amounted to an effective molarity of ∼10-30 μM for the binding partners. There was also a significantly increased proportion of molecular association, manifested in both ensemble population and single-molecule residence time. As an application example, we showed how SIP enabled the observation and quantitative characterization of an unstable complex between Cas9-RNA and noncognate DNA substrates, interactions that had been challenging to characterize previously. Conceptually simple and implementationally robust, SIP was shown to considerably enhance the efficacy in capturing weak interactions and, as demonstrated here, could empower scientists to see the otherwise unseeable.
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Affiliation(s)
- Hao Li
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Tao Liu
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
| | - Haw Yang
- Department of Chemistry, Princeton University,, Princeton, New Jersey 08544, United States
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13
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Hossain MA, Anasti K, Watts B, Cronin K, Derking R, Groschel B, Kane AP, Edwards R, Easterhoff D, Zhang J, Rountree W, Ortiz Y, Saunders K, Schief WR, Sanders RW, Verkoczy L, Reth M, Alam SM. B cells expressing IgM B cell receptors of HIV-1 neutralizing antibodies discriminate antigen affinities by sensing binding association rates. Cell Rep 2022; 39:111021. [PMID: 35767950 PMCID: PMC9837990 DOI: 10.1016/j.celrep.2022.111021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 01/17/2023] Open
Abstract
HIV-1 envelope (Env) proteins designed to induce neutralizing antibody responses allow study of the role of affinities (equilibrium dissociation constant [KD]) and kinetic rates (association/dissociation rates) on B cell antigen recognition. It is unclear whether affinity discrimination during B cell activation is based solely on Env protein binding KD and whether B cells discriminate among proteins of similar affinities that bind with different kinetic rates. Here, we use a panel of Env proteins and Ramos B cell lines expressing immunoglobulin M (IgM) B cell receptors (BCRs) with specificity for CD4-binding-site broadly neutralizing antibodies to study the role of antigen binding kinetic rates on both early (proximal/distal signaling) and late events (BCR/antigen internalization) in B cell activation. Our results support a kinetic model for B cell activation in which Env protein affinity discrimination is based not on overall KD but on sensing of association rate and a threshold antigen-BCR half-life.
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Affiliation(s)
- Md. Alamgir Hossain
- Human Vaccine Institute, Duke University, Durham, NC, USA,These authors contributed equally
| | - Kara Anasti
- Human Vaccine Institute, Duke University, Durham, NC, USA,These authors contributed equally
| | - Brian Watts
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Kenneth Cronin
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Ronald Derking
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Bettina Groschel
- Department of Immunology & Microbiology and Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | | | - R.J. Edwards
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - David Easterhoff
- Human Vaccine Institute, Duke University, Durham, NC, USA,Present address: Moderna, Inc., Cambridge, MA, USA
| | - Jinsong Zhang
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Wes Rountree
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Yaneth Ortiz
- Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Kevin Saunders
- Human Vaccine Institute, Duke University, Durham, NC, USA
| | - William R. Schief
- Department of Immunology & Microbiology and Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, the Netherlands
| | | | - Michael Reth
- Signaling Research Centers BIOSS and CIBSS, Freiburg, Germany,Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - S. Munir Alam
- Human Vaccine Institute, Duke University, Durham, NC, USA,Department of Medicine & Pathology, Duke University, Durham, NC, USA,Lead contact,Correspondence:
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14
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Habibi N, Mauser A, Ko Y, Lahann J. Protein Nanoparticles: Uniting the Power of Proteins with Engineering Design Approaches. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104012. [PMID: 35077010 PMCID: PMC8922121 DOI: 10.1002/advs.202104012] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/12/2021] [Indexed: 05/16/2023]
Abstract
Protein nanoparticles, PNPs, have played a long-standing role in food and industrial applications. More recently, their potential in nanomedicine has been more widely pursued. This review summarizes recent trends related to the preparation, application, and chemical construction of nanoparticles that use proteins as major building blocks. A particular focus has been given to emerging trends related to applications in nanomedicine, an area of research where PNPs are poised for major breakthroughs as drug delivery carriers, particle-based therapeutics or for non-viral gene therapy.
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Affiliation(s)
- Nahal Habibi
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Ava Mauser
- Biointerfaces InstituteDepartment of Biomedical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Yeongun Ko
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Joerg Lahann
- Biointerfaces InstituteDepartments of Chemical EngineeringMaterial Science and EngineeringBiomedical Engineeringand Macromolecular Science and EngineeringUniversity of MichiganAnn ArborMI48109USA
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15
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Ma VPY, Hu Y, Kellner AV, Brockman JM, Velusamy A, Blanchard AT, Evavold BD, Alon R, Salaita K. The magnitude of LFA-1/ICAM-1 forces fine-tune TCR-triggered T cell activation. SCIENCE ADVANCES 2022; 8:eabg4485. [PMID: 35213231 PMCID: PMC8880789 DOI: 10.1126/sciadv.abg4485] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/15/2021] [Indexed: 05/15/2023]
Abstract
T cells defend against cancer and viral infections by rapidly scanning the surface of target cells seeking specific peptide antigens. This key process in adaptive immunity is sparked upon T cell receptor (TCR) binding of antigens within cell-cell junctions stabilized by integrin (LFA-1)/intercellular adhesion molecule-1 (ICAM-1) complexes. A long-standing question in this area is whether the forces transmitted through the LFA-1/ICAM-1 complex tune T cell signaling. Here, we use spectrally encoded DNA tension probes to reveal the first maps of LFA-1 and TCR forces generated by the T cell cytoskeleton upon antigen recognition. DNA probes that control the magnitude of LFA-1 force show that F>12 pN potentiates antigen-dependent T cell activation by enhancing T cell-substrate engagement. LFA-1/ICAM-1 mechanical events with F>12 pN also enhance the discriminatory power of the TCR when presented with near cognate antigens. Overall, our results show that T cells integrate multiple channels of mechanical information through different ligand-receptor pairs to tune function.
