1
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Kohantorabi M, Ugolotti A, Sochor B, Roessler J, Wagstaffe M, Meinhardt A, Beck EE, Dolling DS, Garcia MB, Creutzburg M, Keller TF, Schwartzkopf M, Vayalil SK, Thuenauer R, Guédez G, Löw C, Ebert G, Protzer U, Hammerschmidt W, Zeidler R, Roth SV, Di Valentin C, Stierle A, Noei H. Light-Induced Transformation of Virus-Like Particles on TiO 2. ACS APPLIED MATERIALS & INTERFACES 2024; 16:37275-37287. [PMID: 38959130 PMCID: PMC11261565 DOI: 10.1021/acsami.4c07151] [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: 05/01/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
Titanium dioxide (TiO2) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO2 surface. The in situ GISAXS measurements under an N2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.
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Affiliation(s)
- Mona Kohantorabi
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Aldo Ugolotti
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Benedikt Sochor
- Deutsches
Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Advanced
Light Source, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Johannes Roessler
- Helmholtz
Zentrum München, German Research
Center for Environmental Health, 81377 Munich, Germany
- German Center
for Infection Research (DZIF), Partner Site Munich, 81377 Munich, Germany
| | - Michael Wagstaffe
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Alexander Meinhardt
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- University
of Hamburg, Notkestraße
9-11, 22607 Hamburg, Germany
| | - E. Erik Beck
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- University
of Hamburg, Notkestraße
9-11, 22607 Hamburg, Germany
| | - Daniel Silvan Dolling
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- University
of Hamburg, Notkestraße
9-11, 22607 Hamburg, Germany
| | - Miguel Blanco Garcia
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- University
of Hamburg, Notkestraße
9-11, 22607 Hamburg, Germany
| | - Marcus Creutzburg
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Thomas F. Keller
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Department
of Physics, University of Hamburg, Notkestraße 9-11, 22607 Hamburg, Germany
| | | | - Sarathlal Koyiloth Vayalil
- Deutsches
Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Applied
Science Cluster, UPES, 248007 Dehradun, India
| | - Roland Thuenauer
- Technology
Platform Light Microscopy (TPLM), Universität
Hamburg (UHH), 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
- Technology
Platform Light Microscopy and Image Analysis (TP MIA), Leibniz Institute of Virology (LIV), 20251 Hamburg, Germany
| | - Gabriela Guédez
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
| | - Gregor Ebert
- Institute
of Virology, Technical University of Munich/Helmholtz
Munich, 81675 Munich, Germany
| | - Ulrike Protzer
- Institute
of Virology, Technical University of Munich/Helmholtz
Munich, 81675 Munich, Germany
| | - Wolfgang Hammerschmidt
- Helmholtz
Zentrum München, German Research
Center for Environmental Health, 81377 Munich, Germany
- German Center
for Infection Research (DZIF), Partner Site Munich, 81377 Munich, Germany
| | - Reinhard Zeidler
- Helmholtz
Zentrum München, German Research
Center for Environmental Health, 81377 Munich, Germany
- German Center
for Infection Research (DZIF), Partner Site Munich, 81377 Munich, Germany
- Department
of Otorhinolaryngology, LMU University Hospital, LMU München, 81377 Munich, Germany
| | - Stephan V. Roth
- Deutsches
Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- KTH
Royal Institute of Technology, Teknikringen 56-58, 10044 Stockholm, Sweden
| | - Cristiana Di Valentin
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, Via Cozzi 55, 20125 Milano, Italy
| | - Andreas Stierle
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Department
of Physics, University of Hamburg, Notkestraße 9-11, 22607 Hamburg, Germany
| | - Heshmat Noei
- Centre
for X-ray and Nano Science CXNS, Deutsches
Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- The
Hamburg Centre for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
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2
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Cantero M, Rodríguez-Espinosa MJ, Strobl K, Ibáñez P, Díez-Martínez A, Martín-González N, Jiménez-Zaragoza M, Ortega-Esteban A, de Pablo PJ. Atomic Force Microscopy of Viruses: Stability, Disassembly, and Genome Release. Methods Mol Biol 2024; 2694:317-338. [PMID: 37824011 DOI: 10.1007/978-1-0716-3377-9_15] [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
In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages but also the evaluation of each physicochemical property which is able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter, we start revising some recipes for adsorbing protein shells on surfaces and how the geometrical dilation of tips can affect to the AFM topographies. This work also deals with the abilities of AFM to monitor TGEV coronavirus under changing conditions of the liquid environment. Subsequently, we describe several AFM approaches to study cargo release, aging, and multilayered viruses with single indentation and fatigue assays. Finally, we comment on a combined AFM/fluorescence application to study the influence of crowding on GFP packed within individual P22 bacteriophage capsids.
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Affiliation(s)
- Miguel Cantero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Jesús Rodríguez-Espinosa
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Ibáñez
- Department of Theoretical Physics of Condensed Matter, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alejandro Díez-Martínez
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pedro José de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
- Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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3
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Blaimschein N, Parameswaran H, Nagler G, Manioglu S, Helenius J, Ardelean C, Kuhn A, Guan L, Müller DJ. The insertase YidC chaperones the polytopic membrane protein MelB inserting and folding simultaneously from both termini. Structure 2023; 31:1419-1430.e5. [PMID: 37708891 PMCID: PMC10840855 DOI: 10.1016/j.str.2023.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
The insertion and folding of proteins into membranes is crucial for cell viability. Yet, the detailed contributions of insertases remain elusive. Here, we monitor how the insertase YidC guides the folding of the polytopic melibiose permease MelB into membranes. In vivo experiments using conditionally depleted E. coli strains show that MelB can insert in the absence of SecYEG if YidC resides in the cytoplasmic membrane. In vitro single-molecule force spectroscopy reveals that the MelB substrate itself forms two folding cores from which structural segments insert stepwise into the membrane. However, misfolding dominates, particularly in structural regions that interface the pseudo-symmetric α-helical domains of MelB. Here, YidC takes an important role in accelerating and chaperoning the stepwise insertion and folding process of both MelB folding cores. Our findings reveal a great flexibility of the chaperoning and insertase activity of YidC in the multifaceted folding processes of complex polytopic membrane proteins.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Hariharan Parameswaran
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Gisela Nagler
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | - Jonne Helenius
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland
| | | | - Andreas Kuhn
- Institute of Biology, University of Hohenheim, 70599 Stuttgart, Baden-Württemberg, Germany
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Basel-Stadt, Switzerland.
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4
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Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
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5
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Mari SA, Pluhackova K, Pipercevic J, Leipner M, Hiller S, Engel A, Müller DJ. Gasdermin-A3 pore formation propagates along variable pathways. Nat Commun 2022; 13:2609. [PMID: 35545613 PMCID: PMC9095878 DOI: 10.1038/s41467-022-30232-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/22/2022] [Indexed: 12/31/2022] Open
Abstract
Gasdermins are main effectors of pyroptosis, an inflammatory form of cell death. Released by proteolysis, the N-terminal gasdermin domain assembles large oligomers to punch lytic pores into the cell membrane. While the endpoint of this reaction, the fully formed pore, has been well characterized, the assembly and pore-forming mechanisms remain largely unknown. To resolve these mechanisms, we characterize mouse gasdermin-A3 by high-resolution time-lapse atomic force microscopy. We find that gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane gasdermin-A3 grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolve how the membrane-inserted amphiphilic β-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. The results show that without a vertical collapse gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response.
