1
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Sripada SA, Hosseini M, Ramesh S, Wang J, Ritola K, Menegatti S, Daniele MA. Advances and opportunities in process analytical technologies for viral vector manufacturing. Biotechnol Adv 2024; 74:108391. [PMID: 38848795 DOI: 10.1016/j.biotechadv.2024.108391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/14/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Viral vectors are an emerging, exciting class of biologics whose application in vaccines, oncology, and gene therapy has grown exponentially in recent years. Following first regulatory approval, this class of therapeutics has been vigorously pursued to treat monogenic disorders including orphan diseases, entering hundreds of new products into pipelines. Viral vector manufacturing supporting clinical efforts has spurred the introduction of a broad swath of analytical techniques dedicated to assessing the diverse and evolving panel of Critical Quality Attributes (CQAs) of these products. Herein, we provide an overview of the current state of analytics enabling measurement of CQAs such as capsid and vector identities, product titer, transduction efficiency, impurity clearance etc. We highlight orthogonal methods and discuss the advantages and limitations of these techniques while evaluating their adaptation as process analytical technologies. Finally, we identify gaps and propose opportunities in enabling existing technologies for real-time monitoring from hardware, software, and data analysis viewpoints for technology development within viral vector biomanufacturing.
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Affiliation(s)
- Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Mahshid Hosseini
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA
| | - Srivatsan Ramesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Junhyeong Wang
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA
| | - Kimberly Ritola
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Neuroscience Center, Brain Initiative Neurotools Vector Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Biomanufacturing Training and Education Center, North Carolina State University, 890 Main Campus Dr, Raleigh, NC 27695, USA.
| | - Michael A Daniele
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA.
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2
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by mass photometry. SOFT MATTER 2024; 20:5509-5515. [PMID: 38832814 PMCID: PMC11254546 DOI: 10.1039/d3sm01702h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Nathaniel J S Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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3
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Hitzelhammer F, Dostálová A, Zykov I, Platzer B, Conrad-Billroth C, Juffmann T, Hohenester U. Unified Simulation Platform for Interference Microscopy. ACS PHOTONICS 2024; 11:2745-2756. [PMID: 39036062 PMCID: PMC11258784 DOI: 10.1021/acsphotonics.4c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/23/2024]
Abstract
Interferometric scattering microscopy is a powerful technique that enables various applications, such as mass photometry and particle tracking. Here, we present a numerical toolbox to simulate images obtained in interferometric scattering, coherent bright-field, and dark-field microscopies. The scattered fields are calculated using a boundary element method, facilitating the simulation of arbitrary sample geometries and substrate layer structures. A fully vectorial model is used for simulating the imaging setup. We demonstrate excellent agreement between our simulations and experiments for different shapes of scatterers and excitation angles. Notably, for angles near the Brewster angle, we observe a contrast enhancement which may be beneficial for nanosensing applications. The software is available as a matlab toolbox.
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Affiliation(s)
- Felix Hitzelhammer
- Institute
of Physics, University of Graz Universitätsplatz
5, 8010 Graz, Austria
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
| | - Anežka Dostálová
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
- Department
of Optics Faculty of Science, Palacký
University, 17. Listopadu
12, 77900 Olomouc, Czech Republic
| | - Ilia Zykov
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
| | - Barbara Platzer
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
| | - Clara Conrad-Billroth
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
| | - Thomas Juffmann
- University
of Vienna, Faculty of Physics, VCQ, 1090 Vienna, Austria
- University
of Vienna, Max Perutz Laboratories, Department of Structural and Computational
Biology, 1030 Vienna, Austria
| | - Ulrich Hohenester
- Institute
of Physics, University of Graz Universitätsplatz
5, 8010 Graz, Austria
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4
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Shaw JB, Harvey SR, Du C, Xu Z, Edgington RM, Olmedillas E, Saphire EO, Wysocki VH. Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583498. [PMID: 38496594 PMCID: PMC10942452 DOI: 10.1101/2024.03.07.583498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We illustrate the utility of native mass spectrometry (nMS) combined with a fast, tunable gas-phase charge reduction, electron capture charge reduction (ECCR), for the characterization of protein complex topology and glycoprotein heterogeneity. ECCR efficiently reduces the charge states of tetradecameric GroEL, illustrating Orbitrap m/z measurements to greater than 100,000 m/z. For pentameric C-reactive protein and tetradecameric GroEL, our novel device combining ECCR with surface induced dissociation (SID) reduces the charge states and yields more topologically informative fragmentation. This is the first demonstration that ECCR yields more native-like SID fragmentation. ECCR also significantly improved mass and glycan heterogeneity measurements of heavily glycosylated SARS-CoV-2 spike protein trimer and thyroglobulin dimer. Protein glycosylation is important for structural and functional properties and plays essential roles in many biological processes. The immense heterogeneity in glycosylation sites and glycan structure poses significant analytical challenges that hinder a mechanistic understanding of the biological role of glycosylation. Without ECCR, average mass determination of glycoprotein complexes is available only through charge detection mass spectrometry or mass photometry. With narrow m/z selection windows followed by ECCR, multiple glycoform m/z values are apparent, providing quick global glycoform profiling and providing a future path for glycan localization on individual intact glycoforms.
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Affiliation(s)
- Jared B. Shaw
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588
| | - Sophie R. Harvey
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
| | - Chen Du
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Zhixin Xu
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Regina M. Edgington
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Eduardo Olmedillas
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92037
| | - Vicki H. Wysocki
- Native Mass Spectrometry Guided Structural Biology Center, Ohio State University, Columbus, OH 43210
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
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5
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Velasco L, Islam AN, Kundu K, Oi A, Reinhard BM. Two-color interferometric scattering (iSCAT) microscopy reveals structural dynamics in discrete plasmonic molecules. NANOSCALE 2024; 16:11696-11704. [PMID: 38860984 PMCID: PMC11189637 DOI: 10.1039/d4nr01288g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
Plasmonic molecules are discrete assemblies of noble metal nanoparticles (NPs) that are of interest as transducers in optical nanosensors. So far, NPs with diameters of ∼40 nm have been the preferred building blocks for plasmonic molecules intended as optical single molecule sensors due to difficulties associated with detecting smaller NPs through elastic scattering in conventional darkfield microscopy. Here, we apply 405 nm, 445 nm two-color interferometric scattering (iSCAT) microscopy to characterize polyethylene glycol (PEG) tethered dimers of 10 nm and 20 nm Ag NPs and their monomers. Dimers of both NP sizes can be discerned from their respective monomers through changes in the average iSCAT contrast. In the case of 20 nm Ag NPs, dimer formation induces a change in the sign of the iSCAT contrast, providing a characteristic signal for detecting binding events. 20 nm Ag NP dimers with 0.4 kDa and 3.4 kDa polyethylene glycol (PEG) spacers show iSCAT contrast distributions with significantly different averages on both wavelength channels. The iSCAT contrast measured for individual PEG-tethered 10 nm or 20 nm NP dimers as a function of time shows contrast fluctuations indicative of a rich structural dynamics in the assembled plasmonic molecules, which provides an additional metric to discern dimers from monomers and paves the path to a new class of interferometric plasmon rulers.
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Affiliation(s)
- Leslie Velasco
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Aniqa N Islam
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Koustav Kundu
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Aidan Oi
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02459, USA.
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6
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Wang Q, Wang Q, Qi Z, Moeller W, Wysocki VH, Sun L. Native proteomics by capillary zone electrophoresis-mass spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590970. [PMID: 38712154 PMCID: PMC11071496 DOI: 10.1101/2024.04.24.590970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Native proteomics aims to measure endogenous proteoforms and protein complexes under a near physiological condition using native mass spectrometry (nMS) coupled with liquid-phase separation techniques. Native proteomics should provide the most accurate bird's-eye view of proteome dynamics within cells, which is fundamental for understanding almost all biological processes. nMS has been widely employed to characterize well-purified protein complexes. However, there are only very few trials of utilizing nMS to measure proteoforms and protein complexes in a complex sample (i.e., a whole cell lysate), and those studies are either too time and labor-consuming or only able to detect small proteoforms or protein complexes. Here, we pioneer the native proteomics measurement of large proteoforms or protein complexes up to 400 kDa from a complex proteome via online coupling of native capillary zone electrophoresis (nCZE) to an ultra-high mass range Orbitrap mass spectrometer (UHMR). The nCZE-MS technique enabled the measurement of a 115-kDa standard protein complex while consuming only about 100 pg of protein material, indicating the extremely high sensitivity of the technique. nCZE-MS analysis of an E . coli cell lysate detected 76 and 21 proteoforms or protein complexes in a mass range of 30-400 kDa and over 110 kDa, respectively, in a single run while consuming only 50-ng protein material. The mass distribution of detected proteoforms or protein complexes agreed well with that from mass photometry measurement. This work represents a technical breakthrough of native proteomics for measuring complex proteomes, suggesting that nCZE-MS might be developed as a central technique for native proteomics.