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Affiliation(s)
| | - Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Anna V. Kellner
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
| | - Joshua M. Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
| | - Arventh Velusamy
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Aaron T. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
| | - Brian D. Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ronen Alon
- Department of Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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16
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Mohandas N, Kent LM, Raudsepp A, Jameson GB, Williams MAK. Progress toward Plug-and-Play Polymer Strings for Optical Tweezers Experiments: Concatenation of DNA Using Streptavidin Linkers. ACS OMEGA 2022; 7:6427-6435. [PMID: 35224404 PMCID: PMC8867789 DOI: 10.1021/acsomega.2c00198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Streptavidin is a tetrameric protein that is renowned for its strong binding to biotin. The robustness and strength of this noncovalent coupling has led to multitudinous applications of the pairing. Within the streptavidin tetramer, each protein monomer has the potential to specifically bind one biotin-bearing moiety. Herein, by separating various streptavidin species that have had differing numbers of their four potential binding sites blocked, several different types of "linking hub" were obtained, each with a different valency. The identification of these species and the study of the plugging process used to block sites during their preparation were carried out using capillary electrophoresis. Subsequently, a specific species, namely, a trans-divalent linker, in which the two open biotin-binding pockets are approximately opposite one another, was used to concatenate two ∼5 kb pieces of biotin-terminated double-stranded DNA. Following the incubation of this DNA with the prepared linker, a fraction of ∼10 kb strings was identified using gel electrophoresis. Finally, these concatenated DNA strings were stretched in an optical tweezer experiment, demonstrating the potential of the methodology for coupling and extending molecules for use in single-molecule biophysical experiments.
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Affiliation(s)
- Nimisha Mohandas
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Lisa M. Kent
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Allan Raudsepp
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
- Riddet
Institute, Massey University, Palmerston North 4442, New Zealand
| | - Martin A. K. Williams
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
- Riddet
Institute, Massey University, Palmerston North 4442, New Zealand
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17
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Ayan E, Yuksel B, Destan E, Ertem FB, Yildirim G, Eren M, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Cohen A, Doukov T, Sierra RG, Dağ Ç, DeMirci H. Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature. Commun Biol 2022; 5:73. [PMID: 35058563 PMCID: PMC8776744 DOI: 10.1038/s42003-021-02903-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/28/2021] [Indexed: 11/11/2022] Open
Abstract
Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.
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Affiliation(s)
- Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Fatma Betul Ertem
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Gunseli Yildirim
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Meryem Eren
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | | | - Anton Barty
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Gihan K Ketawala
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Aina Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Çağdaş Dağ
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research, Koc University, 34450, Istanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
- Koc University Isbank Center for Infectious Diseases (KUISCID), 34010, Istanbul, Turkey.
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18
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Monitoring protein conformational changes using fluorescent nanoantennas. Nat Methods 2022; 19:71-80. [PMID: 34969985 DOI: 10.1038/s41592-021-01355-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/10/2021] [Indexed: 01/03/2023]
Abstract
Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as a spectroscopic technique to sense and report protein conformational changes through noncovalent dye-protein interactions. Using experiments and molecular simulations, we detect and characterize five distinct conformational states of intestinal alkaline phosphatase, including the transient enzyme-substrate complex. We also explored the universality of the nanoantenna strategy with another model protein, Protein G and its interaction with antibodies, and demonstrated a rapid screening strategy to identify efficient nanoantennas. These versatile nanoantennas can be used with diverse dyes to monitor small and large conformational changes, suggesting that they could be used to characterize diverse protein movements or in high-throughput screening applications.
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19
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Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
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Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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20
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Avraham O, Bayer EA, Livnah O. Wilavidin* - a novel member of the avidin family that forms unique biotin-binding hexamers. FEBS J 2021; 289:1700-1714. [PMID: 34726340 DOI: 10.1111/febs.16259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 11/28/2022]
Abstract
Nature's optimization of protein functions is a highly intricate evolutionary process. In addition to optimal tertiary folding, the intramolecular recognition among the monomers that generate higher-order quaternary arrangements is driven by stabilizing interactions that have a pivotal role for ideal activity. Homotetrameric avidin and streptavidin are regularly utilized in many applications, whereby their ultra-high affinity toward biotin is dependent on their quaternary arrangements. In recent years, a new subfamily of avidins was discovered that comprises homodimers rather than tetramers, in which the high affinity toward biotin is maintained. Intriguingly, several of the respective dimers have been shown to assemble into higher-order cylindrical hexamers or octamers that dissociate into dimers upon biotin binding. Here, we present wilavidin, a newly discovered member of the dimeric subfamily, forming hexamers in the apo form, which are uniquely maintained upon biotin binding with six high-affinity binding sites. Removal of the short C-terminal segment of wilavidin resulted in the presence of the dimer only, thus emphasizing the role of this segment in stabilizing the hexamer. Utilization of a hexavalent biotin-binding form of avidin would be beneficial for expanding the biotechnological toolbox. Additionally, this unique family of dimeric avidins and their propensity to oligomerize to hexamers or octamers can serve as a basis for protein oligomerization and intermonomeric recognition as well as cumulative interactions that determine molecular assemblies.
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Affiliation(s)
- Orly Avraham
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.,Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
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21
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Schmid S, Stömmer P, Dietz H, Dekker C. Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations. NATURE NANOTECHNOLOGY 2021; 16:1244-1250. [PMID: 34462599 DOI: 10.1038/s41565-021-00958-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Many strategies have been pursued to trap and monitor single proteins over time to detect the molecular mechanisms of these essential nanomachines. Single-protein sensing with nanopores is particularly attractive because it allows label-free high-bandwidth detection on the basis of ion currents. Here we present the nanopore electro-osmotic trap (NEOtrap) that allows trapping and observing single proteins for hours with submillisecond time resolution. The NEOtrap is formed by docking a DNA-origami sphere onto a passivated solid-state nanopore, which seals off a nanocavity of a user-defined size and creates an electro-osmotic flow that traps nearby particles irrespective of their charge. We demonstrate the NEOtrap's ability to sensitively distinguish proteins on the basis of size and shape, and discriminate between nucleotide-dependent protein conformations, as exemplified by the chaperone protein Hsp90. Given the experimental simplicity and capacity for label-free single-protein detection over the broad bio-relevant time range, the NEOtrap opens new avenues to study the molecular kinetics underlying protein function.
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Affiliation(s)
- Sonja Schmid
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | - Pierre Stömmer
- Physik Department, Technische Universität München, Garching near Munich, Germany
| | - Hendrik Dietz
- Physik Department, Technische Universität München, Garching near Munich, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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22
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Hellmeier J, Platzer R, Mühlgrabner V, Schneider MC, Kurz E, Schütz GJ, Huppa JB, Sevcsik E. Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins. ACS NANO 2021; 15:15057-15068. [PMID: 34463486 PMCID: PMC8482763 DOI: 10.1021/acsnano.1c05411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNA origami structures provide flexible scaffolds for the organization of single biomolecules with nanometer precision. While they find increasing use for a variety of biological applications, the functionalization with proteins at defined stoichiometry, high yield, and under preservation of protein function remains challenging. In this study, we applied single molecule fluorescence microscopy in combination with a cell biological functional assay to systematically evaluate different strategies for the site-specific decoration of DNA origami structures, focusing on efficiency, stoichiometry, and protein functionality. Using an activating ligand of the T-cell receptor (TCR) as the protein of interest, we found that two commonly used methodologies underperformed with regard to stoichiometry and protein functionality. While strategies employing tetravalent wildtype streptavidin for coupling of a biotinylated TCR-ligand yielded mixed populations of DNA origami structures featuring up to three proteins, the use of divalent (dSAv) or DNA-conjugated monovalent streptavidin (mSAv) allowed for site-specific attachment of a single biotinylated TCR-ligand. The most straightforward decoration strategy, via covalent DNA conjugation, resulted in a 3-fold decrease in ligand potency, likely due to charge-mediated impairment of protein function. Replacing DNA with charge-neutral peptide nucleic acid (PNA) in a ligand conjugate emerged as the coupling strategy with the best overall performance in our study, as it produced the highest yield with no multivalent DNA origami structures and fully retained protein functionality. With our study we aim to provide guidelines for the stoichiometrically defined, site-specific functionalization of DNA origami structures with proteins of choice serving a wide range of biological applications.