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Affiliation(s)
- Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
| | | | - Matthew Leipner
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | | | - Andreas Engel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
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6
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Dubrovin EV, Klinov DV. Atomic Force Microscopy of Biopolymers on Graphite Surfaces. POLYMER SCIENCE SERIES A 2021. [DOI: 10.1134/s0965545x2106002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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7
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Li M, Xi N, Liu L. Peak force tapping atomic force microscopy for advancing cell and molecular biology. NANOSCALE 2021; 13:8358-8375. [PMID: 33913463 DOI: 10.1039/d1nr01303c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Mei J, Yang H, Sun B, Liu C, Ai H. Small-Molecule Targeted Aβ 42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones. ACS Chem Neurosci 2021; 12:1197-1209. [PMID: 33687193 DOI: 10.1021/acschemneuro.1c00047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heavy evidence has confirmed that Aβ42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aβ42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-β peptide Aβ42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aβ and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aβ42 and Aβ40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aβ42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aβ40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aβ40 oligomer. The HSA distinction between Aβ42 and Aβ40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (β1) and C-terminal (β2) regions of Aβ42 peptide, two key nucleation regions for Aβ intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aβ42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aβ aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aβ aggregates.
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Affiliation(s)
- Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Bo Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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9
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Gupta A, Phang IY, Wohland T. To Hop or not to Hop: Exceptions in the FCS Diffusion Law. Biophys J 2020; 118:2434-2447. [PMID: 32333863 PMCID: PMC7231916 DOI: 10.1016/j.bpj.2020.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Diffusion obstacles in membranes have not been directly visualized because of fast membrane dynamics and the occurrence of subresolution molecular complexes. To understand the obstacle characteristics, mobility-based methods are often used as an indirect way of assessing the membrane structure. Molecular movement in biological plasma membranes is often characterized by anomalous diffusion, but the exact underlying mechanisms are still elusive. Imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS) is a well-established mobility-based method that provides spatially resolved diffusion coefficient maps and is combined with FCS diffusion law analysis to examine subresolution membrane organization. In recent years, although FCS diffusion law analysis has been instrumental in providing new insights into the membrane structure below the optical diffraction limit, there are certain exceptions and anomalies that require further clarification. To this end, we correlate the membrane structural features imaged by atomic force microscopy (AFM) with the dynamics measured using ITIR-FCS. We perform ITIR-FCS measurements on supported lipid bilayers (SLBs) of various lipid compositions to characterize the anomalous diffusion of lipid molecules in distinct obstacle configurations, along with the high-resolution imaging of the membrane structures with AFM. Furthermore, we validate our experimental results by performing simulations on image grids with experimentally determined obstacle configurations. This study demonstrates that FCS diffusion law analysis is a powerful tool to determine membrane heterogeneities implied from dynamics measurements. Our results corroborate the commonly accepted interpretations of imaging FCS diffusion law analysis, and we show that exceptions happen when domains reach the percolation threshold in a biphasic membrane and a network of domains behaves rather like a meshwork, resulting in hop diffusion.
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Affiliation(s)
- Anjali Gupta
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Inn Yee Phang
- Institute of Materials Research and Engineering, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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10
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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11
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Chen S, Xu J, Liu M, Rao ALN, Zandi R, Gill SS, Mohideen U. Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy. PLoS One 2020; 15:e0228036. [PMID: 32015565 PMCID: PMC6996966 DOI: 10.1371/journal.pone.0228036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates depending on the net charges carried. Gag and its complexes consist of monomers, dimers and tetramers, which was confirmed by gel electrophoresis. The addition of specific ΨRNA to Gag is found to increase Gag multimerization. Non-specific TARpolyA RNA was found not to lead to an increase in Gag multimerization. The addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent than ΨRNA. When both ΨRNA and PI(4,5)P2 are present Gag undergoes comformational changes and an even higher degree of multimerization.
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Affiliation(s)
- Shaolong Chen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Jun Xu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Mingyue Liu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - A. L. N. Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, California, United States of America
| | - Roya Zandi
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Sarjeet S. Gill
- Department of Cell Biology & Neuroscience, University of California, Riverside, California, United States of America
| | - Umar Mohideen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
- * E-mail:
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12
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Atomic Force Microscopy of Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 2073:247-285. [PMID: 31612446 DOI: 10.1007/978-1-4939-9869-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Atomic force microscopy (AFM) enables imaging of surface-deposited proteins and protein structures under physiological conditions, which is a benefit compared to ultra-high vacuum techniques such as electron microscopy. AFM also has the potential to provide more information from the phase in tapping mode or from functional AFM modes. The sample preparation, probe selection, and imaging conditions are crucial for successful imaging of proteins. Here we give a detailed account of the steps toward imaging of soft samples in both air and liquid along with the basic theory underpinning these details.
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14
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Mulvihill E, Pfreundschuh M, Thoma J, Ritzmann N, Müller DJ. High-Resolution Imaging of Maltoporin LamB while Quantifying the Free-Energy Landscape and Asymmetry of Sugar Binding. NANO LETTERS 2019; 19:6442-6453. [PMID: 31385710 DOI: 10.1021/acs.nanolett.9b02674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Maltoporins are a family of membrane proteins that facilitate the diffusion of hydrophilic molecules and maltosaccharides across the outer membrane of Gram-negative bacteria. Two contradicting models propose the sugar binding, uptake, and transport by maltoporins to be either symmetric or asymmetric. Here, we address this contradiction and introduce force-distance-based atomic force microscopy to image single maltoporin LamB trimers in the membrane at sub-nanometer resolution and simultaneously quantify the binding of different malto-oligosaccharides. We assay subtle differences of the binding free-energy landscape of maltotriose, maltotetraose, and maltopentaose, which quantifies how binding strength and affinity increase with the malto-oligosaccharide chain length. The ligand-binding parameters change considerably by mutating the extracellular loop 3, which folds into and constricts the transmembrane pore of LamB. By recording LamB topographs and structurally mapping binding events at sub-nanometer resolution, we observe LamB to preferentially bind maltodextrin from the periplasmic side, which shows sugar binding and uptake to be asymmetric. The study introduces atomic force microscopy as an analytical nanoscopic tool that can differentiate among the factors modulating and models describing the binding and uptake of substrates by membrane proteins.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Johannes Thoma
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Noah Ritzmann
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
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15
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The application of atomic force microscopy for viruses and protein shells: Imaging and spectroscopy. Adv Virus Res 2019; 105:161-187. [PMID: 31522704 DOI: 10.1016/bs.aivir.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic force microscopy (AFM) probes surface-adsorbed samples at the nanoscale by using a sharp stylus of nanometric size located at the end of a micro-cantilever. This technique can also work in a liquid environment and offers unique possibilities to study individual protein assemblies, such as viruses, under conditions that resemble their natural liquid milieu. Here, I show how AFM can be used to explore the topography of viruses and protein cages, including that of structures lacking a well-defined symmetry. AFM is not limited for imaging and allows the manipulation of individual viruses with force spectroscopy approaches, such as single indentation and mechanical fatigue assays. These pushing experiments deform the protein cages to obtain their mechanical information and can be used to monitor the structural changes induced by maturation or the exposure to different biochemical environments, such as pH variation. We discuss how studying capsid rupture and self-healing events offers insight into virus uncoating pathways. On the other hand, pulling tests can provide information about the virus-host interaction established between the viral fibers and the cell membrane.