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7
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572878. [PMID: 38187562 PMCID: PMC10769409 DOI: 10.1101/2023.12.21.572878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Nathaniel J. S. Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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8
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Kowal MD, Seifried TM, Brouwer CC, Tavakolizadeh H, Olsén E, Grant E. Electrophoretic Deposition Interferometric Scattering Mass Photometry. ACS NANO 2024; 18:10388-10396. [PMID: 38567867 DOI: 10.1021/acsnano.3c09221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Interferometric scattering microscopy (iSCAT) has rapidly developed as a quantitative tool for the label-free detection of single macromolecules and nanoparticles. In practice, this measurement records the interferometric scattering signal of individual nanoparticles in solution as they land and stick on a coverslip, exhibiting an intensity that varies linearly with particle volume and an adsorption rate that reflects the solution-phase transport kinetics of the system. Together, such measurements provide a multidimensional gauge of the particle size and concentration in solution over time. However, the landing kinetics of particles in solution also manifest a measurement frequency limitation imposed by the slow long-range mobility of particle diffusion to the measurement interface. Here we introduce an effective means to overcome the inherent diffusion-controlled sampling limitation of spontaneous mass photometry. We term this methodology electrophoretic deposition interferometric scattering microscopy (EPD-iSCAT). This approach uses a coverslip supporting a conductive thin film of indium tin oxide (ITO). Charging this ITO film to a potential of around +1 V electrophoretically draws charged nanoparticles from solution and binds them in the focal plane of the microscope. Regulating this potential offers a direct means of controlling particle deposition. Thus, we find for a 0.1 nM solution of 50 nm polystyrene nanoparticles that the application of +1 V to an EPD-iSCAT coverslip assembly drives an electrophoretic deposition rate constant of 1.7 s-1 μm-2 nM-1. Removal of the potential causes deposition to cease. This user control of EPD-iSCAT affords a means to apply single-molecule mass photometry to monitor long-term changes in solution, owing to slow kinetic processes. In contrast with conventional coverslips chemically derivatized with charged thin films, EPD-iSCAT maintains a deposition rate that varies linearly with the bulk concentration.
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Affiliation(s)
- Matthew D Kowal
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Teresa M Seifried
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Carraugh C Brouwer
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hooman Tavakolizadeh
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Erik Olsén
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Edward Grant
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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9
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Zhou X, Chieng A, Wang S. Label-Free Optical Imaging of Nanoscale Single Entities. ACS Sens 2024; 9:543-554. [PMID: 38346398 PMCID: PMC10990724 DOI: 10.1021/acssensors.3c02526] [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: 02/24/2024]
Abstract
The advancement of optical microscopy technologies has achieved imaging of nanoscale objects, including nanomaterials, virions, organelles, and biological molecules, at the single entity level. Recently developed plasmonic and scattering based optical microscopy technologies have enabled label-free imaging of single entities with high spatial and temporal resolutions. These label-free methods eliminate the complexity of sample labeling and minimize the perturbation of the analyte native state. Additionally, these imaging-based methods can noninvasively probe the dynamics and functions of single entities with sufficient throughput for heterogeneity analysis. This perspective will review label-free single entity imaging technologies and discuss their principles, applications, and key challenges.
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Affiliation(s)
- Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Andy Chieng
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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10
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Peters M, McIntosh D, Branzan Albu A, Ying C, Gordon R. Label-Free Tracking of Proteins through Plasmon-Enhanced Interference. ACS NANOSCIENCE AU 2024; 4:69-75. [PMID: 38406310 PMCID: PMC10885339 DOI: 10.1021/acsnanoscienceau.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 02/27/2024]
Abstract
Single unmodified biomolecules in solution can be observed and characterized by interferometric imaging approaches; however, Rayleigh scattering limits this to larger proteins (typically >30 kDa). We observe real-time image tracking of unmodified proteins down to 14 kDa using interference imaging enhanced by surface plasmons launched at an aperture in a metal film. The larger proteins show slower diffusion, quantified by tracking. When the diffusing protein is finally trapped by the nanoaperture, we perform complementary power spectral density and noise amplitude analysis, which gives information about the protein. This approach allows for rapid protein characterization with minimal sample preparation and opens the door to characterizing protein interactions in real time.
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Affiliation(s)
- Matthew Peters
- Department
of Electrical Engineering, University of
Victoria, Victoria, British Columbia V8W 2Y2, Canada
- Centre
for Advanced Materials & Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Declan McIntosh
- Department
of Electrical Engineering, University of
Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Alexandra Branzan Albu
- Department
of Electrical Engineering, University of
Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Cuifeng Ying
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science & Technology, Nottingham
Trent University, Nottingham NG11 8NS, U.K.
| | - Reuven Gordon
- Department
of Electrical Engineering, University of
Victoria, Victoria, British Columbia V8W 2Y2, Canada
- Centre
for Advanced Materials & Related Technologies (CAMTEC), University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
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11
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Olsén E, García Rodríguez B, Skärberg F, Parkkila P, Volpe G, Höök F, Sundås Midtvedt D. Dual-Angle Interferometric Scattering Microscopy for Optical Multiparametric Particle Characterization. NANO LETTERS 2024; 24:1874-1881. [PMID: 38295760 PMCID: PMC10870763 DOI: 10.1021/acs.nanolett.3c03539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/15/2024]
Abstract
Traditional single-nanoparticle sizing using optical microscopy techniques assesses size via the diffusion constant, which requires suspended particles to be in a medium of known viscosity. However, these assumptions are typically not fulfilled in complex natural sample environments. Here, we introduce dual-angle interferometric scattering microscopy (DAISY), enabling optical quantification of both size and polarizability of individual nanoparticles (radius <170 nm) without requiring a priori information regarding the surrounding media or super-resolution imaging. DAISY achieves this by combining the information contained in concurrently measured forward and backward scattering images through twilight off-axis holography and interferometric scattering (iSCAT). Going beyond particle size and polarizability, single-particle morphology can be deduced from the fact that the hydrodynamic radius relates to the outer particle radius, while the scattering-based size estimate depends on the internal mass distribution of the particles. We demonstrate this by differentiating biomolecular fractal aggregates from spherical particles in fetal bovine serum at the single-particle level.
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Affiliation(s)
- Erik Olsén
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | | | - Fredrik Skärberg
- Department
of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Petteri Parkkila
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Giovanni Volpe
- Department
of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Fredrik Höök
- Department
of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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12
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Xu J, Zhang P, Chen Y. Surface Plasmon Resonance Biosensors: A Review of Molecular Imaging with High Spatial Resolution. BIOSENSORS 2024; 14:84. [PMID: 38392003 PMCID: PMC10886473 DOI: 10.3390/bios14020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
Surface plasmon resonance (SPR) is a powerful tool for determining molecular interactions quantitatively. SPR imaging (SPRi) further improves the throughput of SPR technology and provides the spatially resolved capability for observing the molecular interaction dynamics in detail. SPRi is becoming more and more popular in biological and chemical sensing and imaging. However, SPRi suffers from low spatial resolution due to the imperfect optical components and delocalized features of propagating surface plasmonic waves along the surface. Diverse kinds of approaches have been developed to improve the spatial resolution of SPRi, which have enormously impelled the development of the methodology and further extended its possible applications. In this minireview, we introduce the mechanisms for building a high-spatial-resolution SPRi system and present its experimental schemes from prism-coupled SPRi and SPR microscopy (SPRM) to surface plasmonic scattering microscopy (SPSM); summarize its exciting applications, including molecular interaction analysis, molecular imaging and profiling, tracking of single entities, and analysis of single cells; and discuss its challenges in recent decade as well as the promising future.