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Affiliation(s)
| | - René Platzer
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Vanessa Mühlgrabner
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | | | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, Oxford, OX3 7FY, U.K.
| | | | - Johannes B. Huppa
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Eva Sevcsik
- Institute
of Applied Physics, TU Wien, Vienna, 1060, Austria
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23
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Zhang B, Ryan E, Wang X, Lindsay S. Probing Bioelectronic Connections Using Streptavidin Molecules with Modified Valency. J Am Chem Soc 2021; 143:15139-15144. [PMID: 34499834 PMCID: PMC8458255 DOI: 10.1021/jacs.1c05569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As molecular electronic components, proteins are distinguished by a remarkably long electronic decay length (∼10 nm) together with high contact resistance and extreme sensitivity to the chemical details of the contact. As a consequence, the conductance of even a large bioelectronic assembly is largely controlled by the conductance of the contacts. Streptavidin is a versatile linker protein that can tether together biotinylated electrodes and biotinylated proteins but with an ambiguity about the contact geometry that arises from its four possible binding sites for biotin. Here, we use engineered streptavidin tetramers, selected to contain a defined ratio of active monomers to "dead" monomers so as to define the biotin binding sites. We find a strong dependence of conductance on the separation of the biotin molecules, consistent with a short-range tunneling interaction within the streptavidin and in contrast to the long-range transport observed inside larger proteins. Hexaglutamate tails label the active monomers, and the additional negative charge enhances conductance significantly. This effect is quantitatively accounted for by an electronic resonance in the protein conductance.
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Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe AZ 87287, USA
| | - Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe AZ 87287, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe AZ 87287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe AZ 87287, USA
- School of Molecular Sciences, Arizona State University, Tempe AZ 87287, USA
- Department of Physics, Arizona State University, Tempe AZ 87287, USA
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24
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Liu HY, Kumar R, Zhong C, Gorji S, Paniushkina L, Masood R, Wittel UA, Fuchs H, Nazarenko I, Hirtz M. Rapid Capture of Cancer Extracellular Vesicles by Lipid Patch Microarrays. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2008493. [PMID: 34309083 DOI: 10.1002/adma.202008493] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/12/2021] [Indexed: 06/13/2023]
Abstract
Extracellular vesicles (EVs) contain various bioactive molecules such as DNA, RNA, and proteins, and play a key role in the regulation of cancer progression. Furthermore, cancer-associated EVs carry specific biomarkers and can be used in liquid biopsy for cancer detection. However, it is still technically challenging and time consuming to detect or isolate cancer-associated EVs from complex biofluids (e.g., blood). Here, a novel EV-capture strategy based on dip-pen nanolithography generated microarrays of supported lipid membranes is presented. These arrays carry specific antibodies recognizing EV- and cancer-specific surface biomarkers, enabling highly selective and efficient capture. Importantly, it is shown that the nucleic acid cargo of captured EVs is retained on the lipid array, providing the potential for downstream analysis. Finally, the feasibility of EV capture from patient sera is demonstrated. The demonstrated platform offers rapid capture, high specificity, and sensitivity, with only a small need in analyte volume and without additional purification steps. The platform is applied in context of cancer-associated EVs, but it can easily be adapted to other diagnostic EV targets by use of corresponding antibodies.
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Affiliation(s)
- Hui-Yu Liu
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Chunting Zhong
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Saleh Gorji
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Joint Research Laboratory Nanomaterials (KIT and TUD) at Technische Universität Darmstadt (TUD), Jovanka-Bontschits-Str. 2, 64287, Darmstadt, Germany
| | - Liliia Paniushkina
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, Faculty of Medicine, University of Freiburg, Breisacher Straße 115 B, 79106, Freiburg, Germany
| | - Ramsha Masood
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, Faculty of Medicine, University of Freiburg, Breisacher Straße 115 B, 79106, Freiburg, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, Centre of Surgery, Medical Centre, Faculty of Medicine, University of Freiburg, Breisacher Str. 86, 79110, Freiburg, Germany
| | - Harald Fuchs
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Physikalisches Institut & Center for Nanotechnology (CeNTech), Westfälische Wilhelms-Universität, Wilhelm-Klemm-Straße 10, 48149, Münster, Germany
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, Faculty of Medicine, University of Freiburg, Breisacher Straße 115 B, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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25
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Castro A, Carreño JM, Duehr J, Krammer F, Kane RS. Refocusing the Immune Response to Selected Epitopes on a Zika Virus Protein Antigen by Nanopatterning. Adv Healthc Mater 2021; 10:e2002140. [PMID: 33929789 DOI: 10.1002/adhm.202002140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/27/2021] [Indexed: 12/11/2022]
Abstract
Infections with Zika virus (ZIKV) are linked to the development of severe central nervous system disorders, but the need for a ZIKV vaccine remains unmet. Although the design of vaccines that elicit antibodies targeting domain III (DIII) of the ZIKV envelope (E) protein as an antigen is an attractive strategy, poorly neutralizing or cross-reactive antibodies that target the E protein may lead to antibody-dependent enhancement of disease. It is therefore decided to use the previously reported nanopatterning technique, which combines the site-specific incorporation of non-canonical amino acids with site-specific functionalization of the protein with polyethylene glycol (PEG), to shield selected epitopes on DIII. Two different nanopatterned DIII variants are designed and characterized and demonstrate that epitope shielding with PEG completely inhibits the binding of epitope-specific antibodies in vitro. Furthermore, immunization with multivalent nanopatterned DIII antigens results in the refocusing of the antibody response toward the exposed epitopes on the protein surface and away from potentially enhancing epitopes. This ability to redirect the antibody response toward targeted regions of the DIII protein should be useful for the design of effective and safe ZIKV vaccines.