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16
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Hirschi S, Fischer N, Kalbermatter D, Laskowski PR, Ucurum Z, Müller DJ, Fotiadis D. Design and assembly of a chemically switchable and fluorescently traceable light-driven proton pump system for bionanotechnological applications. Sci Rep 2019; 9:1046. [PMID: 30705382 PMCID: PMC6355921 DOI: 10.1038/s41598-018-37260-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Energy-supplying modules are essential building blocks for the assembly of functional multicomponent nanoreactors in synthetic biology. Proteorhodopsin, a light-driven proton pump, is an ideal candidate to provide the required energy in form of an electrochemical proton gradient. Here we present an advanced proteoliposome system equipped with a chemically on-off switchable proteorhodopsin variant. The proton pump was engineered to optimize the specificity and efficiency of chemical deactivation and reactivation. To optically track and characterize the proteoliposome system using fluorescence microscopy and nanoparticle tracking analysis, fluorescenlty labelled lipids were implemented. Fluorescence is a highly valuable feature that enables detection and tracking of nanoreactors in complex media. Cryo-transmission electron microscopy, and correlative atomic force and confocal microscopy revealed that our procedure yields polylamellar proteoliposomes, which exhibit enhanced mechanical stability. The combination of these features makes the presented energizing system a promising foundation for the engineering of complex nanoreactors.
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Affiliation(s)
- S Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - N Fischer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - D Kalbermatter
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - P R Laskowski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Z Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - D J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - D Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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17
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Loading the dice: The orientation of virus-like particles adsorbed on titanate assisted organosilanized surfaces. Biointerphases 2019; 14:011001. [PMID: 30691269 DOI: 10.1116/1.5077010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The organization of virus-like particles (VLPs) on surfaces is a relevant matter for both fundamental and biomedical sciences. In this work, the authors have tailored surfaces with different surface tension components aiming at finding a relationship with the affinity of the different geometric/surface features of icosahedral P22 VLPs. The surfaces have been prepared by titanate assisted organosilanization with glycidyloxy, amino, and perfluoro silanes. Vibrational and photoelectron spectroscopies have allowed identifying the different functional groups of the organosilanes on the surfaces. Atomic force microscopy (AFM) showed that, irrespective of the organosilane used, the final root mean square roughness remains below 1 nm. Contact angle analyses confirm the effective formation of a set of surface chemistries exhibiting different balance among surface tension components. The study of the adsorption of P22 VLPs has involved the analysis of the dynamics of virus immobilization by fluorescence microscopy and the interpretation of the final VLP orientation by AFM. These analyses give rise to statistical distributions pointing to a higher affinity of VLPs toward perfluorinated surfaces, with a dominant fivefold conformation on this hydrophobic surface, but threefold and twofold symmetries dominating on hydrophilic surfaces. These results can be explained in terms of a reinforced hydrophobic interaction between the perfluorinated surface and the dominating hydrophobic residues present at the P22 pentons.
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Ortega-Esteban Á, Martín-González N, Moreno-Madrid F, Llauró A, Hernando-Pérez M, MartÚn CS, de Pablo PJ. Structural and Mechanical Characterization of Viruses with AFM. Methods Mol Biol 2019; 1886:259-278. [PMID: 30374873 DOI: 10.1007/978-1-4939-8894-5_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Microscopes are used to characterize small objects with the help of probes that interact with the specimen, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a micro cantilever which palpates the specimen under study as a blind person manages a walking stick. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages, but also the characterization of every physicochemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted for extracting physical information, such as mechanical and electrostatic properties. We also explain how a convenient combination of AFM and fluorescence methodologies entails monitoring genome release from individual viral shells during mechanical unpacking.
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Affiliation(s)
- Álvaro Ortega-Esteban
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Natália Martín-González
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Moreno-Madrid
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Aida Llauró
- School of Medicine, University of Washington, Seattle, WA, USA
| | - Mercedes Hernando-Pérez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Cármen San MartÚn
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.
- Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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de Pablo PJ, Schaap IAT. Atomic Force Microscopy of Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:159-179. [PMID: 31317500 DOI: 10.1007/978-3-030-14741-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Atomic force microscopy employs a nanometric tip located at the end of a micro-cantilever to probe surface-mounted samples at nanometer resolution. Because the technique can also work in a liquid environment it offers unique possibilities to study individual viruses under conditions that mimic their natural milieu. Here, we review how AFM imaging can be used to study the surface structure of viruses including that of viruses lacking a well-defined symmetry. Beyond imaging, AFM enables the manipulation of single viruses by force spectroscopy experiments. Pulling experiments can provide information about the early events of virus-host interaction between the viral fibers and the cell membrane receptors. Pushing experiments measure the mechanical response of the viral capsid and its contents and can be used to show how virus maturation and exposure to different pH values change the mechanical response of the viruses and the interaction between the capsid and genome. Finally, we discuss how studying capsid rupture and self-healing events offers insight in virus uncoating pathways.
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Affiliation(s)
- P J de Pablo
- Department of Condensed Matter Physics and Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain.
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Donhauser ZJ, Appadoo V, Kliman EJ, Jobs WB, Sheffield EC. Structural Changes in Tubulin Sheets Caused by Immobilization on Solid Supports. ACS OMEGA 2018; 3:18196-18202. [PMID: 30613819 PMCID: PMC6312633 DOI: 10.1021/acsomega.8b02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
In the presence of zinc, the protein tubulin assembles into two-dimensional sheets that are a useful model system for the study of both tubulin and microtubule structure. Tubulin sheets present an ideal protein structure for study with atomic force microscopy because they contain a two-dimensional crystalline protein lattice and retain many of the structural features of tubulin and microtubules. However, high-resolution imaging requires nonperturbative immobilization onto an appropriate imaging substrate. In this report, several substrates commonly used for scanning probe microscopy are evaluated for their ability to effectively immobilize tubulin sheets: mica, gold, highly ordered pyrolytic graphite, and carbon-coated electron microscopy grids. We hypothesize that the different intermolecular interactions presented by these substrates will affect the morphology of adsorbed tubulin sheets as well as the amount of other contaminating adsorbates. Tubulin sheets were successfully imaged on all of these substrates and structural characterization is reported. The most consistent results were obtained on carbon-coated electron microscopy grids, which preserved fine structural features of the sheets and had the least amount of contamination from the adsorption of unpolymerized tubulin. Images of tubulin sheets obtained with atomic force microscopy also compare favorably with published electron micrographs of sheets produced using similar procedures. This work demonstrates the importance of assessing substrate effects when studying two-dimensional protein crystals and identifies suitable substrates for immobilizing tubulin sheets.