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Affiliation(s)
- Jiying Xu
- National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Faculty of Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Zhang
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Chen
- National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, Faculty of Chemical Engineering, Huaiyin Institute of Technology, Huaian 223003, China
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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13
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Wang CR, Harlington AC, Snel MF, Pukala TL. Characterisation of the forest cobra (Naja melanoleuca) venom using a multifaceted mass spectrometric-based approach. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140992. [PMID: 38158032 DOI: 10.1016/j.bbapap.2023.140992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Snake venoms consist of highly biologically active proteins and peptides that are responsible for the lethal physiological effects of snakebite envenomation. In order to guide the development of targeted antivenom strategies, comprehensive understanding of venom compositions and in-depth characterisation of various proteoforms, often not captured by traditional bottom-up proteomic workflows, is necessary. Here, we employ an integrated 'omics' and intact mass spectrometry (MS)-based approach to profile the heterogeneity within the venom of the forest cobra (Naja melanoleuca), adopting different analytical strategies to accommodate for the dynamic molecular mass range of venom proteins present. The venom proteome of N. melanoleuca was catalogued using a venom gland transcriptome-guided bottom-up proteomics approach, revealing a venom consisting of six toxin superfamilies. The subtle diversity present in the venom components was further explored using reversed phase-ultra performance liquid chromatography (RP-UPLC) coupled to intact MS. This approach showed a significant increase in the number of venom proteoforms within various toxin families that were not captured in previous studies. Furthermore, we probed at the higher-order structures of the larger venom proteins using a combination of native MS and mass photometry and revealed significant structural heterogeneity along with extensive post-translational modifications in the form of glycosylation in these larger toxins. Here, we show the diverse structural heterogeneity of snake venom proteins in the venom of N. melanoleuca using an integrated workflow that incorporates analytical strategies that profile snake venom at the proteoform level, complementing traditional venom characterisation approaches.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Alix C Harlington
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Marten F Snel
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia; Proteomics, Metabolomics and MS-Imaging Core Facility, South Australian Health and Medical Research Institute, Adelaide 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia.
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14
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Proctor EJ, Frost HR, Satapathy S, Botquin G, Urbaniec J, Gorman J, De Oliveira DMP, McArthur J, Davies MR, Botteaux A, Smeesters P, Sanderson-Smith M. Molecular characterization of the interaction between human IgG and the M-related proteins from Streptococcus pyogenes. J Biol Chem 2024; 300:105623. [PMID: 38176650 PMCID: PMC10844976 DOI: 10.1016/j.jbc.2023.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Group A Streptococcal M-related proteins (Mrps) are dimeric α-helical-coiled-coil cell membrane-bound surface proteins. During infection, Mrp recruit the fragment crystallizable region of human immunoglobulin G via their A-repeat regions to the bacterial surface, conferring upon the bacteria enhanced phagocytosis resistance and augmented growth in human blood. However, Mrps show a high degree of sequence diversity, and it is currently not known whether this diversity affects the Mrp-IgG interaction. Herein, we report that diverse Mrps all bind human IgG subclasses with nanomolar affinity, with differences in affinity which ranged from 3.7 to 11.1 nM for mixed IgG. Using surface plasmon resonance, we confirmed Mrps display preferential IgG-subclass binding. All Mrps were found to have a significantly weaker affinity for IgG3 (p < 0.05) compared to all other IgG subclasses. Furthermore, plasma pulldown assays analyzed via Western blotting revealed that all Mrp were able to bind IgG in the presence of other serum proteins at both 25 °C and 37 °C. Finally, we report that dimeric Mrps bind to IgG with a 1:1 stoichiometry, enhancing our understanding of this important host-pathogen interaction.
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Affiliation(s)
- Emma-Jayne Proctor
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Hannah R Frost
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Sandeep Satapathy
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia; The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gwenaëlle Botquin
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Joanna Urbaniec
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Jody Gorman
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - David M P De Oliveira
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, QLD, Australia
| | - Jason McArthur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Pierre Smeesters
- Molecular Bacteriology Laboratory, European Plotkins Institute for Vaccinology (EPIV), Université Libre de Bruxelles, Brussels, Belgium
| | - Martina Sanderson-Smith
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.
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15
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Ray S, Mason TO, Boyens-Thiele L, Farzadfard A, Larsen JA, Norrild RK, Jahnke N, Buell AK. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat Chem 2023; 15:1306-1316. [PMID: 37337111 DOI: 10.1038/s41557-023-01244-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Mason
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lars Boyens-Thiele
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jacob Aunstrup Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus K Norrild
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nadin Jahnke
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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16
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Becker J, Peters JS, Crooks I, Helmi S, Synakewicz M, Schuler B, Kukura P. A Quantitative Description for Optical Mass Measurement of Single Biomolecules. ACS PHOTONICS 2023; 10:2699-2710. [PMID: 37602293 PMCID: PMC10436351 DOI: 10.1021/acsphotonics.3c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 08/22/2023]
Abstract
Label-free detection of single biomolecules in solution has been achieved using a variety of experimental approaches over the past decade. Yet, our understanding of the magnitude of the optical contrast and its relationship with the underlying atomic structure as well as the achievable measurement sensitivity and precision remain poorly defined. Here, we use a Fourier optics approach combined with an atomic structure-based molecular polarizability model to simulate mass photometry experiments from first principles. We find excellent agreement between several key experimentally determined parameters such as optical contrast-to-mass conversion, achievable mass accuracy, and molecular shape and orientation dependence. This allows us to determine detection sensitivity and measurement precision mostly independent of the optical detection approach chosen, resulting in a general framework for light-based single-molecule detection and quantification.
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Affiliation(s)
- Jan Becker
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Rd, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Jack S. Peters
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Rd, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Ivor Crooks
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Seham Helmi
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Rd, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Marie Synakewicz
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Department
of Physics, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Philipp Kukura
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Rd, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
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17
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Hiemenz C, Pacios-Michelena A, Helbig C, Vezočnik V, Strebl M, Nikels F, Hawe A, Garidel P, Menzen T. Characterization of Virus Particles and Submicron-Sized Particulate Impurities in Recombinant Adeno-Associated Virus Drug Product. J Pharm Sci 2023; 112:2190-2202. [PMID: 37211315 DOI: 10.1016/j.xphs.2023.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
Characterization of particulate impurities such as aggregates is necessary to develop safe and efficacious adeno-associated virus (AAV) drug products. Although aggregation of AAVs can reduce the bioavailability of the virus, only a limited number of studies focus on the analysis of aggregates. We explored three technologies for their capability to characterize AAV monomers and aggregates in the submicron (<1 µm) size range: (i) mass photometry (MP), (ii) asymmetric flow field flow fractionation coupled to a UV-detector (AF4-UV/Vis) and (iii) microfluidic resistive pulse sensing (MRPS). Although low counts for aggregates impeded a quantitative analysis, MP was affirmed as an accurate and rapid method for quantifying the genome content of empty/filled/double-filled capsids, consistent with sedimentation velocity analytical ultracentrifugation results. MRPS and AF4-UV/Vis enabled the detection and quantification of aggregate content. The developed AF4-UV/Vis method separated AAV monomers from smaller aggregates, thereby enabling a quantification of aggregates <200 nm. MRPS was experienced as a straightforward method to determine the particle concentration and size distribution between 250-2000 nm, provided that the samples do not block the microfluidic cartridge. Overall, within this study we explored the benefits and limitations of the complementary technologies for assessing aggregate content in AAV samples.
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Affiliation(s)
| | | | | | | | - Michael Strebl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Felix Nikels
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany.
| | - Andrea Hawe
- Coriolis Pharma Research GmbH, Martinsried, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, Germany.