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Affiliation(s)
- Ana Castro
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology Atlanta GA 30332 USA
| | - Juan Manuel Carreño
- Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - James Duehr
- Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Florian Krammer
- Department of Microbiology Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology Atlanta GA 30332 USA
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26
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Zahid OK, Rivas F, Wang F, Sethi K, Reiss K, Bearden S, Hall AR. Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2021; 35:102407. [PMID: 33905828 PMCID: PMC8238847 DOI: 10.1016/j.nano.2021.102407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/31/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease.
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Affiliation(s)
- Osama K Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Felipe Rivas
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Fanny Wang
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Katherine Reiss
- Department of Engineering, Wake Forest University, Winston-Salem, NC, USA
| | - Samuel Bearden
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA; Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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27
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Sethi K, Dailey GP, Zahid OK, Taylor EW, Ruzicka JA, Hall AR. Direct Detection of Conserved Viral Sequences and Other Nucleic Acid Motifs with Solid-State Nanopores. ACS NANO 2021; 15:8474-8483. [PMID: 33914524 PMCID: PMC8801185 DOI: 10.1021/acsnano.0c10887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The rapid and reliable recognition of nucleic acid sequences is essential to a broad range of fields including genotyping, gene expression analysis, and pathogen screening. For viral detection in particular, the capability is critical for optimal therapeutic response and preventing disease transmission. Here, we report an approach for detecting identifying sequence motifs within genome-scale single-strand DNA and RNA based on solid-state nanopores. By designing DNA oligonucleotide probes with complementarity to target sequences within a target genome, we establish a protocol to yield affinity-tagged duplex molecules the same length as the probe only if the target is present. The product can subsequently be bound to a protein chaperone and analyzed quantitatively with a selective solid-state nanopore assay. We first use a model DNA genome (M13mp18) to validate the approach, showing the successful isolation and detection of multiple target sequences simultaneously. We then demonstrate the protocol for the detection of RNA viruses by identifying and targeting a highly conserved sequence within human immunodeficiency virus (HIV-1B).
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Affiliation(s)
- Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Gabrielle P. Dailey
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Osama K. Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Ethan W. Taylor
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jan A. Ruzicka
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC 27268, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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28
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Chiba S, Frey SJ, Halfmann PJ, Kuroda M, Maemura T, Yang JE, Wright ER, Kawaoka Y, Kane RS. Multivalent nanoparticle-based vaccines protect hamsters against SARS-CoV-2 after a single immunization. Commun Biol 2021; 4:597. [PMID: 34011948 PMCID: PMC8134492 DOI: 10.1038/s42003-021-02128-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
The COVID-19 pandemic continues to wreak havoc as worldwide SARS-CoV-2 infection, hospitalization, and death rates climb unabated. Effective vaccines remain the most promising approach to counter SARS-CoV-2. Yet, while promising results are emerging from COVID-19 vaccine trials, the need for multiple doses and the challenges associated with the widespread distribution and administration of vaccines remain concerns. Here, we engineered the coat protein of the MS2 bacteriophage and generated nanoparticles displaying multiple copies of the SARS-CoV-2 spike (S) protein. The use of these nanoparticles as vaccines generated high neutralizing antibody titers and protected Syrian hamsters from a challenge with SARS-CoV-2 after a single immunization with no infectious virus detected in the lungs. This nanoparticle-based vaccine platform thus provides protection after a single immunization and may be broadly applicable for protecting against SARS-CoV-2 and future pathogens with pandemic potential. Chiba et al. describe the use of MS2 bacteriophage coat proteins to develop nanocarriers that display the SARS-CoV-2 spike proteins multivalently for vaccine applications. The vaccine elicited high neutralizing antibody titers and protected Syrian hamsters from virus infection after a single immunization.
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Affiliation(s)
- Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Steven J Frey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Tadashi Maemura
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Cryo-EM Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA. .,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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29
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Hellmeier J, Platzer R, Eklund AS, Schlichthaerle T, Karner A, Motsch V, Schneider MC, Kurz E, Bamieh V, Brameshuber M, Preiner J, Jungmann R, Stockinger H, Schütz GJ, Huppa JB, Sevcsik E. DNA origami demonstrate the unique stimulatory power of single pMHCs as T cell antigens. Proc Natl Acad Sci U S A 2021; 118:e2016857118. [PMID: 33468643 PMCID: PMC7848602 DOI: 10.1073/pnas.2016857118] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
T cells detect with their T cell antigen receptors (TCRs) the presence of rare agonist peptide/MHC complexes (pMHCs) on the surface of antigen-presenting cells (APCs). How extracellular ligand binding triggers intracellular signaling is poorly understood, yet spatial antigen arrangement on the APC surface has been suggested to be a critical factor. To examine this, we engineered a biomimetic interface based on laterally mobile functionalized DNA origami platforms, which allow for nanoscale control over ligand distances without interfering with the cell-intrinsic dynamics of receptor clustering. When targeting TCRs via stably binding monovalent antibody fragments, we found the minimum signaling unit promoting efficient T cell activation to consist of two antibody-ligated TCRs within a distance of 20 nm. In contrast, transiently engaging antigenic pMHCs stimulated T cells robustly as well-isolated entities. These results identify pairs of antibody-bound TCRs as minimal receptor entities for effective TCR triggering yet validate the exceptional stimulatory potency of single isolated pMHC molecules.
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Affiliation(s)
| | - Rene Platzer
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Alexandra S Eklund
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | | | | | - Elke Kurz
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Victor Bamieh
- Institute of Applied Physics, TU Wien, 1040 Vienna, Austria
| | | | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
| | - Hannes Stockinger
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Johannes B Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, 1040 Vienna, Austria;
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30
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Glazier R, Shinde P, Ogasawara H, Salaita K. Spectroscopic Analysis of a Library of DNA Tension Probes for Mapping Cellular Forces at Fluid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2145-2164. [PMID: 33417432 DOI: 10.1021/acsami.0c09774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Oligonucleotide-based probes offer the highest spatial resolution, force sensitivity, and molecular specificity for cellular tension sensing and have been developed to measure a variety of molecular forces mediated by individual receptors in T cells, platelets, fibroblasts, B-cells, and immortalized cancer cell lines. These fluorophore-oligonucleotide conjugate probes are designed with a stem-loop structure that engages cell receptors and reversibly unfolds due to mechanical strain. With the growth of recent work bridging molecular mechanobiology and biomaterials, there is a need for a detailed spectroscopic analysis of DNA tension probes that are used for cellular imaging. In this manuscript, we conducted an analysis of 19 DNA hairpin-based tension probe variants using molecular dynamics simulations, absorption spectroscopy, and fluorescence imaging (epifluorescence and fluorescence lifetime imaging microscopy). We find that tension probes are highly sensitive to their molecular design, including donor and acceptor proximity and pairing, DNA stem-loop structure, and conjugation chemistry. We demonstrate the impact of these design features using a supported lipid bilayer model of podosome-like adhesions. Finally, we discuss the requirements for tension imaging in various biophysical contexts and offer a series of experimental recommendations, thus providing a guide for the design and application of DNA hairpin-based molecular tension probes.