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Affiliation(s)
| | | | - Elysa J. Kliman
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
| | - William B. Jobs
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
| | - Evan C. Sheffield
- Vassar College, 124 Raymond Avenue, Poughkeepsie, New York 12604, United States
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POTRA Domains, Extracellular Lid, and Membrane Composition Modulate the Conformational Stability of the β Barrel Assembly Factor BamA. Structure 2018; 26:987-996.e3. [PMID: 29861346 DOI: 10.1016/j.str.2018.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/30/2018] [Accepted: 04/27/2018] [Indexed: 11/21/2022]
Abstract
The core component BamA of the β barrel assembly machinery (BAM) adopts several conformations, which are thought to facilitate the insertion and folding of β barrel proteins into the bacterial outer membrane. Which factors alter the stability of these conformations remains to be quantified. Here, we apply single-molecule force spectroscopy to characterize the mechanical properties of BamA from Escherichia coli. In contrast to the N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, the C-terminal transmembrane β barrel domain of BamA is mechanically much more stable. Exposed to mechanical stress this β barrel stepwise unfolds β hairpins until unfolding has been completed. Thereby, the mechanical stabilities of β barrel and β hairpins are modulated by the POTRA domains, the membrane composition and the extracellular lid closing the β barrel. We anticipate that these differences in stability, which are caused by factors contributing to BAM function, promote conformations of the BamA β barrel required to insert and fold outer membrane proteins.
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Mari SA, Wegmann S, Tepper K, Hyman BT, Mandelkow EM, Mandelkow E, Müller DJ. Reversible Cation-Selective Attachment and Self-Assembly of Human Tau on Supported Brain Lipid Membranes. NANO LETTERS 2018; 18:3271-3281. [PMID: 29644863 PMCID: PMC6588182 DOI: 10.1021/acs.nanolett.8b01085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Misfolding and aggregation of the neuronal, microtubule-associated protein tau is involved in the pathogenesis of Alzheimer's disease and tauopathies. It has been proposed that neuronal membranes could play a role in tau release, internalization, and aggregation and that tau aggregates could exert toxicity via membrane permeabilization. Whether and how tau interacts with lipid membranes remains a matter of discussion. Here, we characterize the interaction of full-length human tau (htau40) with supported lipid membranes (SLMs) made from brain total lipid extract by time-lapse high-resolution atomic force microscopy (AFM). We observe that tau attaches to brain lipid membranes where it self-assembles in a cation-dependent manner. Sodium triggers the attachment, self-assembly, and growth, whereas potassium inhibits these processes. Moreover, tau assemblies are stable in the presence of sodium and lithium but disassemble in the presence of potassium and rubidium. Whereas the pseudorepeat domains (R1-R4) of htau40 promote the sodium-dependent attachment to the membrane and stabilize the tau assemblies, the N-terminal region promotes tau self-assembly and growth.
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Affiliation(s)
- Stefania A. Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Susanne Wegmann
- Department of Neurology, Alzheimer’s Disease Research Laboratory, Harvard Medical School, Massachusetts General Hospital, 114 16th Street, Charlestown, Massachusetts 02129, United States
| | - Katharina Tepper
- Department of Neurology, Alzheimer’s Disease Research Laboratory, Harvard Medical School, Massachusetts General Hospital, 114 16th Street, Charlestown, Massachusetts 02129, United States
- German Center for Neurodegenerative Diseases (DZNE) and CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Bradley T. Hyman
- Department of Neurology, Alzheimer’s Disease Research Laboratory, Harvard Medical School, Massachusetts General Hospital, 114 16th Street, Charlestown, Massachusetts 02129, United States
| | - Eva-Maria Mandelkow
- German Center for Neurodegenerative Diseases (DZNE) and CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- Max-Planck-Institute for Neurological Research Cologne, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE) and CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- Max-Planck-Institute for Neurological Research Cologne, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Corresponding Author. Phone: 0041-61-387-3307
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Pleshakova TO, Bukharina NS, Archakov AI, Ivanov YD. Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization. Int J Mol Sci 2018; 19:E1142. [PMID: 29642632 PMCID: PMC5979402 DOI: 10.3390/ijms19041142] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.
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Affiliation(s)
| | - Natalia S Bukharina
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
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25
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Protein-enriched outer membrane vesicles as a native platform for outer membrane protein studies. Commun Biol 2018; 1:23. [PMID: 30271910 PMCID: PMC6123736 DOI: 10.1038/s42003-018-0027-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/20/2018] [Indexed: 01/15/2023] Open
Abstract
Most studies characterizing the folding, structure, and function of membrane proteins rely on solubilized or reconstituted samples. Whereas solubilized membrane proteins lack the functionally important lipid membrane, reconstitution embeds them into artificial lipid bilayers, which lack characteristic features of cellular membranes including lipid diversity, composition and asymmetry. Here, we utilize outer membrane vesicles (OMVs) released from Escherichia coli to study outer membrane proteins (Omps) in the native membrane environment. Enriched in the native membrane of the OMV we characterize the assembly, folding, and structure of OmpG, FhuA, Tsx, and BamA. Comparing Omps in OMVs to those reconstituted into artificial lipid membranes, we observe different unfolding pathways for some Omps. This observation highlights the importance of the native membrane environment to maintain the native structure and function relationship of Omps. Our fast and easy approach paves the way for functional and structural studies of Omps in the native membrane. Johannes Thoma et al. overexpress outer membrane proteins (Omps) in Escherichia coli and collect the expelled outer membrane vesicles (OMVs) to study Omp assembly, folding and structure. They find that Omps in OMVs show different unfolding pathways compared to Omps reconstituted in artificial lipid membranes.
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26
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Martín-González N, Ortega-Esteban A, Moreno-Madrid F, Llauró A, Hernando-Pérez M, de Pablo PJ. Atomic Force Microscopy of Protein Shells: Virus Capsids and Beyond. Methods Mol Biol 2018; 1665:281-296. [PMID: 28940075 DOI: 10.1007/978-1-4939-7271-5_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In Atomic Force Microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person uses a white cane. In this way AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization a variety physicochemical properties able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In this chapter we start revising some recipes for adsorbing protein shells on surfaces. Then we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties.