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18
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Wu D, Xu P, Kelly M, Ryan ET, Kováč P, Piszczek G. Mass photometry: A powerful tool for carbohydrates-proteins conjugation monitoring and glycoconjugates molecular mass determination. Glycoconj J 2023; 40:401-412. [PMID: 37392327 PMCID: PMC10374364 DOI: 10.1007/s10719-023-10126-7] [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: 05/04/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 07/03/2023]
Abstract
Glycoconjugate vaccines are important additions to the existing means for prevention of diseases caused by bacterial and viral pathogens. Conjugating carbohydrates to proteins is a crucial step in the development of these vaccines. Traditional mass spectrometry techniques, such as MALDI-TOF and SELDI-TOF, have difficulties in detecting glycoconjugates with high molecular masses. Mass photometry (MP) is a single-molecule technique that has been recently developed, which allows mass measurements of individual molecules and generates mass distributions based on hundreds to thousands of these measurements. In this study, we evaluated the performance of MP in monitoring carbohydrate-protein conjugation reactions and characterization of conjugates. Three different glycoconjugates were prepared from carrier protein BSA, and one from a large protein complex, a virus capsid with 3.74 MDa molecular mass. The masses measured by MP were consistent with those obtained by SELDI-TOF-MS and SEC-MALS. The conjugation of BSA dimer to carbohydrate antigen was also successfully characterized. This study shows that the MP technique is a promising alternative to methods developed earlier for monitoring glycoconjugation reactions and characterization of glycoconjugates. It measures intact molecules in solution and it is highly accurate over a wide mass range. MP requires only a very small amount of sample and has no specific buffer constraints. Other MP advantages include minimal cost of consumables and rapid data collection and analysis. Its advantages over other methods make it a valuable tool for researchers in the glycoconjugation field.
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Affiliation(s)
- Di Wu
- Biophysics Core Facility, NHLBI, NIH, Bethesda, MD, 20892, USA.
| | - Peng Xu
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, 20892, USA
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pavol Kováč
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, 20892, USA
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19
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Gaur P, Bain FE, Honda M, Granger SL, Spies M. Single-Molecule Analysis of the Improved Variants of the G-Quadruplex Recognition Protein G4P. Int J Mol Sci 2023; 24:10274. [PMID: 37373425 PMCID: PMC10299155 DOI: 10.3390/ijms241210274] [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: 05/16/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
As many as 700,000 unique sequences in the human genome are predicted to fold into G-quadruplexes (G4s), non-canonical structures formed by Hoogsteen guanine-guanine pairing within G-rich nucleic acids. G4s play both physiological and pathological roles in many vital cellular processes including DNA replication, DNA repair and RNA transcription. Several reagents have been developed to visualize G4s in vitro and in cells. Recently, Zhen et al. synthesized a small protein G4P based on the G4 recognition motif from RHAU (DHX36) helicase (RHAU specific motif, RSM). G4P was reported to bind the G4 structures in cells and in vitro, and to display better selectivity toward G4s than the previously published BG4 antibody. To get insight into G4P- G4 interaction kinetics and selectivity, we purified G4P and its expanded variants, and analyzed their G4 binding using single-molecule total internal reflection fluorescence microscopy and mass photometry. We found that G4P binds to various G4s with affinities defined mostly by the association rate. Doubling the number of the RSM units in the G4P increases the protein's affinity for telomeric G4s and its ability to interact with sequences folding into multiple G4s.
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Affiliation(s)
| | | | | | | | - Maria Spies
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA (M.H.)
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20
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Kremer K, Meier D, Theis L, Miller S, Rost-Nasshan A, Naing YT, Zarzycki J, Paczia N, Serrania J, Blumenkamp P, Goesmann A, Becker A, Thanbichler M, Hochberg GKA, Carter MS, Erb TJ. Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway. Appl Environ Microbiol 2023:e0023823. [PMID: 37318336 PMCID: PMC10370305 DOI: 10.1128/aem.00238-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Metabolic degeneracy describes the phenomenon that cells can use one substrate through different metabolic routes, while metabolic plasticity, refers to the ability of an organism to dynamically rewire its metabolism in response to changing physiological needs. A prime example for both phenomena is the dynamic switch between two alternative and seemingly degenerate acetyl-CoA assimilation routes in the alphaproteobacterium Paracoccus denitrificans Pd1222: the ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMCP and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle toward biomass formation. However, the simultaneous presence of both the EMCP and GC in P. denitrificans Pd1222 raises the question of how this apparent functional degeneracy is globally coordinated during growth. Here, we show that RamB, a transcription factor of the ScfR family, controls expression of the GC in P. denitrificans Pd1222. Combining genetic, molecular biological and biochemical approaches, we identify the binding motif of RamB and demonstrate that CoA-thioester intermediates of the EMCP directly bind to the protein. Overall, our study shows that the EMCP and the GC are metabolically and genetically linked with each other, demonstrating a thus far undescribed bacterial strategy to achieve metabolic plasticity, in which one seemingly degenerate metabolic pathway directly drives expression of the other. IMPORTANCE Carbon metabolism provides organisms with energy and building blocks for cellular functions and growth. The tight regulation between degradation and assimilation of carbon substrates is central for optimal growth. Understanding the underlying mechanisms of metabolic control in bacteria is of importance for applications in health (e.g., targeting of metabolic pathways with new antibiotics, development of resistances) and biotechnology (e.g., metabolic engineering, introduction of new-to-nature pathways). In this study, we use the alphaproteobacterium P. denitrificans as model organism to study functional degeneracy, a well-known phenomenon of bacteria to use the same carbon source through two different (competing) metabolic routes. We demonstrate that two seemingly degenerate central carbon metabolic pathways are metabolically and genetically linked with each other, which allows the organism to control the switch between them in a coordinated manner during growth. Our study elucidates the molecular basis of metabolic plasticity in central carbon metabolism, which improves our understanding of how bacterial metabolism is able to partition fluxes between anabolism and catabolism.
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Affiliation(s)
- Katharina Kremer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Lisa Theis
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stephanie Miller
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | | | - Yadanar T Naing
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for terrestrial Microbiology, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anke Becker
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K A Hochberg
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Chemistry, University of Marburg, Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael S Carter
- Department of Biological Sciences, Salisbury University, Maryland, USA
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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21
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Zhang P, Zhou X, Wang S. Plasmonic Scattering Microscopy for Label-Free Imaging of Molecular Binding Kinetics: From Single Molecules to Single Cells. CHEMISTRY METHODS : NEW APPROACHES TO SOLVING PROBLEMS IN CHEMISTRY 2023; 3:e202200066. [PMID: 37448471 PMCID: PMC10344632 DOI: 10.1002/cmtd.202200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Indexed: 07/15/2023]
Abstract
Measuring molecular binding kinetics represents one of the most important tasks in molecular interaction analysis. Surface plasmon resonance (SPR) is a popular tool for analyzing molecular binding. Plasmonic scattering microscopy (PSM) is a newly developed SPR imaging technology, which detects the out-of-plane scattering of surface plasmons by analytes and has pushed the detection limit of label-free SPR imaging down to a single-protein level. In addition, PSM also allows SPR imaging with high spatiotemporal resolution, making it possible to analyze cellular response to the molecular bindings. In this Mini Review, we present PSM as a method of choice for chemical and biological imaging, introduce its theoretical mechanism, present its experimental schemes, summarize its exciting applications, and discuss its challenges as well as the promising future.
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Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, 85287 (USA)
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (P. R. China)
| | - Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, 85287 (USA)
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287 (USA)
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, 85287 (USA)
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287 (USA)
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22
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Velasco L, Ouyang T, Reinhard BM. Two-Color iSCAT Imaging of Ag Nanoparticles Resolves Size and Ambient Refractive Index Changes. NANO LETTERS 2023; 23:4642-4647. [PMID: 37159328 PMCID: PMC10752631 DOI: 10.1021/acs.nanolett.3c01306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The ability to discern noble metal nanoparticles (NPs) with different sizes and in ambient media with different refractive indices has important applications in imaging and sensing. Here a two-color (405 nm, 445 nm) interferometric scattering (iSCAT) detection scheme is applied to characterize the wavelength-dependent iSCAT contrast of Ag NPs with nominal diameters of 10, 20, 40, and 60 nm and to distinguish between NPs of different sizes. The iSCAT contrast also depends on the ambient refractive index and the relative iSCAT contrast on both channels revealed a spectral red-shift for 40 and 60 nm Ag NPs when the ambient refractive index was increased from n = 1.3892 to n = 1.4328. With the selected wavelength channels, the spectral resolution of the two-color imaging strategy was, however, insufficient to resolve spectral shifts induced by refractive index changes for 10 and 20 nm Ag NPs.
