1
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Yang H, Zhou D, Zhou Z, Duan M, Yu H. Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase. JACS AU 2024; 4:1422-1435. [PMID: 38665647 PMCID: PMC11040704 DOI: 10.1021/jacsau.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/28/2024]
Abstract
The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins. Here, we performed force spectroscopy experiments and multiscale molecular dynamics simulations to study the unfolding pathway of diacylglycerol kinase (DGK), a small trimeric multispan transmembrane enzyme. The remarkable agreement between experiments and simulations allowed precise structural assignment and interaction analysis of unfolding intermediates, bypassing existing limitations on structural mapping, and thus provided mechanistic explanations for the formation of these states. DGK unfolding was found to proceed with structural segments varying in size that do not correlate with its secondary structure. We identified intermolecular side-chain packing interactions as one of the major contributions to the stability of unfolding intermediates. Mutagenesis creating packing defects induced a dramatic decrease in the mechano-stability of corresponding intermediates and also in the thermo-stability of DGK trimer, in good agreement with predictions from simulations. Hence, the molecular determinants of the mechano- and thermo-stability of a membrane protein can be identified at residue resolution. The accurate structural assignment established and microscopic mechanism revealed in this work may substantially expand the scope of single-molecule studies of membrane proteins.
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Affiliation(s)
- Huiying Yang
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Daihong Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Zhangyi Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Mojie Duan
- Innovation
Academy for Precision Measurement Science and Technology, Chinese
Academy of Sciences, Wuhan 430071, China
| | - Hao Yu
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
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2
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Xue Y, Ma Y, Sun Z, Liu X, Zhang M, Zhang J, Xi N. Identification and Measurement of Biomarkers at Single Microorganism Level for In Situ Monitoring Deep Ultraviolet Disinfection Process. IEEE Trans Nanobioscience 2024; 23:242-251. [PMID: 37676797 DOI: 10.1109/tnb.2023.3312754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Since the COVID-19 disease has been further aggravated, the prevention of pathogen transmission becomes a vital issue to restrain casualties. Recent research outcomes have shown the possibilities of the viruses existing on inanimate surfaces up to few days, which carry the risk of touch propagation of the disease. Deep ultraviolet germicide irradiation (UVGI) with the wavelength of 255-280nm has been verified to efficiently disinfect various types of bacteria and virus, which could prevent the aggravation of pandemic spread. Even though considerable experiments and approaches have been applied to evaluate the disinfection effects, there are only few reports about how the individual bio-organism behaves after ultraviolet C (UVC) irradiation, especially in the aspect of mechanical changes. Furthermore, since the standard pathway of virus transmission and reproduction requires the host cell to assemble and transport newly generated virus, the dynamic response of infectious cell is always the vital aspect of virology study. In this work, high power LEDs array has been established with 270nm UVC irradiation to evaluate disinfection capability on various types of bio-organism, and incubator embedded atomic force microscopy (AFM) is used to investigate the single bacterium and virus under UVGI. The real-time tracking of the living Vero cells infected with adenovirus has also been presented in this study. The results show that after sufficient UVGI, the outer shell of bacteria and viruses remain intact in structure, however the bio-organisms lost the capability of reproduction and normal metabolism. The experiment results also indicate that once the host cell is infected with adenovirus, the rapid production of newborn virus capsid will gradually destroy the cellular normal metabolism and lose mechanical integrity.
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3
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do Nascimento RM, Grauby-Heywang C, Kahli H, Debez N, Béven L, Bechtold IH, Bouhacina TC. A 3D physical model predicting favorable bacteria adhesion. Colloids Surf B Biointerfaces 2024; 233:113628. [PMID: 37979480 DOI: 10.1016/j.colsurfb.2023.113628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/20/2023]
Abstract
Predicting the initial steps of bacterial biofilm formation remains a significant challenge accross various fields, such as medical and industrial ones. Here we present a straightforward 3D theoretical model based on thermodynamic rules to assess the early stages of biofilm formation on different material surfaces. This model relying also on morphological aspects of bacteria, we used Atomic Force Microscopy images of two Gram negative bacteria, Pseudomonas fluorescens and Escherichia coli to determine their dimensions and geometries as single cells or in aggregated states. Algorithms developed for our modeling and numerical simulations generated a dataset of energetic minimized states, depending on the substrate. The model was applied to substrates widely used for bacteria immobilization in imaging applications. The results show that the different minimum energy values, depending of the substrate, can be correlated with the bacterial adhesion state, representing a potential tool for evaluating the early stages of biofilm formation on various surfaces.