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Affiliation(s)
- Natalia Martín-González
- Departamento de Física de la Materia Condensada, C-3, Universidad Autónoma de Madrid, Ctra. de Colmenar Viejo, Km 15, 28049, Madrid, Spain
| | - Alvaro Ortega-Esteban
- Departamento de Física de la Materia Condensada, C-3, Universidad Autónoma de Madrid, Ctra. de Colmenar Viejo, Km 15, 28049, Madrid, Spain
| | - F Moreno-Madrid
- Departamento de Física de la Materia Condensada, C-3, Universidad Autónoma de Madrid, Ctra. de Colmenar Viejo, Km 15, 28049, Madrid, Spain
| | - Aida Llauró
- Department of Physiology & Biophysics, University of Washington, Seattle, WA, 98195, USA
| | - Mercedes Hernando-Pérez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, C-3, Universidad Autónoma de Madrid, Ctra. de Colmenar Viejo, Km 15, 28049, Madrid, Spain. .,Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
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27
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Li M, Dang D, Xi N, Wang Y, Liu L. Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells. NANOSCALE 2017; 9:17643-17666. [PMID: 29135007 DOI: 10.1039/c7nr07023c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
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28
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de Pablo PJ. Atomic force microscopy of virus shells. Semin Cell Dev Biol 2017; 73:199-208. [PMID: 28851598 DOI: 10.1016/j.semcdb.2017.08.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/14/2017] [Accepted: 08/18/2017] [Indexed: 11/29/2022]
Abstract
Microscopes are used to characterize small specimens with the help of probes, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM) the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study as a blind person manages a white cane to explore the surrounding. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in liquid milieu. Beyond imaging, AFM also enables the manipulation of single protein cages, and the characterization of every physico-chemical property able of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. Here we describe several AFM approaches to study individual protein cages, including imaging and spectroscopic methodologies for extracting mechanical and electrostatic properties. In addition, AFM allows discovering and testing the self-healing capabilities of protein cages because occasionally they may recover fractures induced by the AFM tip. Beyond the protein shells, AFM also is able of exploring the genome inside, obtaining, for instance, the condensation state of dsDNA and measuring its diffusion when the protein cage breaks.
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Affiliation(s)
- Pedro J de Pablo
- Departamento de Física de la Materia Condensada and Solid Condensed Matter Institute IFIMAC, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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29
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Laskowski PR, Pfreundschuh M, Stauffer M, Ucurum Z, Fotiadis D, Müller DJ. High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox. ACS NANO 2017; 11:8292-8301. [PMID: 28745869 DOI: 10.1021/acsnano.7b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.
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Affiliation(s)
- Pawel R Laskowski
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
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30
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Piantanida L, Bolt HL, Rozatian N, Cobb SL, Voïtchovsky K. Ions Modulate Stress-Induced Nanotexture in Supported Fluid Lipid Bilayers. Biophys J 2017; 113:426-439. [PMID: 28746853 PMCID: PMC5529180 DOI: 10.1016/j.bpj.2017.05.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022] Open
Abstract
Most plasma membranes comprise a large number of different molecules including lipids and proteins. In the standard fluid mosaic model, the membrane function is effected by proteins whereas lipids are largely passive and serve solely in the membrane cohesion. Here we show, using supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers in different saline solutions, that ions can locally induce ordering of the lipid molecules within the otherwise fluid bilayer when the latter is supported. This nanoordering exhibits a characteristic length scale of ∼20 nm, and manifests itself clearly when mechanical stress is applied to the membrane. Atomic force microscopy (AFM) measurements in aqueous solutions containing NaCl, KCl, CaCl2, and Tris buffer show that the magnitude of the effect is strongly ion-specific, with Ca2+ and Tris, respectively, promoting and reducing stress-induced nanotexturing of the membrane. The AFM results are complemented by fluorescence recovery after photobleaching experiments, which reveal an inverse correlation between the tendency for molecular nanoordering and the diffusion coefficient within the bilayer. Control AFM experiments on other lipids and at different temperatures support the hypothesis that the nanotexturing is induced by reversible, localized gel-like solidification of the membrane. These results suggest that supported fluid phospholipid bilayers are not homogenous at the nanoscale, but specific ions are able to locally alter molecular organization and mobility, and spatially modulate the membrane’s properties on a length scale of ∼20 nm. To illustrate this point, AFM was used to follow the adsorption of the membrane-penetrating antimicrobial peptide Temporin L in different solutions. The results confirm that the peptides do not absorb randomly, but follow the ion-induced spatial modulation of the membrane. Our results suggest that ionic effects have a significant impact for passively modulating the local properties of biological membranes, when in contact with a support such as the cytoskeleton.
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Affiliation(s)
- Luca Piantanida
- Department of Physics, Durham University, Durham, United Kingdom
| | - Hannah L Bolt
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Neshat Rozatian
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Steven L Cobb
- Department of Chemistry, Durham University, Durham, United Kingdom
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31
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Zeng C, Hernando-Pérez M, Dragnea B, Ma X, van der Schoot P, Zandi R. Contact Mechanics of a Small Icosahedral Virus. PHYSICAL REVIEW LETTERS 2017; 119:038102. [PMID: 28777631 DOI: 10.1103/physrevlett.119.038102] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Indexed: 06/07/2023]
Abstract
A virus binding to a surface causes stress of the virus cage near the contact area. Here, we investigate the potential role of substrate-induced structural perturbation in the mechanical response of virus particles to adsorption. This is particularly relevant to the broad category of viruses stabilized by weak noncovalent interactions. We utilize atomic force microscopy to measure height distributions of the brome mosaic virus upon adsorption from solution on atomically flat substrates and present a continuum model that captures our observations and provides estimates of elastic properties and of the interfacial energy of the virus, without recourse to indentation.
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Affiliation(s)
- Cheng Zeng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Bogdan Dragnea
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Xiang Ma
- Department of Chemistry, Idaho State University, Pocatello, Idaho 83209, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
| | - Roya Zandi
- Department of Physics and Astronomy, University of California at Riverside, 900 University Avenue, Riverside, California 92521, USA
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32
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Thoma J, Ritzmann N, Wolf D, Mulvihill E, Hiller S, Müller DJ. Maltoporin LamB Unfolds β Hairpins along Mechanical Stress-Dependent Unfolding Pathways. Structure 2017. [DOI: 10.1016/j.str.2017.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Pfreundschuh M, Harder D, Ucurum Z, Fotiadis D, Müller DJ. Detecting Ligand-Binding Events and Free Energy Landscape while Imaging Membrane Receptors at Subnanometer Resolution. NANO LETTERS 2017; 17:3261-3269. [PMID: 28361535 DOI: 10.1021/acs.nanolett.7b00941] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force-distance curve-based atomic force microscopy has emerged into a sophisticated technique for imaging cellular membranes and for detecting specific ligand-binding events of native membrane receptors. However, so far the resolution achieved has been insufficient to structurally map ligand-binding sites onto membrane proteins. Here, we introduce experimental and theoretical approaches for overcoming this limitation. To establish a structurally and functionally well-defined reference sample, we engineer a ligand-binding site to the light-driven proton pump bacteriorhodopsin of purple membrane. Functionalizing the AFM stylus with an appropriate linker-system tethering the ligand and optimizing the AFM conditions allows for imaging the engineered bacteriorhodopsin at subnanometer resolution while structurally mapping the specific ligand-receptor binding events. Improved data analysis allows reconstructing the ligand-binding free energy landscape from the experimental data, thus providing thermodynamic and kinetic insight into the ligand-binding process. The nanoscopic method introduced is generally applicable for imaging receptors in native membranes at subnanometer resolution and for systematically mapping and quantifying the free energy landscape of ligand binding.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
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34
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Atomic force microscopy of virus shells. Biochem Soc Trans 2017; 45:499-511. [PMID: 28408490 DOI: 10.1042/bst20160316] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 11/17/2022]
Abstract
Microscopes are used to characterize small objects with the help of probes that interact with the specimen, such as photons and electrons in optical and electron microscopies, respectively. In atomic force microscopy (AFM), the probe is a nanometric tip located at the end of a microcantilever which palpates the specimen under study just as a blind person manages a walking stick. In this way, AFM allows obtaining nanometric resolution images of individual protein shells, such as viruses, in a liquid milieu. Beyond imaging, AFM also enables not only the manipulation of single protein cages, but also the characterization of every physicochemical property capable of inducing any measurable mechanical perturbation to the microcantilever that holds the tip. In the present revision, we start revising some recipes for adsorbing protein shells on surfaces. Then, we describe several AFM approaches to study individual protein cages, ranging from imaging to spectroscopic methodologies devoted to extracting physical information, such as mechanical and electrostatic properties. We also explain how a convenient combination of AFM and fluorescence methodologies entails monitoring genome release from individual viral shells during mechanical unpacking.