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Affiliation(s)
- Leslie Velasco
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
| | - Tianhong Ouyang
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
| | - Björn M. Reinhard
- Department of Chemistry and The Photonics Center, Boston University, Boston, MA 02215, United States
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23
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [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: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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24
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Liu L, Tibbs J, Li N, Bacon A, Shepherd S, Lee H, Chauhan N, Demirci U, Wang X, Cunningham BT. A photonic resonator interferometric scattering microscope for label-free detection of nanometer-scale objects with digital precision in point-of-use environments. Biosens Bioelectron 2023; 228:115197. [PMID: 36905862 PMCID: PMC10072782 DOI: 10.1016/j.bios.2023.115197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/27/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic source. The use of a photonic crystal substrate for interferemetric scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosome, and ferritin protein.
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Affiliation(s)
- Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joseph Tibbs
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Amanda Bacon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hankeun Lee
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Neha Chauhan
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Stanford School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Cancer Center at Illinois, Urbana, IL, 61801, USA.
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25
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Gaur P, Bain FE, Honda M, Granger SL, Spies M. Single-molecule analysis of the improved variants of the G-quadruplex recognition protein G4P. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539902. [PMID: 37214990 PMCID: PMC10197523 DOI: 10.1101/2023.05.08.539902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As many as 700,000 unique sequences in the human genome are predicted to fold into G-quadruplexes (G4s), non-canonical structures formed by Hoogsteen guanine-guanine pairing within G-rich nucleic acids. G4s play both physiological and pathological roles in many vital cellular processes including DNA replication, DNA repair and RNA transcription. Several reagents have been developed to visualize G4s in vitro and in cells. Recently, Zhen et al . synthesized a small protein G4P based on the G4 recognition motif from RHAU (DHX36) helicase (RHAU specific motif, RSM). G4P was reported to bind the G4 structures in cells and in vitro , and to display better selectivity towards G4s than the previously published BG4 antibody. To get insight into the G4P-G4 interaction kinetics and selectivity, we purified G4P and its expanded variants, and analyzed their G4 binding using single-molecule total internal reflection fluorescence microscopy and mass photometry. We found that G4P binds to various G4s with affinities defined mostly by the association rate. Doubling the number of the RSM units in the G4P increases the protein's affinity for telomeric G4s and its ability to interact with sequences folding into multiple G4s.
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26
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Boyle MJ, Goldman YE, Composto RJ. Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN. J Phys Chem B 2023; 127:3737-3745. [PMID: 37074024 DOI: 10.1021/acs.jpcb.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Interferometric scattering microscopy (iSCAT) is a label-free optical microscopy technique that enables imaging of individual nano-objects such as nanoparticles, viruses, and proteins. Essential to this technique is the suppression of background scattering and identification of signals from nano-objects. In the presence of substrates with high roughness, scattering heterogeneities in the background, when coupled with tiny stage movements, cause features in the background to be manifested in background-suppressed iSCAT images. Traditional computer vision algorithms detect these background features as particles, limiting the accuracy of object detection in iSCAT experiments. Here, we present a pathway to improve particle detection in such situations using supervised machine learning via a mask region-based convolutional neural network (mask R-CNN). Using a model iSCAT experiment of 19.2 nm gold nanoparticles adsorbing to a rough layer-by-layer polyelectrolyte film, we develop a method to generate labeled datasets using experimental background images and simulated particle signals and train the mask R-CNN using limited computational resources via transfer learning. We then compare the performance of the mask R-CNN trained with and without inclusion of experimental backgrounds in the dataset against that of a traditional computer vision object detection algorithm, Haar-like feature detection, by analyzing data from the model experiment. Results demonstrate that including representative backgrounds in training datasets improved the mask R-CNN in differentiating between background and particle signals and elevated performance by markedly reducing false positives. The methodology for creating a labeled dataset with representative experimental backgrounds and simulated signals facilitates the application of machine learning in iSCAT experiments with strong background scattering and thus provides a useful workflow for future researchers to improve their image processing capabilities.
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Affiliation(s)
- Michael J Boyle
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Center for Engineered Materials and Manufacturing, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Yale E Goldman
- Department of Physiology and Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Russell J Composto
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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27
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Takeda K, Noda M, Maruno T, Uchiyama S. Critical Calibration of Mass Photometry for Higher-Mass Samples Such as Adeno-Associated Virus Vectors. J Pharm Sci 2023; 112:1145-1150. [PMID: 36334808 DOI: 10.1016/j.xphs.2022.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Mass photometry (MP) is a label-free, single-molecule technique that can determine molecular mass distribution with very low sample consumption in a short time. Because of the established experimental instrument and analytical software, MP measurements may be readily obtained; thus, the application of MP is expanding, especially in the fields of bioscience and biotechnology. However, because the MP data quality is strongly focus-dependent, optical settings must be intrinsically strict. In this study, we report the importance of the critical calibration of the mass photometer, which is required for the accurate estimation of high-molecular mass samples, such as adeno-associated virus vectors. Additionally, a method for optimizing the instrument settings, including the calibration of the stage, is presented.
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Affiliation(s)
| | - Masanori Noda
- U-medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | - Susumu Uchiyama
- U-medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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28
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Needham LM, Saavedra C, Rasch JK, Sole-Barber D, Schweitzer BS, Fairhall AJ, Vollbrecht CH, Mehlenbacher B, Zhang Z, Tenbrake L, Pfeifer H, Chapman ER, Goldsmith RH. Label-free observation of individual solution phase molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534170. [PMID: 36993572 PMCID: PMC10055403 DOI: 10.1101/2023.03.24.534170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The vast majority of chemistry and biology occurs in solution, and new label-free analytical techniques that can help resolve solution-phase complexity at the single-molecule level can provide new microscopic perspectives of unprecedented detail. Here, we use the increased light-molecule interactions in high-finesse fiber Fabry-Pérot microcavities to detect individual biomolecules as small as 1.2 kDa with signal-to-noise ratios >100, even as the molecules are freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of sub-populations in mixed samples. Strikingly, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight can also be resolved. Detection is based on a novel molecular velocity filtering and dynamic thermal priming mechanism leveraging both photo-thermal bistability and Pound-Drever-Hall cavity locking. This technology holds broad potential for applications in life and chemical sciences and represents a major advancement in label-free in vitro single-molecule techniques.
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Affiliation(s)
- Lisa-Maria Needham
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Carlos Saavedra
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | - Julia K. Rasch
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | | | | | - Alex J. Fairhall
- Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | | | | | - Zhao Zhang
- Howard Hughes Medical Institute and the Department of Neuroscience, University of Wisconsin-Madison, WI, USA
| | - Lukas Tenbrake
- Institut für Angewandte Physik, Universität Bonn, Wegelerstr. 8, 53115 Bonn, Germany
| | - Hannes Pfeifer
- Institut für Angewandte Physik, Universität Bonn, Wegelerstr. 8, 53115 Bonn, Germany
| | - Edwin R. Chapman
- Howard Hughes Medical Institute and the Department of Neuroscience, University of Wisconsin-Madison, WI, USA
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29
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Dahmardeh M, Mirzaalian Dastjerdi H, Mazal H, Köstler H, Sandoghdar V. Self-supervised machine learning pushes the sensitivity limit in label-free detection of single proteins below 10 kDa. Nat Methods 2023; 20:442-447. [PMID: 36849549 PMCID: PMC9998267 DOI: 10.1038/s41592-023-01778-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/06/2023] [Indexed: 03/01/2023]
Abstract
Interferometric scattering (iSCAT) microscopy is a label-free optical method capable of detecting single proteins, localizing their binding positions with nanometer precision, and measuring their mass. In the ideal case, iSCAT is limited by shot noise such that collection of more photons should extend its detection sensitivity to biomolecules of arbitrarily low mass. However, a number of technical noise sources combined with speckle-like background fluctuations have restricted the detection limit in iSCAT. Here, we show that an unsupervised machine learning isolation forest algorithm for anomaly detection pushes the mass sensitivity limit by a factor of 4 to below 10 kDa. We implement this scheme both with a user-defined feature matrix and a self-supervised FastDVDNet and validate our results with correlative fluorescence images recorded in total internal reflection mode. Our work opens the door to optical investigations of small traces of biomolecules and disease markers such as α-synuclein, chemokines and cytokines.
