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Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 2024; 7:1005. [PMID: 39152195 PMCID: PMC11329788 DOI: 10.1038/s42003-024-06690-9] [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: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ziane Izri
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Oleg Dmytrenko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Patrick Fischer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Chase Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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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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3
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Ibrahim KA, Naidu AS, Miljkovic H, Radenovic A, Yang W. Label-Free Techniques for Probing Biomolecular Condensates. ACS NANO 2024; 18:10738-10757. [PMID: 38609349 DOI: 10.1021/acsnano.4c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.
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4
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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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5
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Sülzle J, Yang W, Shimoda Y, Ronceray N, Mayner E, Manley S, Radenovic A. Label-Free Imaging of DNA Interactions with 2D Materials. ACS PHOTONICS 2024; 11:737-744. [PMID: 38405387 PMCID: PMC10885193 DOI: 10.1021/acsphotonics.3c01604] [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: 11/05/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/27/2024]
Abstract
Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.
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Affiliation(s)
- Jenny Sülzle
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Wayne Yang
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Yuta Shimoda
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Nathan Ronceray
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Eveline Mayner
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Suliana Manley
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Aleksandra Radenovic
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
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6
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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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7
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Shaked NT, Boppart SA, Wang LV, Popp J. Label-free biomedical optical imaging. NATURE PHOTONICS 2023; 17:1031-1041. [PMID: 38523771 PMCID: PMC10956740 DOI: 10.1038/s41566-023-01299-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/22/2023] [Indexed: 03/22/2024]
Abstract
Label-free optical imaging employs natural and nondestructive approaches for the visualisation of biomedical samples for both biological assays and clinical diagnosis. Currently, this field revolves around multiple broad technology-oriented communities, each with a specific focus on a particular modality despite the existence of shared challenges and applications. As a result, biologists or clinical researchers who require label-free imaging are often not aware of the most appropriate modality to use. This manuscript presents a comprehensive review of and comparison among different label-free imaging modalities and discusses common challenges and applications. We expect this review to facilitate collaborative interactions between imaging communities, push the field forward and foster technological advancements, biophysical discoveries, as well as clinical detection, diagnosis, and monitoring of disease.
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Affiliation(s)
- Natan T Shaked
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Stephen A Boppart
- Beckman Institute for Advanced Science and Technology, Department of Electrical and Computer Engineering,; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lihong V Wang
- Caltech Optical Imaging Laboratory, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research, Jena, Germany; Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
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8
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Carlquist WC, Cytrynbaum EN. The mechanism of MinD stability modulation by MinE in Min protein dynamics. PLoS Comput Biol 2023; 19:e1011615. [PMID: 37976301 PMCID: PMC10691731 DOI: 10.1371/journal.pcbi.1011615] [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] [Received: 12/23/2022] [Revised: 12/01/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
The patterns formed both in vivo and in vitro by the Min protein system have attracted much interest because of the complexity of their dynamic interactions given the apparent simplicity of the component parts. Despite both the experimental and theoretical attention paid to this system, the details of the biochemical interactions of MinD and MinE, the proteins responsible for the patterning, are still unclear. For example, no model consistent with the known biochemistry has yet accounted for the observed dual role of MinE in the membrane stability of MinD. Until now, a statistical comparison of models to the time course of Min protein concentrations on the membrane has not been carried out. Such an approach is a powerful way to test existing and novel models that are difficult to test using a purely experimental approach. Here, we extract time series from previously published fluorescence microscopy time lapse images of in vitro experiments and fit two previously described and one novel mathematical model to the data. We find that the novel model, which we call the Asymmetric Activation with Bridged Stability Model, fits the time-course data best. It is also consistent with known biochemistry and explains the dual MinE role via MinE-dependent membrane stability that transitions under the influence of rising MinE to membrane instability with positive feedback. Our results reveal a more complex network of interactions between MinD and MinE underlying Min-system dynamics than previously considered.
