1
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Jiang Y, Miyagi A, Wang X, Qiu B, Boudker O, Scheuring S. HS-AFM single-molecule structural biology uncovers basis of transporter wanderlust kinetics. Nat Struct Mol Biol 2024; 31:1286-1295. [PMID: 38632360 DOI: 10.1038/s41594-024-01260-3] [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: 07/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
The Pyrococcus horikoshii amino acid transporter GltPh revealed, like other channels and transporters, activity mode switching, previously termed wanderlust kinetics. Unfortunately, to date, the basis of these activity fluctuations is not understood, probably due to a lack of experimental tools that directly access the structural features of transporters related to their instantaneous activity. Here, we take advantage of high-speed atomic force microscopy, unique in providing simultaneous structural and temporal resolution, to uncover the basis of kinetic mode switching in proteins. We developed membrane extension membrane protein reconstitution that allows the analysis of isolated molecules. Together with localization atomic force microscopy, principal component analysis and hidden Markov modeling, we could associate structural states to a functional timeline, allowing six structures to be solved from a single molecule, and an inward-facing state, IFSopen-1, to be determined as a kinetic dead-end in the conformational landscape. The approaches presented on GltPh are generally applicable and open possibilities for time-resolved dynamic single-molecule structural biology.
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Affiliation(s)
- Yining Jiang
- Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology Program, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Atsushi Miyagi
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Xiaoyu Wang
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Biao Qiu
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Olga Boudker
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA.
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2
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [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] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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3
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Fukuda S, Ando T. Technical advances in high-speed atomic force microscopy. Biophys Rev 2023; 15:2045-2058. [PMID: 38192344 PMCID: PMC10771405 DOI: 10.1007/s12551-023-01171-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/19/2023] [Indexed: 01/10/2024] Open
Abstract
It has been 30 years since the outset of developing high-speed atomic force microscopy (HS-AFM), and 15 years have passed since its establishment in 2008. This advanced microscopy is capable of directly visualizing individual biological macromolecules in dynamic action and has been widely used to answer important questions that are inaccessible by other approaches. The number of publications on the bioapplications of HS-AFM has rapidly increased in recent years and has already exceeded 350. Although less visible than these biological studies, efforts have been made for further technical developments aimed at enhancing the fundamental performance of HS-AFM, such as imaging speed, low sample disturbance, and scan size, as well as expanding its functionalities, such as correlative microscopy, temperature control, buffer exchange, and sample manipulations. These techniques can expand the range of HS-AFM applications. After summarizing the key technologies underlying HS-AFM, this article focuses on recent technical advances and discusses next-generation HS-AFM.
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Affiliation(s)
- Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-Machi, Kanazawa, 920-1192 Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-Machi, Kanazawa, 920-1192 Japan
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4
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Pan Y, Zhan J, Jiang Y, Xia D, Scheuring S. A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1. Nat Commun 2023; 14:6369. [PMID: 37821516 PMCID: PMC10567702 DOI: 10.1038/s41467-023-41806-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023] Open
Abstract
Bcs1, a homo-heptameric transmembrane AAA-ATPase, facilitates folded Rieske iron-sulfur protein translocation across the inner mitochondrial membrane. Structures in different nucleotide states (ATPγS, ADP, apo) provided conformational snapshots, but the kinetics and structural transitions of the ATPase cycle remain elusive. Here, using high-speed atomic force microscopy (HS-AFM) and line scanning (HS-AFM-LS), we characterized single-molecule Bcs1 ATPase cycling. While the ATP conformation had ~5600 ms lifetime, independent of the ATP-concentration, the ADP/apo conformation lifetime was ATP-concentration dependent and reached ~320 ms at saturating ATP-concentration, giving a maximum turnover rate of 0.17 s-1. Importantly, Bcs1 ATPase cycle conformational changes occurred in concert. Furthermore, we propose that the transport mechanism involves opening the IMS gate through energetically costly straightening of the transmembrane helices, potentially driving rapid gate resealing. Overall, our results establish a concerted ATPase cycle mechanism in Bcs1, distinct from other AAA-ATPases that use a hand-over-hand mechanism.
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Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Jingyu Zhan
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA.