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Affiliation(s)
- Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Pushkar Shinde
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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31
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Martinent R, Du D, López-Andarias J, Sakai N, Matile S. Oligomers of Cyclic Oligochalcogenides for Enhanced Cellular Uptake. Chembiochem 2020; 22:253-259. [PMID: 32975867 DOI: 10.1002/cbic.202000630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/24/2020] [Indexed: 12/20/2022]
Abstract
Monomeric cyclic oligochalcogenides (COCs) are emerging as attractive transporters to deliver substrates of interest into the cytosol through thiol-mediated uptake. The objective of this study was to explore COC oligomers. We report a systematic evaluation of monomers, dimers, and trimers of asparagusic, lipoic, and diselenolipoic acid as well as their supramolecular monomers, dimers, trimers, and tetramers. COC dimers were more than twice as active as the monomers on both the covalent and noncovalent levels, whereas COC trimers were not much better than dimers. These trends might suggest that thiol-mediated uptake of COCs is synergistic over both short and long distances, that is, it involves more than two COCs and more than one membrane protein, although other interpretations cannot be excluded at this level of complexity. These results thus provide attractive perspectives for structural evolution as well as imminent use in practice. Moreover, they validate automated HC-CAPA as an invaluable method to collect comprehensive data on cytosolic delivery within a reasonable time at a level of confidence that is otherwise inconceivable.
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Affiliation(s)
- Rémi Martinent
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Dongchen Du
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Javier López-Andarias
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
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32
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Platzer R, Rossboth BK, Schneider MC, Sevcsik E, Baumgart F, Stockinger H, Schütz GJ, Huppa JB, Brameshuber M. Unscrambling fluorophore blinking for comprehensive cluster detection via photoactivated localization microscopy. Nat Commun 2020; 11:4993. [PMID: 33020470 PMCID: PMC7536177 DOI: 10.1038/s41467-020-18726-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
Determining nanoscale protein distribution via Photoactivated Localization Microscopy (PALM) mandates precise knowledge of the applied fluorophore's blinking properties to counteract overcounting artifacts that distort the resulting biomolecular distributions. Here, we present a readily applicable methodology to determine, optimize and quantitatively account for the blinking behavior of any PALM-compatible fluorophore. Using a custom-designed platform, we reveal complex blinking of two photoswitchable fluorescence proteins (PS-CFP2 and mEOS3.2) and two photoactivatable organic fluorophores (PA Janelia Fluor 549 and Abberior CAGE 635) with blinking cycles on time scales of several seconds. Incorporating such detailed information in our simulation-based analysis package allows for robust evaluation of molecular clustering based on individually recorded single molecule localization maps.
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Affiliation(s)
- René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | | | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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33
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Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt M, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Sci Immunol 2020; 5:5/49/eabc3979. [PMID: 32646852 DOI: 10.1126/sciimmunol.abc3979] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022]
Abstract
The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1-/- mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.
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Affiliation(s)
- Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Máté G Kiss
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Frieda Kage
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christina Rashkova
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Stephanie Stahnke
- Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Michael Caldera
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Rico Chandra Ardy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Birgit Hoeger
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Block
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - David Medgyesi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Celine Sin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sepideh Shahkarami
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Renate Kain
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Vahid Ziaee
- Pediatric Rheumatology Research Group, Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran
| | - Peter Hammerl
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Loïc Dupré
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,Center for Pathophysiology of Toulouse Purpan, INSERM UMR1043, CNRS UMR5282, Paul Sabatier University, Toulouse, France
| | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Alexis Lomakin
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Klemens Rottner
- Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.,Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christoph J Binder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Theresia E B Stradal
- Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Kaan Boztug
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria. .,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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34
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Transmembrane protein rotaxanes reveal kinetic traps in the refolding of translocated substrates. Commun Biol 2020; 3:159. [PMID: 32246060 PMCID: PMC7125113 DOI: 10.1038/s42003-020-0840-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/20/2020] [Indexed: 01/22/2023] Open
Abstract
Understanding protein folding under conditions similar to those found in vivo remains challenging. Folding occurs mainly vectorially as a polypeptide emerges from the ribosome or from a membrane translocon. Protein folding during membrane translocation is particularly difficult to study. Here, we describe a single-molecule method to characterize the folded state of individual proteins after membrane translocation, by monitoring the ionic current passing through the pore. We tag both N and C termini of a model protein, thioredoxin, with biotinylated oligonucleotides. Under an electric potential, one of the oligonucleotides is pulled through a α-hemolysin nanopore driving the unfolding and translocation of the protein. We trap the protein in the nanopore as a rotaxane-like complex using streptavidin stoppers. The protein is subjected to cycles of unfolding-translocation-refolding switching the voltage polarity. We find that the refolding pathway after translocation is slower than in bulk solution due to the existence of kinetic traps. Feng et al address the technical challenge of monitoring the protein folding during membrane translocation. Using thioredoxin as a model and with electric potential driving its translocation through single a-hemolysin nanopore, they observe that after translocation, folding is slower than in bulk due to existence of kinetic traps.
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35
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Abstract
The complex of the small molecule biotin and the homotetrameric protein streptavidin is key to a broad range of biotechnological applications. Therefore, the behavior of this extraordinarily high-affinity interaction under mechanical force is intensively studied by single-molecule force spectroscopy. Recently, steered molecular dynamics simulations have identified a low force pathway for the dissociation of biotin from streptavidin, which involves partial unfolding of the N-terminal β-sheet structure of monovalent streptavidin's functional subunit. Based on these results, we now introduced two mutations (T18C,A33C) in the functional subunit of monovalent streptavidin to establish a switchable connection (disulfide bridge) between the first two β-strands to prevent this unfolding. In atomic force microscopy-based single-molecule force spectroscopy experiments, we observed unbinding forces of about 350 pN (at a force-loading rate of 10 nN s-1) for pulling a single biotin out of an N-terminally anchored monovalent streptavidin binding pocket - about 1.5-fold higher compared with what has been reported for N-terminal force loading of native monovalent streptavidin. Upon addition of a reducing agent, the unbinding forces dropped back to 200 pN, as the disulfide bridge was destroyed. Switching from reducing to oxidizing buffer conditions, the inverse effect was observed. Our work illustrates how the mechanics of a receptor-ligand system can be tuned by engineering the receptor protein far off the ligand-binding pocket.
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Affiliation(s)
- Leonard C Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany.