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35
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Kumar S, Cartron ML, Mullin N, Qian P, Leggett GJ, Hunter CN, Hobbs JK. Direct Imaging of Protein Organization in an Intact Bacterial Organelle Using High-Resolution Atomic Force Microscopy. ACS NANO 2017; 11:126-133. [PMID: 28114766 PMCID: PMC5269641 DOI: 10.1021/acsnano.6b05647] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The function of bioenergetic membranes is strongly influenced by the spatial arrangement of their constituent membrane proteins. Atomic force microscopy (AFM) can be used to probe protein organization at high resolution, allowing individual proteins to be identified. However, previous AFM studies of biological membranes have typically required that curved membranes are ruptured and flattened during sample preparation, with the possibility of disruption of the native protein arrangement or loss of proteins. Imaging native, curved membranes requires minimal tip-sample interaction in both lateral and vertical directions. Here, long-range tip-sample interactions are reduced by optimizing the imaging buffer. Tapping mode AFM with high-resonance-frequency small and soft cantilevers, in combination with a high-speed AFM, reduces the forces due to feedback error and enables application of an average imaging force of tens of piconewtons. Using this approach, we have imaged the membrane organization of intact vesicular bacterial photosynthetic "organelles", chromatophores. Despite the highly curved nature of the chromatophore membrane and lack of direct support, the resolution was sufficient to identify the photosystem complexes and quantify their arrangement in the native state. Successive imaging showed the proteins remain surprisingly static, with minimal rotation or translation over several-minute time scales. High-order assemblies of RC-LH1-PufX complexes are observed, and intact ATPases are successfully imaged. The methods developed here are likely to be applicable to a broad range of protein-rich vesicles or curved membrane systems, which are an almost ubiquitous feature of native organelles.
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Affiliation(s)
- Sandip Kumar
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - Michaël L. Cartron
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - Nic Mullin
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - Pu Qian
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - Graham J. Leggett
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - C. Neil Hunter
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
| | - Jamie K. Hobbs
- Department
of Physics and Astronomy, Department of Molecular Biology
and Biotechnology, Department of Chemistry, and Krebs Institute, University of Sheffield, Sheffield, South Yorkshire S10 2TN, U.K.
- E-mail:
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36
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van Pee K, Mulvihill E, Müller DJ, Yildiz Ö. Unraveling the Pore-Forming Steps of Pneumolysin from Streptococcus pneumoniae. NANO LETTERS 2016; 16:7915-7924. [PMID: 27796097 DOI: 10.1021/acs.nanolett.6b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Pneumolysin (PLY) is the main virulence factor of Streptococcus pneumoniae that causes pneumonia, meningitis, and invasive pneumococcal infection. PLY is produced as monomers, which bind to cholesterol-containing membranes, where they oligomerize into large pores. To investigate the pore-forming mechanism, we determined the crystal structure of PLY at 2.4 Å and used it to design mutants on the surface of monomers. Electron microscopy of liposomes incubated with PLY mutants revealed that several mutations interfered with ring formation. Mutants that formed incomplete rings or linear arrays had strongly reduced hemolytic activity. By high-resolution time-lapse atomic force microscopy of wild-type PLY, we observed two different ring-shaped complexes. Most of the complexes protruded ∼8 nm above the membrane surface, while a smaller number protruded ∼11 nm or more. The lower complexes were identified as pores or prepores by the presence or absence of a lipid bilayer in their center. The taller complexes were side-by-side assemblies of monomers of soluble PLY that represent an early form of the prepore. Our observations suggest a four-step mechanism of membrane attachment and pore formation by PLY, which is discussed in the context of recent structural models. The functional separation of these steps is necessary for the understanding how cholesterol-dependent cytolysins form pores and lyse cells.
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Affiliation(s)
- Katharina van Pee
- Department of Structural Biology, Max PIanck Institute of Biophysics , Max von Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Estefania Mulvihill
- Department of Biosystems Science and Engineering, ETH Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
| | - Özkan Yildiz
- Department of Structural Biology, Max PIanck Institute of Biophysics , Max von Laue Strasse 3, 60438 Frankfurt am Main, Germany
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37
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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38
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Sborgi L, Rühl S, Mulvihill E, Pipercevic J, Heilig R, Stahlberg H, Farady CJ, Müller DJ, Broz P, Hiller S. GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death. EMBO J 2016; 35:1766-78. [PMID: 27418190 PMCID: PMC5010048 DOI: 10.15252/embj.201694696] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/28/2016] [Indexed: 12/18/2022] Open
Abstract
Pyroptosis is a lytic type of cell death that is initiated by inflammatory caspases. These caspases are activated within multi‐protein inflammasome complexes that assemble in response to pathogens and endogenous danger signals. Pyroptotic cell death has been proposed to proceed via the formation of a plasma membrane pore, but the underlying molecular mechanism has remained unclear. Recently, gasdermin D (GSDMD), a member of the ill‐characterized gasdermin protein family, was identified as a caspase substrate and an essential mediator of pyroptosis. GSDMD is thus a candidate for pyroptotic pore formation. Here, we characterize GSDMD function in live cells and in vitro. We show that the N‐terminal fragment of caspase‐1‐cleaved GSDMD rapidly targets the membrane fraction of macrophages and that it induces the formation of a plasma membrane pore. In vitro, the N‐terminal fragment of caspase‐1‐cleaved recombinant GSDMD tightly binds liposomes and forms large permeability pores. Visualization of liposome‐inserted GSDMD at nanometer resolution by cryo‐electron and atomic force microscopy shows circular pores with variable ring diameters around 20 nm. Overall, these data demonstrate that GSDMD is the direct and final executor of pyroptotic cell death.