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5
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Sanganna Gari RR, Tagiltsev G, Pumroy RA, Jiang Y, Blackledge M, Moiseenkova-Bell VY, Scheuring S. Intrinsically disordered regions in TRPV2 mediate protein-protein interactions. Commun Biol 2023; 6:966. [PMID: 37736816 PMCID: PMC10516966 DOI: 10.1038/s42003-023-05343-7] [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: 08/12/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
Transient receptor potential (TRP) ion channels are gated by diverse intra- and extracellular stimuli leading to cation inflow (Na+, Ca2+) regulating many cellular processes and initiating organismic somatosensation. Structures of most TRP channels have been solved. However, structural and sequence analysis showed that ~30% of the TRP channel sequences, mainly the N- and C-termini, are intrinsically disordered regions (IDRs). Unfortunately, very little is known about IDR 'structure', dynamics and function, though it has been shown that they are essential for native channel function. Here, we imaged TRPV2 channels in membranes using high-speed atomic force microscopy (HS-AFM). The dynamic single molecule imaging capability of HS-AFM allowed us to visualize IDRs and revealed that N-terminal IDRs were involved in intermolecular interactions. Our work provides evidence about the 'structure' of the TRPV2 IDRs, and that the IDRs may mediate protein-protein interactions.
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Affiliation(s)
| | - Grigory Tagiltsev
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yining Jiang
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, New York, USA
| | - Martin Blackledge
- Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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6
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Pan Y, Pohjolainen E, Schmidpeter PAM, Vaiana AC, Nimigean CM, Grubmüller H, Scheuring S. Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nat Struct Mol Biol 2023; 30:512-520. [PMID: 36973509 DOI: 10.1038/s41594-023-00955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Cyclic nucleotide-gated ion channels are crucial in many physiological processes such as vision and pacemaking in the heart. SthK is a prokaryotic homolog with high sequence and structure similarities to hyperpolarization-activated and cyclic nucleotide-modulated and cyclic nucleotide-gated channels, especially at the level of the cyclic nucleotide binding domains (CNBDs). Functional measurements showed that cyclic adenosine monophosphate (cAMP) is a channel activator while cyclic guanosine monophosphate (cGMP) barely leads to pore opening. Here, using atomic force microscopy single-molecule force spectroscopy and force probe molecular dynamics simulations, we unravel quantitatively and at the atomic level how CNBDs discriminate between cyclic nucleotides. We find that cAMP binds to the SthK CNBD slightly stronger than cGMP and accesses a deep-bound state that a cGMP-bound CNBD cannot reach. We propose that the deep binding of cAMP is the discriminatory state that is essential for cAMP-dependent channel activation.
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Affiliation(s)
- Yangang Pan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Emmi Pohjolainen
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | | | - Andrea C Vaiana
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
- Institute of Biophysics, National Research Council, Palermo, Italy
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Helmut Grubmüller
- Max Planck Institute for Multidisciplinary Sciences, Theoretical and Computational Biophysics Department, Goettingen, Germany
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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7
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Jiang Y, Thienpont B, Sapuru V, Hite RK, Dittman JS, Sturgis JN, Scheuring S. Membrane-mediated protein interactions drive membrane protein organization. Nat Commun 2022; 13:7373. [PMID: 36450733 PMCID: PMC9712761 DOI: 10.1038/s41467-022-35202-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
The plasma membrane's main constituents, i.e., phospholipids and membrane proteins, are known to be organized in lipid-protein functional domains and supercomplexes. No active membrane-intrinsic process is known to establish membrane organization. Thus, the interplay of thermal fluctuations and the biophysical determinants of membrane-mediated protein interactions must be considered to understand membrane protein organization. Here, we used high-speed atomic force microscopy and kinetic and membrane elastic theory to investigate the behavior of a model membrane protein in oligomerization and assembly in controlled lipid environments. We find that membrane hydrophobic mismatch modulates oligomerization and assembly energetics, and 2D organization. Our experimental and theoretical frameworks reveal how membrane organization can emerge from Brownian diffusion and a minimal set of physical properties of the membrane constituents.