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Affiliation(s)
- William C. Carlquist
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Eric N. Cytrynbaum
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
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9
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Kabashin AV, Kravets VG, Grigorenko AN. Label-free optical biosensing: going beyond the limits. Chem Soc Rev 2023; 52:6554-6585. [PMID: 37681251 DOI: 10.1039/d3cs00155e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Label-free optical biosensing holds great promise for a variety of applications in biomedical diagnostics, environmental and food safety, and security. It is already used as a key tool in the investigation of biomolecular binding events and reaction constants in real time and offers further potential additional functionalities and low-cost designs. However, the sensitivity of this technology does not match the routinely used but expensive and slow labelling methods. Therefore, label-free optical biosensing remains predominantly a research tool. Here we discuss how one can go beyond the limits of detection provided by standard optical biosensing platforms and achieve a sensitivity of label-free biosensing that is superior to labelling methods. To this end we review newly emerging optical implementations that overcome current sensitivity barriers by employing novel structural architectures, artificial materials (metamaterials and hetero-metastructures) and using phase of light as a sensing parameter. Furthermore, we elucidate the mechanism of plasmonic phase biosensing and review hyper-sensitive transducers, which can achieve detection limits at the single molecule level (less than 1 fg mm-2) and make it possible to detect analytes at several orders of magnitude lower concentrations than so far reported in literature. We finally discuss newly emerging layouts based on dielectric nanomaterials, bound states in continuum, and exceptional points.
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Affiliation(s)
- Andrei V Kabashin
- Aix Marseille Université, CNRS, UMR 7341 CNRS, LP3, Campus de Luminy-case 917, 13288, Marseille Cedex 9, France.
| | - Vasyl G Kravets
- School of Physics and Astronomy, University of Manchester, Manchester, M13 9PL, UK.
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10
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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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11
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Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Dev Cell 2023; 58:1315-1332. [PMID: 37419118 DOI: 10.1016/j.devcel.2023.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/22/2023] [Accepted: 06/08/2023] [Indexed: 07/09/2023]
Abstract
Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.
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Affiliation(s)
- Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria; Medical University of Vienna, Center for Medical Biochemistry, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
| | - Martin Loose
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria; University of Vienna, Center for Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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12
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Reinhardt R, Leonard TA. A critical evaluation of protein kinase regulation by activation loop autophosphorylation. eLife 2023; 12:e88210. [PMID: 37470698 PMCID: PMC10359097 DOI: 10.7554/elife.88210] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Phosphorylation of proteins is a ubiquitous mechanism of regulating their function, localization, or activity. Protein kinases, enzymes that use ATP to phosphorylate protein substrates are, therefore, powerful signal transducers in eukaryotic cells. The mechanism of phosphoryl-transfer is universally conserved among protein kinases, which necessitates the tight regulation of kinase activity for the orchestration of cellular processes with high spatial and temporal fidelity. In response to a stimulus, many kinases enhance their own activity by autophosphorylating a conserved amino acid in their activation loop, but precisely how this reaction is performed is controversial. Classically, kinases that autophosphorylate their activation loop are thought to perform the reaction in trans, mediated by transient dimerization of their kinase domains. However, motivated by the recently discovered regulation mechanism of activation loop cis-autophosphorylation by a kinase that is autoinhibited in trans, we here review the various mechanisms of autoregulation that have been proposed. We provide a framework for critically evaluating biochemical, kinetic, and structural evidence for protein kinase dimerization and autophosphorylation, and share some thoughts on the implications of these mechanisms within physiological signaling networks.
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Affiliation(s)
- Ronja Reinhardt
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
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13
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. RESEARCH SQUARE 2023:rs.3.rs-3060076. [PMID: 37461524 PMCID: PMC10350206 DOI: 10.21203/rs.3.rs-3060076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
HIV-1 capsid assembly is an essential process in the virus infection cycle. Initiation of capsid assembly involves viral proteins, genomic RNA, and the inner leaflet of the plasma membrane, facilitated by a number of cellular factors1. The viral structural protein Gag plays a number of central roles in this process, including association with the membrane, selective binding of genomic RNA, and oligomerization and packaging to ultimately produce an immature budded pro-viral particle2. While there have been intensive studies regarding the early stages of Gag assembly, there is a lack of consensus on the mechanism for nucleation and growth of Gag complexes3-7. Here we show that myristoylated Gag forms a trimer nucleus in a model membrane that can selectively bind a dimeric RNA containing the packaging signal. Subsequent growth of myristoyl-Gag oligomers requires vRNA, and occurs by addition of 1 or 2 Gag monomers at a time from solution. These data support a model where the immature capsid lattice formation occurs by a gradual lattice edge expansion, following a trimeric nucleation event. The dynamic single molecule data that support this model were recorded using mass photometry, involving full length myristoylated protein, RNA, and lipid together. These data are the first to support a lattice edge expansion model of Gag during early stages of assembly in a biological-relevant setting, providing insights to the fundamental models of virus structural protein assembly process.