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Affiliation(s)
| | | | - Estefania Mulvihill
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | | | | | | | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Petr Broz
- Biozentrum, University of Basel, Basel, Switzerland
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39
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Borrell JH, Montero MT, Domènech Ò. Mapping phase diagrams of supported lipid bilayers by atomic force microscopy. Microsc Res Tech 2016; 80:4-10. [PMID: 27001606 DOI: 10.1002/jemt.22655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/16/2016] [Accepted: 02/05/2016] [Indexed: 12/18/2022]
Abstract
In this work, we present the method followed to construct a pseudophase diagram of two phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol). Two different techniques, DSC and AFM, have been used based in the determination of the onset (Tonset ) and completion (Toffset ) temperatures of the gel-to-liquid crystalline phases (Lβ →Lα ), the first from the endotherms from liposomes and the second from the topographic images of supported lipid bilayers. The features of both phase diagrams are discussed emphasizing the influence of Ca2+ presence and the substrate (mica) on the transition undergone by the phospholipid mixture. Microsc. Res. Tech. 80:4-10, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jordi H Borrell
- Departament de Fisicoquímica, Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona (UB), Barcelona, Catalonia, 08028, Spain
| | - M Teresa Montero
- Departament de Fisicoquímica, Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona (UB), Barcelona, Catalonia, 08028, Spain
| | - Òscar Domènech
- Departament de Fisicoquímica, Facultat de Farmàcia and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona (UB), Barcelona, Catalonia, 08028, Spain
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40
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Xiao X, Nie G, Zhang X, Tian D, Li H. Protein Adsorption Switch Constructed by a Pillar[5]arene-Based Host-Guest Interaction. Chemistry 2015; 22:941-5. [DOI: 10.1002/chem.201504076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Xuan Xiao
- Key Laboratory of Pesticide and Chemical Biology (CCNU); Ministry of Education; College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Guanrong Nie
- Key Laboratory of Pesticide and Chemical Biology (CCNU); Ministry of Education; College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Xiaoyan Zhang
- Key Laboratory of Pesticide and Chemical Biology (CCNU); Ministry of Education; College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Demei Tian
- Key Laboratory of Pesticide and Chemical Biology (CCNU); Ministry of Education; College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU); Ministry of Education; College of Chemistry; Central China Normal University; Wuhan 430079 P.R. China
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41
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Hernando-Pérez M, Cartagena-Rivera AX, Lošdorfer Božič A, Carrillo PJP, San Martín C, Mateu MG, Raman A, Podgornik R, de Pablo PJ. Quantitative nanoscale electrostatics of viruses. NANOSCALE 2015; 7:17289-98. [PMID: 26228582 DOI: 10.1039/c5nr04274g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.
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Affiliation(s)
- M Hernando-Pérez
- Departamento de Física de la Materia Condensada and Condensed Matter Physics Center - IFIMAC, Universidad Autónoma de Madrid, Spain.
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42
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Mulvihill E, van Pee K, Mari SA, Müller DJ, Yildiz Ö. Directly Observing the Lipid-Dependent Self-Assembly and Pore-Forming Mechanism of the Cytolytic Toxin Listeriolysin O. NANO LETTERS 2015; 15:6965-6973. [PMID: 26302195 DOI: 10.1021/acs.nanolett.5b02963] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Listeriolysin O (LLO) is the major virulence factor of Listeria monocytogenes and a member of the cholesterol-dependent cytolysin (CDC) family. Gram-positive pathogenic bacteria produce water-soluble CDC monomers that bind cholesterol-dependent to the lipid membrane of the attacked cell or of the phagosome, oligomerize into prepores, and insert into the membrane to form transmembrane pores. However, the mechanisms guiding LLO toward pore formation are poorly understood. Using electron microscopy and time-lapse atomic force microscopy, we show that wild-type LLO binds to membranes, depending on the presence of cholesterol and other lipids. LLO oligomerizes into arc- or slit-shaped assemblies, which merge into complete rings. All three oligomeric assemblies can form transmembrane pores, and their efficiency to form pores depends on the cholesterol and the phospholipid composition of the membrane. Furthermore, the dynamic fusion of arcs, slits, and rings into larger rings and their formation of transmembrane pores does not involve a height difference between prepore and pore. Our results reveal new insights into the pore-forming mechanism and introduce a dynamic model of pore formation by LLO and other CDC pore-forming toxins.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
| | - Katharina van Pee
- Department of Structural Biology, Max-Planck-Institute of Biophysics , Max von Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
| | - Özkan Yildiz
- Department of Structural Biology, Max-Planck-Institute of Biophysics , Max von Laue Str. 3, 60438 Frankfurt am Main, Germany
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43
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Llauró A, Coppari E, Imperatori F, Bizzarri AR, Castón JR, Santi L, Cannistraro S, de Pablo PJ. Calcium ions modulate the mechanics of tomato bushy stunt virus. Biophys J 2015; 109:390-7. [PMID: 26200875 PMCID: PMC4621496 DOI: 10.1016/j.bpj.2015.05.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/25/2015] [Accepted: 05/30/2015] [Indexed: 01/27/2023] Open
Abstract
Viral particles are endowed with physicochemical properties whose modulation confers certain metastability to their structures to fulfill each task of the viral cycle. Here, we investigate the effects of swelling and ion depletion on the mechanical stability of individual tomato bushy stunt virus nanoparticles (TBSV-NPs). Our experiments show that calcium ions modulate the mechanics of the capsid: the sequestration of calcium ions from the intracapsid binding sites reduces rigidity and resilience in ∼24% and 40%, respectively. Interestingly, mechanical deformations performed on native TBSV-NPs induce an analogous result. In addition, TBSV-NPs do not show capsomeric vacancies after surpassing the elastic limit. We hypothesize that even though there are breakages among neighboring capsomers, RNA-capsid protein interaction prevents the release of capsid subunits. This work shows the mechanical role of calcium ions in viral shell stability and identifies TBSV-NPs as malleable platforms based on protein cages for cargo transportation at the nanoscale.
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Affiliation(s)
- Aida Llauró
- Department of Condensed Matter Physics and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid,. Madrid, Spain
| | - Emilia Coppari
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | - Francesca Imperatori
- Department of Agriculture, Forests, Nature and Energy (DAFNE), Università della Tuscia, Viterbo, Italy
| | - Anna R Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | - José R Castón
- Department of Macromolecular Structure, Centro Nacional de Biotecnología/CSIC, Madrid Spain
| | - Luca Santi
- Department of Agriculture, Forests, Nature and Energy (DAFNE), Università della Tuscia, Viterbo, Italy
| | | | - Pedro J de Pablo
- Department of Condensed Matter Physics and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid,. Madrid, Spain.