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Affiliation(s)
- Rodney Marcelo do Nascimento
- Centro de Ciências Físicas e Matemáticas, Universidade Federal de Santa Catarina, UFSC, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Christine Grauby-Heywang
- Laboratoire Ondes et Matière d'Aquitaine, Université de Bordeaux, CNRS, UMR 5798, 351 cours de la Libération, 33400 Talence, France
| | - Houssem Kahli
- Laboratoire Ondes et Matière d'Aquitaine, Université de Bordeaux, CNRS, UMR 5798, 351 cours de la Libération, 33400 Talence, France
| | - Nesrine Debez
- Laboratoire Ondes et Matière d'Aquitaine, Université de Bordeaux, CNRS, UMR 5798, 351 cours de la Libération, 33400 Talence, France
| | - Laure Béven
- Université de Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, 33140 Villenave d'Ornon, France
| | - Ivan Helmuth Bechtold
- Centro de Ciências Físicas e Matemáticas, Universidade Federal de Santa Catarina, UFSC, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Touria Cohen Bouhacina
- Laboratoire Ondes et Matière d'Aquitaine, Université de Bordeaux, CNRS, UMR 5798, 351 cours de la Libération, 33400 Talence, France
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4
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Cruz-Wegener C, Kutell J, Aldaher L, deHaseth N, Bhattacharya SK, Ziebarth N. Quantifying ABCA1/apoA-1 Signaling Pathways with AFM Imaging and Lipidomic Analysis. Methods Mol Biol 2024; 2816:205-222. [PMID: 38977601 DOI: 10.1007/978-1-0716-3902-3_19] [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: 07/10/2024]
Abstract
The role of lipid metabolic pathways in the pathophysiology of primary open-angle glaucoma (POAG) has been thoroughly elucidated, with pathways involved in lipid-related disorders such as hypercholesterolemia and hyperlipoprotein accumulation being of particular interest. The ABCA1/apoA-1 transduction pathway moderates reverse cholesterol transport (RCT), facilitating the transport of free cholesterol (FC) and phospholipids (PL) and preventing intracellular lipid aggregates in retinal ganglion cells (RGCs) due to excess FCs and PLs. A deficiency of ABCA1 transporters, and thus, dysregulation of the ABCA1/apoA-1 transduction pathway, may potentiate cellular lipid accumulation, which affects the structural and mechanical features of the cholesterol-rich RGC membranes. Atomic force microscopy (AFM) is a cutting-edge imaging technique suitable for imaging topographical surfaces of a biological specimen and determining its mechanical properties and structural features. The versatility and precision of this technique may prove beneficial in understanding the effects of ABCA1/apoA-1 pathway downregulation and decreased cholesterol efflux in RGCs and their membranes. In this protocol, ABCA1-/- RGC mouse models are prepared over the course of 3 days and are then compared with non-knockout ABCA1 RGC mouse models through AFM imaging of topographical surfaces to examine the difference in membrane dynamics of knockout vs. non-knockout models. Intracellular and extracellular levels of lipids are quantified through high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS).
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Affiliation(s)
- Carolina Cruz-Wegener
- Bascom Palmer Eye Institute, Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Jonah Kutell
- Bascom Palmer Eye Institute, Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Louay Aldaher
- Bascom Palmer Eye Institute, Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Noa deHaseth
- Bascom Palmer Eye Institute, Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
- Department of Biomedical Engineering, University of Miami, Coral Gables, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, Miller School of Medicine at University of Miami, Miami, FL, USA
- Miami Integrative Metabolomics Research Center, Miami, FL, USA
| | - Noel Ziebarth
- Bascom Palmer Eye Institute, Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA.