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Affiliation(s)
- Yining Jiang
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA
| | - Batiste Thienpont
- grid.5399.60000 0001 2176 4817Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Unité Mixte de Recherche (UMR) 7255, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université, Marseille, France
| | - Vinay Sapuru
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA ,Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065 USA
| | - Richard K. Hite
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Jeremy S. Dittman
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Biochemistry, 1300 York Avenue, New York, NY 10065 USA
| | - James N. Sturgis
- grid.5399.60000 0001 2176 4817Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Unité Mixte de Recherche (UMR) 7255, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université, Marseille, France
| | - Simon Scheuring
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XKavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 USA
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8
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Jiao F, Dehez F, Ni T, Yu X, Dittman JS, Gilbert R, Chipot C, Scheuring S. Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism. Nat Commun 2022; 13:5039. [PMID: 36028507 PMCID: PMC9418332 DOI: 10.1038/s41467-022-32757-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
Perforin-2 (PFN2, MPEG1) is a pore-forming protein that acts as a first line of defense in the mammalian immune system, rapidly killing engulfed microbes within the phagolysosome in macrophages. PFN2 self-assembles into hexadecameric pre-pore rings that transition upon acidification into pores damaging target cell membranes. Here, using high-speed atomic force microscopy (HS-AFM) imaging and line-scanning and molecular dynamics simulation, we elucidate PFN2 pre-pore to pore transition pathways and dynamics. Upon acidification, the pre-pore rings (pre-pore-I) display frequent, 1.8 s-1, ring-opening dynamics that eventually, 0.2 s-1, initiate transition into an intermediate, short-lived, ~75 ms, pre-pore-II state, inducing a clockwise pre-pore-I to pre-pore-II propagation. Concomitantly, the first pre-pore-II subunit, undergoes a major conformational change to the pore state that propagates also clockwise at a rate ~15 s-1. Thus, the pre-pore to pore transition is a clockwise hand-over-hand mechanism that is accomplished within ~1.3 s. Our findings suggest a clockwise mechanism of membrane insertion that with variations may be general for the MACPF/CDC superfamily.
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Affiliation(s)
- Fang Jiao
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, USA.
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - François Dehez
- Laboratoire International Associé, Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no 7019, Université de Lorraine, Vandœuvre-lès-Nancy cedex, France
| | - Tao Ni
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Xiulian Yu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Calleva Research Centre for Evolution and Human Sciences, Magdalen College, University of Oxford, Oxford, UK
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Robert Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Calleva Research Centre for Evolution and Human Sciences, Magdalen College, University of Oxford, Oxford, UK
| | - Christophe Chipot
- Laboratoire International Associé, Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche no 7019, Université de Lorraine, Vandœuvre-lès-Nancy cedex, France
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, USA.
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9
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Sharma M, Biela AP, Kowalczyk A, Borzęcka-Solarz K, Piette BMAG, Gaweł S, Bishop J, Kukura P, Benesch JLP, Imamura M, Scheuring S, Heddle JG. Shape-Morphing of an Artificial Protein Cage with Unusual Geometry Induced by a Single Amino Acid Change. ACS NANOSCIENCE AU 2022; 2:404-413. [PMID: 36281256 PMCID: PMC9585630 DOI: 10.1021/acsnanoscienceau.2c00019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Artificial protein
cages are constructed from multiple protein
subunits. The interaction between the subunits, notably the angle
formed between them, controls the geometry of the resulting cage.
Here, using the artificial protein cage, “TRAP-cage”,
we show that a simple alteration in the position of a single amino
acid responsible for Au(I)-mediated subunit–subunit interactions
in the constituent ring-shaped building blocks results in a more acute
dihedral angle between them. In turn, this causes a dramatic shift
in the structure from a 24-ring cage with an octahedral symmetry to
a 20-ring cage with a C2 symmetry. This symmetry change is accompanied
by a decrease in the number of Au(I)-mediated bonds between cysteines
and a concomitant change in biophysical properties of the cage.
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Affiliation(s)
- Mohit Sharma
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
- School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Artur P. Biela
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
| | - Agnieszka Kowalczyk
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
- Faculty of Mathematics and Computer Science, Jagiellonian University, Kraków 30-348, Poland
| | - Kinga Borzęcka-Solarz
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
| | | | - Szymon Gaweł
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
| | - Joshua Bishop
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, U.K
| | - Philipp Kukura
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, U.K
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, U.K
| | - Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York City, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, New York 10065, United States
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, New York 10065, United States
| | - Jonathan G. Heddle
- Malopolska Center of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków 30-387, Poland
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10
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Stupka I, Azuma Y, Biela AP, Imamura M, Scheuring S, Pyza E, Woźnicka O, Maskell DP, Heddle JG. Chemically induced protein cage assembly with programmable opening and cargo release. SCIENCE ADVANCES 2022; 8:eabj9424. [PMID: 34985943 PMCID: PMC8730398 DOI: 10.1126/sciadv.abj9424] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.