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Affiliation(s)
- Anne X.-Z. Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John A. Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
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14
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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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15
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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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16
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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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17
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525415. [PMID: 36747785 PMCID: PMC9901173 DOI: 10.1101/2023.01.27.525415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mass photometry (MP) was used to investigate the assembly of myristoylated full-length HIV-1 Gag (myr-Gag) and vRNA 5’ UTR fragment in a supported lipid bilayer (SLB) model system. The MP trajectories demonstrated that Gag trimerization on the membrane is a key step of early Gag assembly in the presence of vRNA. Growth of myr-Gag oligomers requires vRNA, occuring by addition of 1 or 2 monomers at a time from solution. These data support a model where formation of the Gag hexamers characteristic of the immature capsid lattice occurs by a gradual edge expansion, following a trimeric nucleation event. These dynamic single molecule data involving protein, RNA, and lipid components together, provide novel and fundamental insights into the initiation of virus capsid assembly.
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18
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Meindlhumer S, Brauns F, Finžgar JR, Kerssemakers J, Dekker C, Frey E. Directing Min protein patterns with advective bulk flow. Nat Commun 2023; 14:450. [PMID: 36707506 PMCID: PMC9883515 DOI: 10.1038/s41467-023-35997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD concentration ratios, upstream propagation for large ratios, but multistability of both propagation directions in between. Whereas downstream propagation can be described by a minimal model that disregards MinE conformational switching, upstream propagation can be reproduced by a reduced switch model, where increased MinD bulk concentrations on the upstream side promote protein attachment. Our study demonstrates that a differential flow, where bulk flow advects protein concentrations in the bulk, but not on the surface, can control surface-pattern propagation. This suggests that flow can be used to probe molecular features and to constrain mathematical models for pattern-forming systems.
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Affiliation(s)
- Sabrina Meindlhumer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Jernej Rudi Finžgar
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, 80539, Munich, Germany.
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19
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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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20
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Niebling S, Burastero O, García-Alai M. Biophysical Characterization of Membrane Proteins. Methods Mol Biol 2023; 2652:215-230. [PMID: 37093478 DOI: 10.1007/978-1-0716-3147-8_12] [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] [Indexed: 04/25/2023]
Abstract
Membrane proteins are responsible for a large variety of tasks in organisms and of particular interesting as drug targets. At the same time, they are notoriously difficult to work with and require a thorough characterization before proceeding with structural studies. Here, we present a biophysical pipeline to characterize membrane proteins focusing on the optimization of stability, aggregation behavior, and homogeneity. The pipeline shown here is built on three biophysical techniques: differential scanning fluorimetry using native protein fluorescence (nano differential scanning fluorimetry), dynamic light scattering, and mass photometry. For each of these techniques, we provide detailed protocols for performing experiments and data analysis.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
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21
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Loose M, Auer A, Brognara G, Budiman HR, Kowalski L, Matijević I. In vitro
reconstitution of small
GTPase
regulation. FEBS Lett 2022; 597:762-777. [PMID: 36448231 DOI: 10.1002/1873-3468.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.