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Affiliation(s)
- Mahyar Dahmardeh
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Houman Mirzaalian Dastjerdi
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Department of Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hisham Mazal
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Harald Köstler
- Department of Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany. .,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany. .,Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
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30
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Margheritis E, Kappelhoff S, Cosentino K. Pore-Forming Proteins: From Pore Assembly to Structure by Quantitative Single-Molecule Imaging. Int J Mol Sci 2023; 24:ijms24054528. [PMID: 36901959 PMCID: PMC10003378 DOI: 10.3390/ijms24054528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Pore-forming proteins (PFPs) play a central role in many biological processes related to infection, immunity, cancer, and neurodegeneration. A common feature of PFPs is their ability to form pores that disrupt the membrane permeability barrier and ion homeostasis and generally induce cell death. Some PFPs are part of the genetically encoded machinery of eukaryotic cells that are activated against infection by pathogens or in physiological programs to carry out regulated cell death. PFPs organize into supramolecular transmembrane complexes that perforate membranes through a multistep process involving membrane insertion, protein oligomerization, and finally pore formation. However, the exact mechanism of pore formation varies from PFP to PFP, resulting in different pore structures with different functionalities. Here, we review recent insights into the molecular mechanisms by which PFPs permeabilize membranes and recent methodological advances in their characterization in artificial and cellular membranes. In particular, we focus on single-molecule imaging techniques as powerful tools to unravel the molecular mechanistic details of pore assembly that are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is critical for understanding the physiological role of PFPs and developing therapeutic approaches.
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31
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Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation. Commun Biol 2023; 6:121. [PMID: 36717706 PMCID: PMC9887055 DOI: 10.1038/s42003-023-04512-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Small heat shock proteins (sHSPs) are chaperones with well-characterized roles in heat stress, but potential roles for sHSPs in desiccation tolerance have not been as thoroughly explored. We identified nine sHSPs from the tardigrade Hypsibius exemplaris, each containing a conserved alpha-crystallin domain flanked by disordered regions. Many of these sHSPs are highly expressed. Multiple tardigrade and human sHSPs could improve desiccation tolerance of E. coli, suggesting that the capacity to contribute to desicco-protection is a conserved property of some sHSPs. Purification and subsequent analysis of two tardigrade sHSPs, HSP21 and HSP24.6, revealed that these proteins can oligomerize in vitro. These proteins limited heat-induced aggregation of the model enzyme citrate synthase. Heterologous expression of HSP24.6 improved bacterial heat shock survival, and the protein significantly reduced heat-induced aggregation of soluble bacterial protein. Thus, HSP24.6 likely chaperones against protein aggregation to promote heat tolerance. Furthermore, HSP21 and HSP24.6 limited desiccation-induced aggregation and loss of function of citrate synthase. This suggests a mechanism by which tardigrade sHSPs promote desiccation tolerance, by limiting desiccation-induced protein aggregation, thereby maintaining proteostasis and supporting survival. These results suggest that sHSPs provide a mechanism of general stress resistance that can also be deployed to support survival during anhydrobiosis.
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32
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Zhou X, Wang R, Wan Z, Zhang P, Wang S. Multiplexed Protein Detection and Parallel Binding Kinetics Analysis with Label-Free Digital Single-Molecule Counting. Anal Chem 2023; 95:1541-1548. [PMID: 36595491 PMCID: PMC10316747 DOI: 10.1021/acs.analchem.2c04582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multiplexed protein detection is critical for improving the drug and biomarker screening efficiency. Here, we show that multiplexed protein detection and parallel protein interaction analysis can be realized by evanescent scattering microscopy (ESM). ESM enables binding kinetics measurement with label-free digital single-molecule counting. We implemented an automatic single-molecule counting strategy with high temporal resolution to precisely determine the binding time, which improves the counting efficiency and accuracy. We show that digital single-molecule counting can recognize proteins with different molecular weights, thus making it possible to monitor the protein binding processes in the solution by real-time tracking of the numbers of free and bound proteins landing on the sensor surface. Furthermore, we show that this strategy can simultaneously analyze the kinetics of two different protein interaction processes on the surface and in the solution. This work may pave a way to investigate complicated protein interactions, such as the competition of biomarker-antibody binding in biofluids with biomarker-protein binding on the cellular membrane.
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Affiliation(s)
- Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Rui Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, USA
| | - Zijian Wan
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, USA
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, USA
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33
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Proctor EJ, Satapathy S, Sanderson-Smith M. Elucidating the Stoichiometries of Host-Pathogen Protein Interactions with Mass Photometry. Methods Mol Biol 2023; 2674:201-208. [PMID: 37258969 DOI: 10.1007/978-1-0716-3243-7_13] [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: 06/02/2023]
Abstract
Mass photometry (MP) is a single molecule technique that enables the characterization of individual proteins. Here we show a detailed workflow using the Refeyn OneMP to investigate molecular complexes, using the M53 protein, a plasminogen-binding group A streptococcal M-like protein (PAM), and human plasminogen as exemplar proteins. The methodology described herein confirmed a 1:1 binding stoichiometry for the M53-plasminogen complex. Additionally, MP was used to identify the oligomerization state, homogeneity, purity, and approximate molecular weights of each protein.
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Affiliation(s)
- Emma-Jayne Proctor
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Sandeep Satapathy
- Blavatnik Institute of Cell Biology, Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martina Sanderson-Smith
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.
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34
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Liu L, Tibbs J, Li N, Bacon A, Shepherd S, Lee H, Chauhan N, Demirci U, Wang X, Cunningham BT. A Photonic Resonator Interferometric Scattering Microscope for Label-free Detection of Nanometer-Scale Objects with Digital Precision in Point-of-Use Environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.13.520266. [PMID: 36561182 PMCID: PMC9774210 DOI: 10.1101/2022.12.13.520266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.
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Affiliation(s)
- Leyang Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Joseph Tibbs
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Amanda Bacon
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hankeun Lee
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Neha Chauhan
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Stanford School of Medicine, Stanford University, Palo Alto, California 94304, USA
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, Urbana, Illinois 61801, USA
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35
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Wu D, Hwang P, Li T, Piszczek G. Rapid characterization of adeno-associated virus (AAV) gene therapy vectors by mass photometry. Gene Ther 2022; 29:691-697. [PMID: 35046529 PMCID: PMC9296698 DOI: 10.1038/s41434-021-00311-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 11/16/2021] [Accepted: 12/07/2021] [Indexed: 02/08/2023]
Abstract
Recombinant adeno-associated viruses (rAAV) are used extensively as gene delivery vectors in clinical studies, and several rAAV based treatments have already been approved. Significant progress has been made in rAAV manufacturing; however, better and more precise capsid characterization techniques are still needed to guarantee the purity and safety of rAAV preparations. Current analytical techniques used to characterize rAAV preparations are susceptible to background signals, have limited accuracy, or require a large amount of time and material. A recently developed single-molecule technique, mass photometry (MP), measures mass distributions of biomolecules with high-resolution and sensitivity. Here we explore applications of MP for the characterization of capsid fractions. We demonstrate that MP is able to resolve and quantify not only empty and full-genome containing capsid populations but also identify partially packaged capsid impurities. MP data accurately measures full and empty capsid ratios, and can be used to estimate the size of the encapsidated genome. MP distributions provide information on sample heterogeneity and on the presence of aggregates. Sub-picomole quantities of sample are sufficient for MP analysis, and data can be obtained and analyzed within minutes. This method provides a simple, robust, and effective tool to monitor the physical attributes of rAAV vectors.