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Affiliation(s)
- Izabela Stupka
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Postgraduate School of Molecular Medicine, 02-091 Warsaw, Poland
| | - Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Artur P. Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York City, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Daniel P. Maskell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jonathan G. Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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11
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Shimizu M, Okamoto C, Umeda K, Watanabe S, Ando T, Kodera N. An ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz for high-speed atomic force microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:013701. [PMID: 35104993 DOI: 10.1063/5.0072722] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The Z-scanner is the major component limiting the speed performance of all current high-speed atomic force microscopy systems. Here, we present an ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz, achieving a record response time of ∼0.14 µs, approximately twice as fast as conventional piezoelectric-based Z-scanners. In the mechanical design, a small piezo-stack is supported at its bottom four vertices on a cone-like hollow, allowing the resonance frequency of the Z-scanner to remain as high as that of the piezo in free vibration. Its maximum displacement, ∼190 nm at 50 V, is large enough for imaging bio-molecules. For imaging bio-molecules in a buffer solution, the upper half of the Z-scanner is wrapped in a thin film resistant to water and chemicals, providing an excellent waterproof and mechanical durability without lowering the resonance frequency. We demonstrate that this Z-scanner can observe actin filaments, fragile biological polymers, for more than five times longer than the conventional Z-scanner at a tip velocity of 800 µm/s.
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Affiliation(s)
- Masahiro Shimizu
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Chihiro Okamoto
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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13
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Heath GR, Lin YC, Matin TR, Scheuring S. Structural dynamics of channels and transporters by high-speed atomic force microscopy. Methods Enzymol 2021; 652:127-159. [PMID: 34059280 DOI: 10.1016/bs.mie.2021.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Channels and transporters are vital for transmembrane transport of ions and solutes, and also of larger compounds such as lipids and macromolecules. Therefore, they are crucial in many biological processes such as sensing, signal transduction, and the regulation of the distribution of molecules. Dysfunctions of these membrane proteins are associated to numerous diseases, and their interaction with drugs is critical in medicine. Understanding the behavior of channels and transporters requires structural and dynamic information to decipher the molecular mechanisms underlying their function. High-Speed Atomic Force Microscopy (HS-AFM) now allows the study of single transmembrane channels and transporters in action under physiological conditions, i.e., at ambient temperature and pressure, in physiological buffer and in a membrane, and in a most direct, label-free manner. In this chapter, we discuss the HS-AFM sample preparation, application, and data analysis protocols to study the structural and conformational dynamics of membrane-embedded channels and transporters.
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Affiliation(s)
- George R Heath
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | - Yi-Chih Lin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Tina R Matin
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, United States; Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, United States.
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Fukuda S, Ando T. Faster high-speed atomic force microscopy for imaging of biomolecular processes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:033705. [PMID: 33820001 DOI: 10.1063/5.0032948] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) has enabled observing protein molecules during their functional activity at rates of 1-12.5 frames per second (fps), depending on the imaging conditions, sample height, and fragility. To meet the increasing demand for the great expansion of observable dynamic molecular processes, faster HS-AFM with less disturbance is imperatively needed. However, even a 50% improvement in the speed performance imposes tremendous challenges, as the optimization of major rate-limiting components for their fast response is nearly matured. This paper proposes an alternative method that can lower the feedback control error and thereby enhance the imaging rate. This method can be implemented in any HS-AFM system by minor modifications of the software and hardware. The resulting faster and less-disturbing imaging capabilities are demonstrated by the imaging of relatively fragile actin filaments and microtubules near the video rate, and of actin polymerization that occurs through weak intermolecular interactions, at ∼8 fps.