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Affiliation(s)
- Martin Loose
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Albert Auer
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Gabriel Brognara
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | | | - Lukasz Kowalski
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Ivana Matijević
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
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22
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Lavania A, Carpenter WB, Oltrogge LM, Perez D, Turnšek JB, Savage DF, Moerner WE. Exploring Masses and Internal Mass Distributions of Single Carboxysomes in Free Solution Using Fluorescence and Interferometric Scattering in an Anti-Brownian Trap. J Phys Chem B 2022; 126:8747-8759. [PMID: 36282790 PMCID: PMC9639131 DOI: 10.1021/acs.jpcb.2c05939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Carboxysomes are self-assembled bacterial microcompartments that facilitate carbon assimilation by colocalizing the enzymes of CO2 fixation within a protein shell. These microcompartments can be highly heterogeneous in their composition and filling, so measuring the mass and loading of an individual carboxysome would allow for better characterization of its assembly and function. To enable detailed and extended characterizations of single nanoparticles in solution, we recently demonstrated an improved interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which tracks the position of a single nanoparticle via its scattering of a near-infrared beam and applies feedback to counteract its Brownian motion. Importantly, the scattering signal can be related to the mass of nanoscale proteinaceous objects, whose refractive indices are well-characterized. We calibrate single-particle scattering cross-section measurements in the ISABEL trap and determine individual carboxysome masses in the 50-400 MDa range by analyzing their scattering cross sections with a core-shell model. We further investigate carboxysome loading by combining mass measurements with simultaneous fluorescence reporting from labeled internal components. This method may be extended to other biological objects, such as viruses or extracellular vesicles, and can be combined with orthogonal fluorescence reporters to achieve precise physical and chemical characterization of individual nanoscale biological objects.
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Affiliation(s)
- Abhijit
A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California94305, United States,Department
of Applied Physics, Stanford University, Stanford, California94305, United States
| | - William B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California94305, United States
| | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California94305, United States,Department
of Applied Physics, Stanford University, Stanford, California94305, United States,
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23
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Ding L, Shan X, Wang D, Liu B, Du Z, Di X, Chen C, Maddahfar M, Zhang L, Shi Y, Reece P, Halkon B, Aharonovich I, Xu X, Wang F. Lanthanide Ion Resonance-Driven Rayleigh Scattering of Nanoparticles for Dual-Modality Interferometric Scattering Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203354. [PMID: 35975425 PMCID: PMC9661846 DOI: 10.1002/advs.202203354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Light scattering from nanoparticles is significant in nanoscale imaging, photon confinement. and biosensing. However, engineering the scattering spectrum, traditionally by modifying the geometric feature of particles, requires synthesis and fabrication with nanometre accuracy. Here it is reported that doping lanthanide ions can engineer the scattering properties of low-refractive-index nanoparticles. When the excitation wavelength matches the ion resonance frequency of lanthanide ions, the polarizability and the resulted scattering cross-section of nanoparticles are dramatically enhanced. It is demonstrated that these purposely engineered nanoparticles can be used for interferometric scattering (iSCAT) microscopy. Conceptually, a dual-modality iSCAT microscopy is further developed to identify different nanoparticle types in living HeLa cells. The work provides insight into engineering the scattering features by doping elements in nanomaterials, further inspiring exploration of the geometry-independent scattering modulation strategy.
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Affiliation(s)
- Lei Ding
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
- School of Electrical and Data EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Xuchen Shan
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
- School of Electrical and Data EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
- School of PhysicsBeihang UniversityBeijing100191China
| | - Dejiang Wang
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Baolei Liu
- School of PhysicsBeihang UniversityBeijing100191China
| | - Ziqing Du
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Xiangjun Di
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Chaohao Chen
- School of Electrical and Data EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Mahnaz Maddahfar
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Ling Zhang
- School of Electrical and Data EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Yuzhi Shi
- National Key Laboratory of Science and Technology on Micro/Nano FabricationDepartment of Micro/Nano ElectronicsShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Peter Reece
- School of PhysicsThe University of New South WalesKensingtonNew South Wales2033Australia
| | - Benjamin Halkon
- Centre for Audio, Acoustics & VibrationFaculty of Engineering & ITUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Igor Aharonovich
- School of Mathematical and Physical SciencesFaculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
- ARC Centre of Excellence for Transformative Meta‐Optical Systems (TMOS)Faculty of ScienceUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Xiaoxue Xu
- School of Biomedical Engineering, Faculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
| | - Fan Wang