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36
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Krndija D, Fairhead M. IGF1R undergoes active and directed centripetal transport on filopodia upon receptor activation. Biochem J 2019; 476:3583-3593. [PMID: 31738383 DOI: 10.1042/bcj20190665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022]
Abstract
Filopodia are thin, actin-based membrane protrusions with roles in sensing external mechanical and chemical cues, such as growth factor gradients in tissues. It was proposed that the chemical sensing role of filopodia is achieved through clearance of activated signaling receptors from filopodia. Type I insulin-like growth factor receptor (IGF1R) is a key regulator of normal development and growth, as well as tumor development and progression. Its biological roles depend on its activation upon IGF1 binding at the cell membrane. IGF1R behavior at the cell membrane and in particular in filopodia, has not been established. We found that IGF1 activation led to a gradual reduction in IGF1R puncta in filopodia, and that this clearance depended on actin, non-muscle myosin II, and IGF1R kinase activity. Using single particle tracking of filopodial IGF1R, we established that ligand-free IGF1R undergoes non-directional unidimensional diffusion along the filopodium. Moreover, after initial diffusion, the ligand-bound IGF1R is actively transported along the filopodium towards the filopodium base, and consequently cleared from the filopodium. Our results show that IGF1R can move directionally on the plasma membrane protrusions, supporting a sensory role for filopodia in interpreting local IGF1 gradients.
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Affiliation(s)
- Denis Krndija
- Department of Biochemistry, University of Oxford, Oxford, U.K
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37
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Denham EM, Barton MI, Black SM, Bridge MJ, de Wet B, Paterson RL, van der Merwe PA, Goyette J. A generic cell surface ligand system for studying cell-cell recognition. PLoS Biol 2019; 17:e3000549. [PMID: 31815943 PMCID: PMC6922461 DOI: 10.1371/journal.pbio.3000549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/19/2019] [Accepted: 11/12/2019] [Indexed: 01/11/2023] Open
Abstract
Dose-response experiments are a mainstay of receptor biology studies and can reveal valuable insights into receptor function. Such studies of receptors that bind cell surface ligands are currently limited by the difficulty in manipulating the surface density of ligands at a cell–cell interface. Here, we describe a generic cell surface ligand system that allows precise manipulation of cell surface ligand densities over several orders of magnitude. These densities are robustly quantifiable, a major advance over previous studies. We validate the system for a range of immunoreceptors, including the T-cell receptor (TCR), and show that this generic ligand stimulates via the TCR at a similar surface density as its native ligand. We also extend our work to the activation of chimeric antigen receptors. This novel system allows the effect of varying the surface density, valency, dimensions, and affinity of the ligand to be investigated. It can be readily broadened to other receptor–cell surface ligand interactions and will facilitate investigation into the activation of, and signal integration between, cell surface receptors. This study describes a generic cell-surface ligand system that allows precise manipulation of ligand densities, valency, dimensions, and affinity. The system is validated for a range of immunoreceptors, including the T-cell receptor, and can be readily broadened to other cell-surface receptor-ligand interactions.
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Affiliation(s)
- Eleanor M. Denham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Michael I. Barton
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Susannah M. Black
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Marcus J. Bridge
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ben de Wet
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Rachel L. Paterson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - P. Anton van der Merwe
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- * E-mail: (JG); (PAvdM)
| | - Jesse Goyette
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (JG); (PAvdM)
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38
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Liao YH, Lin CH, Cheng CY, Wong WC, Juo JY, Hsieh CL. Monovalent and Oriented Labeling of Gold Nanoprobes for the High-Resolution Tracking of a Single-Membrane Molecule. ACS NANO 2019; 13:10918-10928. [PMID: 31259529 DOI: 10.1021/acsnano.9b01176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-molecule tracking is a powerful method to study molecular dynamics in living systems including biological membranes. High-resolution single-molecule tracking requires a bright and stable signal, which has typically been facilitated by nanoparticles due to their superb optical properties. However, there are concerns about using a nanoparticle to label a single molecule because of its relatively large size and the possibility of cross-linking multiple target molecules, both of which could affect the original molecular dynamics. In this work, using various labeling schemes, we investigate the effects using nanoparticles to measure the diffusion of single-membrane molecules. By conjugating a low density of streptavidin (sAv) to gold nanoparticles (AuNPs) of different sizes (10, 15, 20, 30, and 40 nm), we isolate and quantify the effect of the particle size on the diffusion of biotinylated lipids in supported lipid bilayers (SLBs). We find that single sAv tends to cross-link two biotinylated lipids, leading to a much slower diffusion in SLBs. We further demonstrate a simple and robust strategy for the monovalent and oriented labeling of a single lipid molecule with a AuNP by using naturally dimeric rhizavidin (rAv) as a bridge, thus connecting the biotinylated nanoparticle surface and biotinylated target molecule. The rAv-AuNP conjugate demonstrates fast and free diffusion in SLBs (2-3 μm2/s for rAv-AuNP sizes of 10-40 nm), which is comparable to the diffusion of dye-labeled lipids, indicating that the adverse size and cross-linking effects are successfully avoided. We also note that the diffusion of dye-labeled lipids critically depends on the choice of dye, which could report different diffusion coefficients by about 20% (2.2 μm2/s of ATTO647N and 2.6 μm2/s of ATTO532). By comparing the diffusion of the uniformly and randomly oriented labeling of a single lipid molecule with a AuNP, we conclude that oriented labeling is favorable for measuring the diffusion of single-membrane molecules. Our work shows that the measured diffusion of the membrane molecule is highly sensitive to the molecular design of the cross-linker for labeling. The demonstrated approach of monovalent and oriented AuNP labeling provides the opportunity to study single-molecule membrane dynamics at much higher spatiotemporal resolutions and, most importantly, without labeling artifacts.
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Affiliation(s)
- Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Wai Cheng Wong
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Jz-Yuan Juo
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS) , Academia Sinica , Taipei 10617 , Taiwan
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39
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Liu X, Zhang Y, Nagel R, Reisner W, Dunbar WB. Controlling DNA Tug-of-War in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901704. [PMID: 31192541 DOI: 10.1002/smll.201901704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a "tug-of-war" whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug-of-war state is limited purely by diffusive sliding of the DNA between the pores. A tug-of-war state is produced on 76.8% of molecules that are captured with a maximum two-order of magnitude increase in average pore translocation time relative to the average time for single-pore translocation. Moreover, the translocation slow-down is quantified as a function of voltage tuning and it is shown that the slow-down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual-pore applications include genome mapping and enzyme-free sequencing.