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Affiliation(s)
- Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892-8012, USA
| | - Philsang Hwang
- Ocular Gene Therapy Core Facility, National Eye Institute, 6 Center Drive, Bethesda, MD 20892, USA
| | - Tiansen Li
- Ocular Gene Therapy Core Facility, National Eye Institute, 6 Center Drive, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892-8012, USA,correspondence to:
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36
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Lin S, He Y, Feng D, Piliarik M, Chen XW. Optical Fingerprint of Flat Substrate Surface and Marker-Free Lateral Displacement Detection with Angstrom-Level Precision. PHYSICAL REVIEW LETTERS 2022; 129:213201. [PMID: 36461964 DOI: 10.1103/physrevlett.129.213201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
We report that flat substrates such as glass coverslips with surface roughness well below 0.5 nm feature notable speckle patterns when observed with high-sensitivity interference microscopy. We uncover that these speckle patterns unambiguously originate from the subnanometer surface undulations, and develop an intuitive model to illustrate how subnanometer nonresonant dielectric features could generate pronounced interference contrast in the far field. We introduce the concept of optical fingerprint for the deterministic speckle pattern associated with a particular substrate surface area and intentionally enhance the speckle amplitudes for potential applications. We demonstrate such optical fingerprints can be leveraged for reproducible position identification and marker-free lateral displacement detection with an experimental precision of 0.22 nm. The reproducible position identification allows us to detect new nanoscopic features developed during laborious processes performed outside of the microscope. The demonstrated capability for ultrasensitive displacement detection may find applications in the semiconductor industry and superresolution optical microscopy.
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Affiliation(s)
- Shupei Lin
- School of Physics and Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, People's Republic of China
| | - Yong He
- School of Physics and Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, People's Republic of China
| | - Delong Feng
- School of Physics and Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, People's Republic of China
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, 18251 Prague, Czech Republic
| | - Xue-Wen Chen
- School of Physics and Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, People's Republic of China and Institute for Quantum Science and Engineering and Hubei Key Laboratory of Gravitation and Quantum Physics, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan 430074, People's Republic of China
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37
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Adhikari S, Orrit M. Optically Probing the Chirality of Single Plasmonic Nanostructures and of Single Molecules: Potential and Obstacles. ACS PHOTONICS 2022; 9:3486-3497. [PMID: 36411819 PMCID: PMC9673138 DOI: 10.1021/acsphotonics.2c01205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Circular dichroism (CD) is a standard method for the analysis of biomolecular conformation. It is very reliable when applied to molecules, but requires relatively large amounts of solution. Plasmonics offer the perspective of enhancement of CD signals, which would extend CD spectrometry to smaller amounts of molecules and to weaker chiral signals. However, plasmonic enhancement comes at the cost of additional complications: averaging over all orientations is no longer possible or reliable, linear dichroism leaks into CD signals because of experimental imperfections, scattering and its interference with the incident beam must be taken into account, and the interaction between chiral molecules and possibly chiral plasmonic structures considerably complicates the interpretation of measured signals. This Perspective aims to explore the motivations and problems of plasmonic chirality and to re-evaluate present and future solutions.
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38
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Yang W, Wei Z, Nie Y, Tian Y. Optical Detection and Imaging of Nonfluorescent Matter at the Single-Molecule/Particle Level. J Phys Chem Lett 2022; 13:9618-9631. [PMID: 36214484 DOI: 10.1021/acs.jpclett.2c02228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the first optical detection of single molecules in 1989, single-molecule spectroscopy has developed rapidly and been widely applied in many areas. However, the vast majority of matter is extremely inefficient at emitting photons in our physical world, which seriously limits the applications of optical methods based on photoluminescence. In addition to indirect detection by fluorescence labeling, many efforts have been made to directly image nonfluorescent matter at the single-particle or single-molecule level in different ways based on the absorption or scattering interaction between light and matter. Herein, we review five popular methods for imaging nonfluorescent particles/molecules, including dark-field microscopy (DFM), surface plasmon resonance microscopy (SPRM), surface enhanced Raman microscopy (SERM), interferometric scattering microscopy (iSCAT), and photothermal microscopy (PTM). After summarizing the principles and applications of these methods, we compare the advantages and disadvantages of each method and describe further potential development and applications.
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Affiliation(s)
- Weiqing Yang
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing210023, China
| | - Zhihong Wei
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing210023, China
| | - Yan Nie
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing210023, China
| | - Yuxi Tian
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing210023, China
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39
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Zhang P, Zhou X, Jiang J, Kolay J, Wang R, Ma G, Wan Z, Wang S. In Situ Analysis of Membrane-Protein Binding Kinetics and Cell-Surface Adhesion Using Plasmonic Scattering Microscopy. Angew Chem Int Ed Engl 2022; 61:e202209469. [PMID: 35922374 PMCID: PMC9561081 DOI: 10.1002/anie.202209469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 11/09/2022]
Abstract
Surface plasmon resonance microscopy (SPRM) is an excellent platform for in situ studying cell-substrate interactions. However, SPRM suffers from poor spatial resolution and small field of view. Herein, we demonstrate plasmonic scattering microscopy (PSM) by adding a dry objective on a popular prism-coupled surface plasmon resonance (SPR) system. PSM not only retains SPRM's high sensitivity and real-time analysis capability, but also provides ≈7 times higher spatial resolution and ≈70 times larger field of view than the typical SPRM, thus providing more details about membrane protein response to ligand binding on over 100 cells simultaneously. In addition, PSM allows quantifying the target movements in the axial direction with a high spatial resolution, thus allowing mapping adhesion spring constants for quantitatively describing the mechanical properties of the cell-substrate contacts. This work may offer a powerful and cost-effective strategy for upgrading current SPR products.
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Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Jiapei Jiang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Jayeeta Kolay
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Rui Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Zijian Wan
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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40
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Hundt N, Cole D, Hantke MF, Miller JJ, Struwe WB, Kukura P. Direct observation of the molecular mechanism underlying protein polymerization. SCIENCE ADVANCES 2022; 8:eabm7935. [PMID: 36044567 PMCID: PMC9432825 DOI: 10.1126/sciadv.abm7935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Protein assembly is a main route to generating complexity in living systems. Revealing the relevant molecular details is challenging because of the intrinsic heterogeneity of species ranging from few to hundreds of molecules. Here, we use mass photometry to quantify and monitor the full range of actin oligomers during polymerization with single-molecule sensitivity. We find that traditional nucleation-based models cannot account for the observed distributions of actin oligomers. Instead, the key step of filament formation is a slow transition between distinct states of an actin filament mediated by cation exchange or ATP hydrolysis. The resulting model reproduces important aspects of actin polymerization, such as the critical concentration for filament formation and bulk growth behavior. Our results revise the mechanism of actin nucleation, shed light on the role and function of actin-associated proteins, and introduce a general and quantitative means to studying protein assembly at the molecular level.
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Affiliation(s)
- Nikolas Hundt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Daniel Cole
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Max F. Hantke
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Jack J. Miller
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PT, UK
- The PET Research Centre and The MR Research Centre, Aarhus University, Aarhus, Denmark
| | - Weston B. Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- The Kavli Institute for Nanoscience Discovery, Oxford, UK
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41
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Heide F, Legare S, To V, Gupta M, Gabir H, Imhof T, Moya‐Torres A, McDougall M, Meier M, Koch M, Stetefeld J. Heparins mediate the multimer assembly of secreted Noggin. Protein Sci 2022. [DOI: 10.1002/pro.4419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fabian Heide
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Scott Legare
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Vu To
- AbCellera Biologics Inc. Vancouver British Columbia Canada
| | - Monika Gupta
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Haben Gabir
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty University of Cologne Cologne Germany
| | | | - Matthew McDougall
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Markus Meier
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Center for Molecular Medicine, Medical Faculty University of Cologne Cologne Germany
| | - Jörg Stetefeld
- Department of Chemistry University of Manitoba Winnipeg Manitoba Canada
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42
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Zhang P, Zhou X, Jiang J, Kolay J, Wang R, Ma G, Wan Z, Wang S. In Situ Analysis of Membrane‐Protein Binding Kinetics and Cell–Surface Adhesion Using Plasmonic Scattering Microscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pengfei Zhang
- Arizona State University Biodesign Center for Bioelectronics and Biosensors 1001 S. McAllister Ave. 85287 Tempe UNITED STATES
| | - Xinyu Zhou
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Jiapei Jiang
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Jayeeta Kolay
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Rui Wang
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Guangzhong Ma
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Zijian Wan
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Shaopeng Wang
- Arizona State University Biodesign Institute Center for Bioelectronics and Biosensors 1001 S McAllister AvenuePO BOX 875801 85248 Tempe UNITED STATES
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43
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Lyu PT, Li QY, Wu P, Sun C, Kang B, Chen HY, Xu JJ. Decrypting Material Performance by Wide-field Femtosecond Interferometric Imaging of Energy Carrier Evolution. J Am Chem Soc 2022; 144:13928-13937. [PMID: 35866699 DOI: 10.1021/jacs.2c05735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Energy carrier evolution is crucial for material performance. Ultrafast microscopy has been widely applied to visualize the spatiotemporal evolution of energy carriers. However, direct imaging of a small amount of energy carriers on the nanoscale remains difficult due to extremely weak transient signals. Here, we present a method for ultrasensitive and high-throughput imaging of energy carrier evolution in space and time. This method combines femtosecond pump-probe techniques with interferometric scattering microscopy (iSCAT), named Femto-iSCAT. The interferometric principle and unique spatially modulated contrast enhancement enable the exploration of new science. We address three important and challenging problems: transport of different energy carriers at various interfaces, heterogeneous hot-electron distribution and relaxation in single plasmonic resonators, and distinct structure-dependent edge-state dynamics of carriers and excitons in optoelectronic semiconductors. Femto-iSCAT holds great potential as a universal tool for ultrasensitive imaging of energy carrier evolution in space and time.