- School of Electrical and Data EngineeringFaculty of Engineering and Information TechnologyUniversity of Technology SydneyUltimoNew South Wales2007Australia
- School of PhysicsBeihang UniversityBeijing100191China
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24
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Paul S, Lyons A, Kirchner R, Woodside MT. Quantifying Oligomer Populations in Real Time during Protein Aggregation Using Single-Molecule Mass Photometry. ACS NANO 2022; 16:16462-16470. [PMID: 36126253 PMCID: PMC9620981 DOI: 10.1021/acsnano.2c05739] [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: 06/10/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Protein aggregation is a hallmark of many neurodegenerative diseases. The early stages of the aggregation cascade are crucial because small oligomers are thought to be key neurotoxic species, but they are difficult to study because they feature heterogeneous mixtures of transient states. We show how the populations of different oligomers can be tracked as they evolve over time during aggregation using single-molecule mass photometry to measure individually the masses of the oligomers present in solution. By applying the approach to tau protein, whose aggregates are linked to diseases including Alzheimer's and frontotemporal dementia, we found that tau existed in an equilibrium between monomers, dimers, and trimers before aggregation was triggered. Once aggregation commenced, the monomer population dropped continuously, paired first with a rise in the population of the smallest oligomers and then a steep drop as the protein was incorporated into larger oligomers and fibrils. Fitting these populations to kinetic models allowed different models of aggregation to be tested, identifying the most likely mechanism and quantifying the microscopic rates for each step in the mechanism. This work demonstrates a powerful approach for the characterization of previously inaccessible regimes in protein aggregation and building quantitative mechanistic models.
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Affiliation(s)
- Simanta
Sarani Paul
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Aaron Lyons
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Russell Kirchner
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Michael T. Woodside
- Department
of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada
- Centre
for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G2E1, Canada
- Li Ka
Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G2E1, Canada
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25
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Niebling S, Veith K, Vollmer B, Lizarrondo J, Burastero O, Schiller J, Struve García A, Lewe P, Seuring C, Witt S, García-Alai M. Biophysical Screening Pipeline for Cryo-EM Grid Preparation of Membrane Proteins. Front Mol Biosci 2022; 9:882288. [PMID: 35813810 PMCID: PMC9259969 DOI: 10.3389/fmolb.2022.882288] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Successful sample preparation is the foundation to any structural biology technique. Membrane proteins are of particular interest as these are important targets for drug design, but also notoriously difficult to work with. For electron cryo-microscopy (cryo-EM), the biophysical characterization of sample purity, homogeneity, and integrity as well as biochemical activity is the prerequisite for the preparation of good quality cryo-EM grids as these factors impact the result of the computational reconstruction. Here, we present a quality control pipeline prior to single particle cryo-EM grid preparation using a combination of biophysical techniques to address the integrity, purity, and oligomeric states of membrane proteins and its complexes to enable reproducible conditions for sample vitrification. Differential scanning fluorimetry following the intrinsic protein fluorescence (nDSF) is used for optimizing buffer and detergent conditions, whereas mass photometry and dynamic light scattering are used to assess aggregation behavior, reconstitution efficiency, and oligomerization. The data collected on nDSF and mass photometry instruments can be analyzed with web servers publicly available at spc.embl-hamburg.de. Case studies to optimize conditions prior to cryo-EM sample preparation of membrane proteins present an example quality assessment to corroborate the usefulness of our pipeline.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Benjamin Vollmer
- Centre for Structural Systems Biology (CSSB), Leibniz Institute of Virology (LIV), Hamburg, Germany
| | | | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Janina Schiller
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Angelica Struve García
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- *Correspondence: María García-Alai,
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26
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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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27
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles. Nat Methods 2022; 19:751-758. [PMID: 35637303 PMCID: PMC9184284 DOI: 10.1038/s41592-022-01491-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/12/2022] [Indexed: 12/18/2022]
Abstract
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes. Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.
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Priest L, Peters JS, Kukura P. Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins. Chem Rev 2021; 121:11937-11970. [PMID: 34587448 PMCID: PMC8517954 DOI: 10.1021/acs.chemrev.1c00271] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 02/02/2023]
Abstract
Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.
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Affiliation(s)
| | | | - Philipp Kukura
- Physical and Theoretical
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Vala M, Piliarik M. Weighing single protein complexes on the go. Nat Methods 2021; 18:1159-1160. [PMID: 34608317 DOI: 10.1038/s41592-021-01263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Milan Vala
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, Czech Republic.
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