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Affiliation(s)
- Xu Liu
- Ontera, Inc., Santa Cruz, CA, 95060, USA
| | - Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | | | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
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40
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Bearden S, Wang F, Hall AR. Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection. Anal Chem 2019; 91:7996-8001. [PMID: 31144812 DOI: 10.1021/acs.analchem.9b01873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biotin-streptavidin bond is the strongest noncovalent bond in nature and is thus used extensively in biotechnology applications. However, the difficulty of releasing the bond without high temperatures or corrosive solutions can be a barrier to applications involving nucleic acids and other delicate substrates. Here, room-temperature phenol is employed to release biotin-tagged DNA constructs from streptavidin rapidly and efficiently. It is demonstrated that synthetic biotinylated DNA can be recovered at yields approaching 100% from both solution-phase and bead-bound streptavidin with as little as 12% (v/v) phenol, leaving the biotin tag active and reusable after extraction. As an application of this recovery method, biotinylated DNA fragments are isolated from a mixed solution to provide selectivity for solid-state nanopore detection.
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Affiliation(s)
- Samuel Bearden
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States
| | - Fanny Wang
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States
| | - Adam R Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences , Wake Forest School of Medicine , Winston-Salem , North Carolina 27101 , United States.,Comprehensive Cancer Center , Wake Forest School of Medicine , Winston-Salem , North Carolina 27157 , United States
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41
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Abstract
Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.
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Affiliation(s)
- Alberto Osuna Gálvez
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
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42
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Molecular basis of chromatin remodeling by Rhp26, a yeast CSB ortholog. Proc Natl Acad Sci U S A 2019; 116:6120-6129. [PMID: 30867290 DOI: 10.1073/pnas.1818163116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
CSB/ERCC6 belongs to an orphan subfamily of SWI2/SNF2-related chromatin remodelers and plays crucial roles in gene expression, DNA damage repair, and the maintenance of genome integrity. The molecular basis of chromatin remodeling by Cockayne syndrome B protein (CSB) is not well understood. Here we investigate the molecular mechanism of chromatin remodeling by Rhp26, a Schizosaccharomyces pombe CSB ortholog. The molecular basis of chromatin remodeling and nucleosomal epitope recognition by Rhp26 is distinct from that of canonical chromatin remodelers, such as imitation switch protein (ISWI). We reveal that the remodeling activities are bidirectionally regulated by CSB-specific motifs: the N-terminal leucine-latch motif and the C-terminal coupling motif. Rhp26 remodeling activities depend mainly on H4 tails and to a lesser extent on H3 tails, but not on H2A and H2B tails. Rhp26 promotes the disruption of histone cores and the release of free DNA. Finally, we dissected the distinct contributions of two Rhp26 C-terminal regions to chromatin remodeling and DNA damage repair.
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43
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Wu SC, Wang C, Chin J, Wong SL. A bio-coupling approach using a dextran-binding domain to immobilize an engineered streptavidin to Sephadex for easy preparation of affinity matrix. Sci Rep 2019; 9:3359. [PMID: 30833609 PMCID: PMC6399347 DOI: 10.1038/s41598-019-40044-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
An engineered streptavidin, SAVSBPM18 with reversible biotin binding capability, has been successfully applied to purify biotinylated and streptavidin-binding peptide (SBP) tagged proteins. To simplify the preparation for the SAVSBPM18 affinity matrix without chemical conjugation, two bio-coupling approaches were developed based on a 14-kDa dextran-binding domain (DBD) from a Leuconostoc mesenteroides dextransucrase. The first approach offers simplicity for bio-coupling by creating a direct fusion, SAVSBPM18-Linker-DBD. Purification of the fusion from crude extract and its immobilization to Sephadex can be consolidated in one-step. The second approach aims at flexibility. A SnoopCatcher (SC) was fused to DBD to create SC-Linker-DBD. This fusion can covalently capture any recombinant proteins tagged with a SnoopTag (ST) including SAVSBPM18-Linker-ST via the formation of an isopeptide bond at the interface through the SnoopCatcher-SnoopTag interaction. Although monomeric DBD binds to dextran with nanomolar affinity, DBD tetramerized via streptavidin (SAVSBPM18-Linker-ST·SC-Linker-DBD) showed an even tighter binding to Sephadex. The majority of the fluorescently labelled DBD tetramers were retained on the Sephadex surface even after four months. Affinity columns generated using either approach effectively purified both SBP-tagged and biotinylated proteins. These columns are reusable and functional even after a year of frequent use.
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Affiliation(s)
- Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Chris Wang
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,Biology Program, Faculty of Arts & Science, Ambrose University, 150 Ambrose Circle SW, Calgary, Alberta, T3H 0L5, Canada
| | - Jonathan Chin
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Chamma I, Sainlos M, Thoumine O. Biophysical mechanisms underlying the membrane trafficking of synaptic adhesion molecules. Neuropharmacology 2019; 169:107555. [PMID: 30831159 DOI: 10.1016/j.neuropharm.2019.02.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/14/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
Abstract
Adhesion proteins play crucial roles at synapses, not only by providing a physical trans-synaptic linkage between axonal and dendritic membranes, but also by connecting to functional elements including the pre-synaptic neurotransmitter release machinery and post-synaptic receptors. To mediate these functions, adhesion proteins must be organized on the neuronal surface in a precise and controlled manner. Recent studies have started to describe the mobility, nanoscale organization, and turnover rate of key synaptic adhesion molecules including cadherins, neurexins, neuroligins, SynCAMs, and LRRTMs, and show that some of these proteins are highly mobile in the plasma membrane while others are confined at sub-synaptic compartments, providing evidence for different regulatory pathways. In this review article, we provide a biophysical view of the diffusional trapping of adhesion molecules at synapses, involving both extracellular and intracellular protein interactions. We review the methodology underlying these measurements, including biomimetic systems with purified adhesion proteins, means to perturb protein expression or function, single molecule imaging in cultured neurons, and analytical models to interpret the data. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Ingrid Chamma
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France
| | - Matthieu Sainlos
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France
| | - Olivier Thoumine
- Univ. Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000, Bordeaux, France.