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Affiliation(s)
- Pin-Tian Lyu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing-Yue Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Pei Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chao Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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44
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Zhang P, Wang R, Wan Z, Zhou X, Ma G, Kolay J, Jiang J, Wang S. Label-Free Imaging of Single Proteins and Binding Kinetics Using Total Internal Reflection-Based Evanescent Scattering Microscopy. Anal Chem 2022; 94:10781-10787. [PMID: 35852494 PMCID: PMC9467297 DOI: 10.1021/acs.analchem.2c01510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Single-molecule detection can push beyond ensemble averages and reveal the statistical distributions of molecular properties. Measuring the binding kinetics of single proteins also represents one of the critical and challenging tasks in protein analysis. Here, we report total internal reflection-based evanescent scattering microscopy with label-free single-protein detection capability. Total internal reflection is employed to excite the evanescent field to enhance light-analyte interaction and reduce environmental noise. As a result, the system provides wide-field imaging capability and allows excitation and observation using one objective. In addition, this system quantifies protein binding kinetics by simultaneously counting the binding of individual molecules and recording their binding sites with nanometer precision, providing a digital method to measure binding kinetics with high spatiotemporal resolution. This approach does not employ specially designed microspheres or nanomaterials and may pave a way for label-free single-protein analysis in conventional microscopy.
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Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Rui Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Zijian Wan
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Jayeeta Kolay
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Jiapei Jiang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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45
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Characterising biomolecular interactions and dynamics with mass photometry. Curr Opin Chem Biol 2022; 68:102132. [DOI: 10.1016/j.cbpa.2022.102132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/22/2022] [Indexed: 12/25/2022]
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46
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Evanescent scattering imaging of single protein binding kinetics and DNA conformation changes. Nat Commun 2022; 13:2298. [PMID: 35484120 PMCID: PMC9051210 DOI: 10.1038/s41467-022-30046-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 04/04/2022] [Indexed: 11/08/2022] Open
Abstract
Evanescent illumination has been widely used to detect single biological macromolecules because it can notably enhance light-analyte interaction. However, the current evanescent single-molecule detection system usually requires specially designed microspheres or nanomaterials. Here we show that single protein detection and imaging can be realized on a plain glass surface by imaging the interference between the evanescent lights scattered by the single proteins and by the natural roughness of the cover glass. This allows us to quantify the sizes of single proteins, characterize the protein-antibody interactions at the single-molecule level, and analyze the heterogeneity of single protein binding behaviors. In addition, owing to the exponential distribution of evanescent field intensity, the evanescent imaging system can track the analyte axial movement with high resolution, which can be used to analyze the DNA conformation changes, providing one solution for detecting small molecules, such as microRNA. This work demonstrates a label-free single protein imaging method with ordinary consumables and may pave a road for detecting small biological molecules.
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47
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Adhikari S, Orrit M. Progress and perspectives in single-molecule optical spectroscopy. J Chem Phys 2022; 156:160903. [PMID: 35489995 DOI: 10.1063/5.0087003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.
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Affiliation(s)
- Subhasis Adhikari
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
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48
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Katsikis G, Hwang IE, Wang W, Bhat VS, McIntosh NL, Karim OA, Blus BJ, Sha S, Agache V, Wolfrum JM, Springs SL, Sinskey AJ, Barone PW, Braatz RD, Manalis SR. Weighing the DNA Content of Adeno-Associated Virus Vectors with Zeptogram Precision Using Nanomechanical Resonators. NANO LETTERS 2022; 22:1511-1517. [PMID: 35148107 DOI: 10.1021/acs.nanolett.1c04092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-associated virus (AAV) vectors, which are the most widely used viral vectors for in vivo gene therapy, are typically characterized using PCR, ELISA, and analytical ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as charge-detection mass spectroscopy, static light scattering, and mass photometry offer turnaround times of minutes for measuring AAV mass using optical or charge properties of AAV. Here, we demonstrate an orthogonal method where suspended nanomechanical resonators (SNR) are used to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a precision near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.
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Affiliation(s)
- Georgios Katsikis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Iris E Hwang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wade Wang
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Vikas S Bhat
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Nicole L McIntosh
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Omair A Karim
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Bartlomiej J Blus
- BioMarin Pharmaceutical, Inc., San Rafael, California 94901, United States
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent Agache
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard D Braatz
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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49
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Baaske MD, Asgari N, Punj D, Orrit M. Nanosecond time scale transient optoplasmonic detection of single proteins. SCIENCE ADVANCES 2022; 8:eabl5576. [PMID: 35030027 PMCID: PMC8759745 DOI: 10.1126/sciadv.abl5576] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Optical detection of individual proteins with high bandwidth holds great promise for understanding important biological processes on the nanoscale and for high-throughput fingerprinting applications. As fluorescent labels impose restrictions on detection bandwidth and require time-intensive and invasive processes, label-free optical techniques are highly desirable. Here, we read out changes in the resonantly scattered field of individual gold nanorods interferometrically and use photothermal spectroscopy to optimize the experiment’s parameters. This interferometric plasmonic scattering enables the observation of single proteins as they traverse plasmonic near fields of gold nanorods with unprecedented temporal resolution in the nanosecond-to-microsecond range.
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50
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Seraphim TV, Nano N, Cheung YWS, Aluksanasuwan S, Colleti C, Mao YQ, Bhandari V, Young G, Höll L, Phanse S, Gordiyenko Y, Southworth DR, Robinson CV, Thongboonkerd V, Gava LM, Borges JC, Babu M, Barbosa LRS, Ramos CHI, Kukura P, Houry WA. Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes. Structure 2022; 30:156-171.e12. [PMID: 34492227 DOI: 10.1016/j.str.2021.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
R2TP is a highly conserved chaperone complex formed by two AAA+ ATPases, RUVBL1 and RUVBL2, that associate with PIH1D1 and RPAP3 proteins. R2TP acts in promoting macromolecular complex formation. Here, we establish the principles of R2TP assembly. Three distinct RUVBL1/2-based complexes are identified: R2TP, RUVBL1/2-RPAP3 (R2T), and RUVBL1/2-PIH1D1 (R2P). Interestingly, we find that PIH1D1 does not bind to RUVBL1/RUVBL2 in R2TP and does not function as a nucleotide exchange factor; instead, RPAP3 is found to be the central subunit coordinating R2TP architecture and linking PIH1D1 and RUVBL1/2. We also report that RPAP3 contains an intrinsically disordered N-terminal domain mediating interactions with substrates whose sequences are primarily enriched for Armadillo repeat domains and other helical-type domains. Our work provides a clear and consistent model of R2TP complex structure and gives important insights into how a chaperone machine concerned with assembly of folded proteins into multisubunit complexes might work.
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Affiliation(s)
- Thiago V Seraphim
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Nardin Nano
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Yiu Wing Sunny Cheung
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Siripat Aluksanasuwan
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Carolina Colleti
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada
| | - Gavin Young
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Larissa Höll
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Yuliya Gordiyenko
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Lisandra M Gava
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Júlio C Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo, São Paulo, SP 05508-090, Brazil; Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-100, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 661 University Avenue, MaRS Centre, West Tower, Room 1612, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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