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Petrosyan R, Bippes CA, Walheim S, Harder D, Fotiadis D, Schimmel T, Alsteens D, Müller DJ. Single-molecule force spectroscopy of membrane proteins from membranes freely spanning across nanoscopic pores. NANO LETTERS 2015; 15:3624-3633. [PMID: 25879249 DOI: 10.1021/acs.nanolett.5b01223] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy (SMFS) provides detailed insight into the mechanical (un)folding pathways and structural stability of membrane proteins. So far, SMFS could only be applied to membrane proteins embedded in native or synthetic membranes adsorbed to solid supports. This adsorption causes experimental limitations and raises the question to what extent the support influences the results obtained by SMFS. Therefore, we introduce here SMFS from native purple membrane freely spanning across nanopores. We show that correct analysis of the SMFS data requires extending the worm-like chain model, which describes the mechanical stretching of a polypeptide, by the cubic extension model, which describes the bending of a purple membrane exposed to mechanical stress. This new experimental and theoretical approach allows to characterize the stepwise (un)folding of the membrane protein bacteriorhodopsin and to assign the stability of single and grouped secondary structures. The (un)folding and stability of bacteriorhodopsin shows no significant difference between freely spanning and directly supported purple membranes. Importantly, the novel experimental SMFS setup opens an avenue to characterize any protein from freely spanning cellular or synthetic membranes.
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Affiliation(s)
- Rafayel Petrosyan
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Christian A Bippes
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Stefan Walheim
- †Institute of Applied Physics and Center for Functional Nanostructures (CFN) and Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Daniel Harder
- §Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- §Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Thomas Schimmel
- †Institute of Applied Physics and Center for Functional Nanostructures (CFN) and Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - David Alsteens
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Daniel J Müller
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
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Bosshart PD, Engel A, Fotiadis D. High-resolution atomic force microscopy imaging of rhodopsin in rod outer segment disk membranes. Methods Mol Biol 2015; 1271:189-203. [PMID: 25697525 DOI: 10.1007/978-1-4939-2330-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows recording topographical information of membrane proteins under near-physiological conditions. Remarkable results have been obtained on membrane proteins that were reconstituted into lipid bilayers. High-resolution AFM imaging of native disk membranes from vertebrate rod outer segments has unveiled the higher-order oligomeric state of the G protein-coupled receptor rhodopsin, which is highly expressed in disk membranes. Based on AFM imaging, it has been demonstrated that rhodopsin assembles in rows of dimers and paracrystals and that the rhodopsin dimer is the fundamental building block of higher-order structures.
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Affiliation(s)
- Patrick D Bosshart
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, Bern, CH-3012, Switzerland
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46
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van Rosmalen MGM, Roos WH, Wuite GJL. Material properties of viral nanocages explored by atomic force microscopy. Methods Mol Biol 2015; 1252:115-137. [PMID: 25358778 DOI: 10.1007/978-1-4939-2131-7_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-particle nanoindentation by atomic force microscopy (AFM) is an emergent technique to characterize the material properties of nano-sized proteinaceous systems. AFM uses a very small tip attached to a cantilever to scan the surface of the substrate. As a result of the sensitive feedback loop of AFM, the force applied by the tip on the substrate during scanning can be controlled and monitored. By accurately controlling this scanning force, topographical maps of fragile substrates can be acquired to study the morphology of the substrate. In addition, mechanical properties of the substrate like stiffness and breaking point can be determined by using the force spectroscopy capability of AFM. Here we discuss basics of AFM operation and how this technique is used to determine the structure and mechanical properties of protein nanocages, in particular viral particles. Knowledge of morphology as well as mechanical properties is essential for understanding viral life cycles, including genome packaging, capsid maturation, and uncoating, but also contributes to the development of diagnostics, vaccines, imaging modalities, and targeted therapeutic devices based on viruslike particles.
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Pfreundschuh M, Alsteens D, Hilbert M, Steinmetz MO, Müller DJ. Localizing chemical groups while imaging single native proteins by high-resolution atomic force microscopy. NANO LETTERS 2014; 14:2957-2964. [PMID: 24766578 DOI: 10.1021/nl5012905] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Simultaneous high-resolution imaging and localization of chemical interaction sites on single native proteins is a pertinent biophysical, biochemical, and nanotechnological challenge. Such structural mapping and characterization of binding sites is of importance in understanding how proteins interact with their environment and in manipulating such interactions in a plethora of biotechnological applications. Thus far, this challenge remains to be tackled. Here, we introduce force-distance curve-based atomic force microscopy (FD-based AFM) for the high-resolution imaging of SAS-6, a protein that self-assembles into cartwheel-like structures. Using functionalized AFM tips bearing Ni(2+)-N-nitrilotriacetate groups, we locate specific interaction sites on SAS-6 at nanometer resolution and quantify the binding strength of the Ni(2+)-NTA groups to histidine residues. The FD-based AFM approach can readily be applied to image any other native protein and to locate and structurally map histidine residues. Moreover, the surface chemistry used to functionalize the AFM tip can be modified to map other chemical interaction sites.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , Mattenstrasse 26, 4058 Basel, Switzerland
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48
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Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc 2014; 9:1113-30. [DOI: 10.1038/nprot.2014.070] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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de Pablo PJ, Carrión-Vázquez M. Imaging biological samples with atomic force microscopy. Cold Spring Harb Protoc 2014; 2014:167-77. [PMID: 24492779 DOI: 10.1101/pdb.top080473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atomic force microscopy (AFM) is an invaluable tool both for obtaining high-resolution topographical images and for determining the values of mechanical and structural properties of specimens adsorbed onto a surface. AFM is useful in an array of fields and applications, from materials science to biology. It is an extremely versatile technique that can be applied to almost any surface-mounted sample and can be operated in ambient air, ultrahigh vacuum, and, most importantly for biology, liquids. AFM can be used to explore samples ranging in size from atoms to molecules, molecular aggregates, and cells. Individual biomolecules can be viewed and manipulated at the nanoscale, providing fundamental biological information. In particular, the study of the mechanical properties of biomolecular aggregates at the nanoscale constitutes an important source of data to elaborate mechanochemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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50
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Zhu L, Gregurec D, Reviakine I. Nanoscale departures: excess lipid leaving the surface during supported lipid bilayer formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:15283-15292. [PMID: 24266399 DOI: 10.1021/la401354j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The behavior of small liposomes on surfaces of inorganic oxides remains enigmatic. Under appropriate conditions it results in the formation of supported lipid bilayers (SLBs). During this process, some lipids leave the surface (desorb). We were able to visualize this by a combination of time-resolved fluorescence microscopy and fluorescence recovery after photobleaching studies. Our observations also allowed us to analyze the kinetics of bilayer patch growth during the late stages of SLB formation. We found that it entails a balance between desorption of excess lipids and further adsorption of liposomes from solution. These studies were performed with liposomes containing zwitterionic phospholipids (dioleoylphosphatidylcholine alone or a mixture of dioleoylphosphatidylcholine, dipalmitoylphosphatidylcholine, and cholesterol) on TiO2 in the presence of Ca(2+) but in the absence of other salts.
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Affiliation(s)
- Ling Zhu
- Biosurfaces, CIC biomaGUNE , Paseo Miramón 182, 20009 San Sebastián, Spain
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