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Affiliation(s)
- Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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15
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Chillón I, Marcia M. The molecular structure of long non-coding RNAs: emerging patterns and functional implications. Crit Rev Biochem Mol Biol 2020; 55:662-690. [PMID: 33043695 DOI: 10.1080/10409238.2020.1828259] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts that regulate vital cellular processes and are crucially connected to diseases. Despite their unprecedented molecular complexity, it is emerging that lncRNAs possess distinct structural motifs. Remarkably, the 3D shape and topology of full-length, native lncRNAs have been visualized for the first time in the last year. These studies reveal that lncRNA structures dictate lncRNA functions. Here, we review experimentally determined lncRNA structures and emphasize that lncRNA structural characterization requires synergistic integration of computational, biochemical and biophysical approaches. Based on these emerging paradigms, we discuss how to overcome the challenges posed by the complex molecular architecture of lncRNAs, with the goal of obtaining a detailed understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
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16
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Uroda T, Chillón I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M. Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques. Nat Protoc 2020; 15:2107-2139. [PMID: 32451442 DOI: 10.1038/s41596-020-0323-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered transcripts that regulate vital cellular processes, such as cellular differentiation and DNA replication, and are crucially connected to diseases. Although the 3D structures of lncRNAs are key determinants of their function, the unprecedented molecular complexity of lncRNAs has so far precluded their 3D structural characterization at high resolution. It is thus paramount to develop novel approaches for biochemical and biophysical characterization of these challenging targets. Here, we present a protocol that integrates non-denaturing lncRNA purification with in-solution hydrodynamic analysis and single-particle atomic force microscopy (AFM) imaging to produce highly homogeneous lncRNA preparations and visualize their 3D topology at ~15-Å resolution. Our protocol is suitable for imaging lncRNAs in biologically active conformations and for measuring structural defects of functionally inactive mutants that have been identified by cell-based functional assays. Once optimized for the specific target lncRNA of choice, our protocol leads from cloning to AFM imaging within 3-4 weeks and can be implemented using state-of-the-art biochemical and biophysical instrumentation by trained researchers familiar with RNA handling and supported by AFM and small-angle X-ray scattering (SAXS) experts.
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Affiliation(s)
- Tina Uroda
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.,Department of BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Marie Teulon
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Ombeline Pessey
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | | | - Jean-Luc Pellequer
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France.
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17
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Ando T. High-speed atomic force microscopy. Curr Opin Chem Biol 2019; 51:105-112. [DOI: 10.1016/j.cbpa.2019.05.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
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Heath GR, Scheuring S. Advances in high-speed atomic force microscopy (HS-AFM) reveal dynamics of transmembrane channels and transporters. Curr Opin Struct Biol 2019; 57:93-102. [PMID: 30878714 DOI: 10.1016/j.sbi.2019.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
Recent advances in high-speed atomic force microscopy (HS-AFM) have made it possible to study the conformational dynamics of single unlabeled transmembrane channels and transporters. Improving environmental control with the integration of a non-disturbing buffer exchange system, which in turn allows the gradual change of conditions during HS-AFM operation, has provided a breakthrough toward the performance of structural titration experiments. Further advancements in temporal resolution with the use of line scanning and height spectroscopy techniques show how high-speed atomic force microscopy can measure millisecond to microsecond dynamics, pushing this method beyond current spatial and temporal limits offered by less direct techniques.
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Affiliation(s)
- George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA.
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Heath GR, Scheuring S. High-speed AFM height spectroscopy reveals µs-dynamics of unlabeled biomolecules. Nat Commun 2018; 9:4983. [PMID: 30478320 PMCID: PMC6255864 DOI: 10.1038/s41467-018-07512-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/02/2018] [Indexed: 01/21/2023] Open
Abstract
Dynamics are fundamental to the functions of biomolecules and can occur on a wide range of time and length scales. Here we develop and apply high-speed AFM height spectroscopy (HS-AFM-HS), a technique whereby we monitor the sensing of a HS-AFM tip at a fixed position to directly detect the motions of unlabeled molecules underneath. This gives Angstrom spatial and microsecond temporal resolutions. In conjunction with HS-AFM imaging modes to precisely locate areas of interest, HS-AFM-HS measures simultaneously surface concentrations, diffusion coefficients and oligomer sizes of annexin-V on model membranes to decipher key kinetics allowing us to describe the entire annexin-V membrane-association and self-assembly process in great detail and quantitatively. This work displays how HS-AFM-HS can assess the dynamics of unlabeled bio-molecules over several orders of magnitude and separate the various dynamic components spatiotemporally. The dynamics of biomolecules can occur over a wide range of time and length scales. Here the authors develop a high-speed AFM height spectroscopy method to directly detect the motion of unlabeled molecules at Angstrom spatial and microsecond temporal resolution.
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Affiliation(s)
- George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY, 10065, USA.,Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY, 10065, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY, 10065, USA. .,Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY, 10065, USA.
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