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Bartolami E, Basagiannis D, Zong L, Martinent R, Okamoto Y, Laurent Q, Ward TR, Gonzalez‐Gaitan M, Sakai N, Matile S. Diselenolane‐Mediated Cellular Uptake: Efficient Cytosolic Delivery of Probes, Peptides, Proteins, Artificial Metalloenzymes and Protein‐Coated Quantum Dots. Chemistry 2019; 25:4047-4051. [DOI: 10.1002/chem.201805900] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/29/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Eline Bartolami
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
| | - Dimitris Basagiannis
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
| | - Lili Zong
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
- Current Address: School of Chemistry and Chemical EngineeringSoutheast University Nanjing 210096 China
| | - Rémi Martinent
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
| | - Yasunori Okamoto
- Department of ChemistryUniversity of Basel Basel Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
| | - Quentin Laurent
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of Basel Basel Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
| | - Marcos Gonzalez‐Gaitan
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
| | - Naomi Sakai
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
| | - Stefan Matile
- National Centre of Competence in Research (NCCR) Chemical Biology, School of Chemistry and BiochemistryUniversity of Geneva CH-1211 Geneva Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering CH-4002 Basel Switzerland
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Waner MJ, Hiznay JM, Mustovich AT, Patton W, Ponyik C, Mascotti DP. Streptavidin cooperative allosterism upon binding biotin observed by differential changes in intrinsic fluorescence. Biochem Biophys Rep 2019; 17:127-131. [PMID: 30805560 PMCID: PMC6372923 DOI: 10.1016/j.bbrep.2018.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/02/2022] Open
Abstract
While the binding of biotin by streptavidin does not appear to be cooperative in the traditional sense of altered binding strength, it has been suggested that it may be cooperative in terms of differential structural changes in the protein. In this work we present intrinsic tryptophan fluorescence data as evidence of a cooperative structural change. The technique involves examination of the differences in fluorescence emission corresponding to distinct tryptophan populations accompanying protein-ligand binding. Specifically we note that the 335 nm emission population (i.e. more hydrophobic) saturates prior to the saturation of the 350 nm emission population commonly used in the standard binding activity assay. We also note that the wavelength of maximum emission, total integrated fluorescence emission and full width at half maximum during the titration of ligand into streptavidin also reach saturation before the expected 4:1 stoichiometric end point. This suggests that the binding of the first 3 biotins effect greater structural changes in the protein than the final ligand. Structurally sensitive intrinsic Trp fluorescence changes upon biotin addition. Key features of this fluorescence stops changing prior to full biotin saturation. This suggests that ligand-induced structural changes are allosteric. We introduce use of ‘cooperative allosterism’ to distinguish from traditional usage.
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Goujon A, Straková K, Sakai N, Matile S. Streptavidin interfacing as a general strategy to localize fluorescent membrane tension probes in cells. Chem Sci 2019; 10:310-319. [PMID: 30713639 PMCID: PMC6333237 DOI: 10.1039/c8sc03620a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
To image the mechanical properties of biological membranes, twisted push-pull mechanophores that respond to membrane tension by planarization in the ground state have been introduced recently. For their application in biological systems, these so-called fluorescent flippers will have to be localized to specific environments of cellular membranes. In this report, we explore streptavidin as a versatile connector between biotinylated flipper probes and biotinylated targets. Fluorescence spectroscopy and microscopy with LUVs and GUVs reveal the specific conditions needed for desthiobiotin-loaded streptavidin to deliver biotinylated flippers selectively to biotinylated membranes. Selectivity for biotinylated plasma membranes is also observed in HeLa cells, confirming the compatibility of this strategy with biological systems. Streptavidin interfacing does not affect the mechanosensitivity of the flipper probes, red shift in the excitation maximum and fluorescence lifetime increase with membrane order and tension, as demonstrated, inter alia, using FLIM.
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Affiliation(s)
- Antoine Goujon
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Karolína Straková
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Naomi Sakai
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
| | - Stefan Matile
- School of Chemistry and Biochemistry , National Centre of Competence in Research (NCCR) Chemical Biology , University of Geneva , Geneva , Switzerland . ; http://www.unige.ch/sciences/chiorg/matile/
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Villares A, Moreau C, Cathala B. Star-like Supramolecular Complexes of Reducing-End-Functionalized Cellulose Nanocrystals. ACS OMEGA 2018; 3:16203-16211. [PMID: 31458256 PMCID: PMC6643679 DOI: 10.1021/acsomega.8b02559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/16/2018] [Indexed: 05/27/2023]
Abstract
In this work, we take advantage of the parallel organization of cellulose chains in cellulose I yielding an inherent chemical asymmetry of cellulose nanocrystals, i.e., reducing vs nonreducing end, to selectively modify only one end of these rigid rodlike crystals to be used as a linking point for the formation of supramolecular structures. We have prepared biotin-functionalized tunicate cellulose nanocrystals at the reducing end capable of forming new complex supramolecular hierarchies by the addition of the protein streptavidin. Biotin-streptavidin coupling was chosen because streptavidin has a multivalency of four and the biotin-streptavidin bond is known to be highly selective and stable. Hence, streptavidin molecules would link up to four cellulose nanocrystals through their biotin-modified reducing end. Two biotin derivatives were studied, consisting of an anchoring group, i.e., amine or hydrazine; the biotin moiety; and the linker between them. Results show that the length of the linker significantly affects the bond between the biotinylated cellulose nanocrystals and streptavidin, and a certain chain length is necessary for the supramolecular assembly of several cellulose nanocrystals by streptavidin.
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Affiliation(s)
- Ana Villares
- INRA, UR1268 Biopolymères
Interactions Assemblages, Rue de la Géraudière, 44316 Nantes, France
| | - Céline Moreau
- INRA, UR1268 Biopolymères
Interactions Assemblages, Rue de la Géraudière, 44316 Nantes, France
| | - Bernard Cathala
- INRA, UR1268 Biopolymères
Interactions Assemblages, Rue de la Géraudière, 44316 Nantes, France
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Yoon HR, Choi H, Choi YA, Kim JA, Jung J, Kim HM, Jung Y. Fabrication of Oligomeric Avidin Scaffolds for Valency-Controlled Surface Display of Functional Ligands. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hye Ryeon Yoon
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
| | - Hyeongjoo Choi
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
| | - Yoon-Aa Choi
- Bionano Health Guard Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
| | - Jung A. Kim
- Graduate School of Nanoscience and Technology; KAIST; Korea
| | - Juyeon Jung
- Bionano Health Guard Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
- Hazards Monitoring Bionano Research Center; KRIBB; Daejeon 34141 Korea
- Nanobiotechnology Major; KRIBB School of Engineering; UST; Daejeon 34113 Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering; KAIST; Korea
| | - Yongwon Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
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50
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Yoon HR, Choi H, Choi YA, Kim JA, Jung J, Kim HM, Jung Y. Fabrication of Oligomeric Avidin Scaffolds for Valency-Controlled Surface Display of Functional Ligands. Angew Chem Int Ed Engl 2018; 57:12410-12414. [DOI: 10.1002/anie.201805749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/14/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Hye Ryeon Yoon
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
| | - Hyeongjoo Choi
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
| | - Yoon-Aa Choi
- Bionano Health Guard Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
| | - Jung A. Kim
- Graduate School of Nanoscience and Technology; KAIST; Korea
| | - Juyeon Jung
- Bionano Health Guard Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 34141 Korea
- Hazards Monitoring Bionano Research Center; KRIBB; Daejeon 34141 Korea
- Nanobiotechnology Major; KRIBB School of Engineering; UST; Daejeon 34113 Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering; KAIST; Korea
| | - Yongwon Jung
- Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Korea
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