- Department of Biomedical Engineering, University of Miami, Coral Gables, USA.
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5
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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6
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Hall D. Simulating biological surface dynamics in high-speed atomic force microscopy experiments. Biophys Rev 2023; 15:2069-2079. [PMID: 38192349 PMCID: PMC10771409 DOI: 10.1007/s12551-023-01169-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 01/10/2024] Open
Abstract
High-speed atomic force microscopy (HSAFM) is an important tool for studying the dynamic behavior of large biomolecular assemblies at surfaces. However, unlike light microscopy techniques, which visualize each point in the field of view at the same time, in HSAFM, the surface is literally imaged pixel-by-pixel with a variable extent of time separation existing between recordings made at one pixel and all others within the surface image. Such "temporal asynchronicity" in the recording of the spatial information can introduce distortions into the image when the surface components move at a rate comparable to that at which the surface is imaged. This Letter describes recently released software developments that are able to predict the likely form of these distortions and estimate confidence levels when assigning the identity of observed structures. These described approaches may facilitate both the design and optimization of future HSAFM experimental protocols. Further to this, they may assist in the interpretation of results from already published HSAFM studies.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
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7
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Zerbetto M, Saint-Pierre C, Piserchia A, Torrengo S, Gambarelli S, Abergel D, Polimeno A, Gasparutto D, Sicoli G. Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach. J Phys Chem Lett 2023; 14:10032-10038. [PMID: 37906734 DOI: 10.1021/acs.jpclett.3c02383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.
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Affiliation(s)
- Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrea Piserchia
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Simona Torrengo
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Daniel Abergel
- Laboratoire des biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Antonino Polimeno
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Giuseppe Sicoli
- CNRS UMRS 8516, LASIRE, University of Lille, Avenue Paul Langevin - C4 building, F-59655 Villeneuve d'Ascq Cedex, France
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8
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Staii C. Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy. Molecules 2023; 28:4632. [PMID: 37375186 DOI: 10.3390/molecules28124632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM-force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function.
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Affiliation(s)
- Cristian Staii
- Department of Physics and Astronomy, Tufts University, Medford, MA 02155, USA
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9
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Waite JR, Tan SY, Saha H, Sarkar S, Sarkar A. Few-shot deep learning for AFM force curve characterization of single-molecule interactions. PATTERNS (NEW YORK, N.Y.) 2023; 4:100672. [PMID: 36699737 PMCID: PMC9868661 DOI: 10.1016/j.patter.2022.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 12/07/2022] [Indexed: 01/09/2023]
Abstract
Deep learning (DL)-based analytics has the scope to transform the field of atomic force microscopy (AFM) with regard to fast and bias-free measurement characterization. For example, AFM force-distance curves can help estimate important parameters of binding kinetics, such as the most probable rupture force, binding probability, association, and dissociation constants, as well as receptor density on live cells. Other than the ideal single-rupture event in the force-distance curves, there can be no-rupture, double-rupture, or multiple-rupture events. The current practice is to go through such datasets manually, which can be extremely tedious work for the experimentalists. We address this issue by adopting a few-shot learning approach to build sample-efficient DL models that demonstrate better performance than shallow ML models while matching the performance of moderately trained humans. We also release our AFM force curve dataset and annotations publicly as a benchmark for the research community.
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Affiliation(s)
- Joshua R. Waite
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Sin Yong Tan
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Homagni Saha
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, USA
| | - Anwesha Sarkar
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA,Corresponding author
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10
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Ekar J, Kovač J. AFM Study of Roughness Development during ToF-SIMS Depth Profiling of Multilayers with a Cs + Ion Beam in a H 2 Atmosphere. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12871-12880. [PMID: 36239688 PMCID: PMC9609309 DOI: 10.1021/acs.langmuir.2c01837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The influence of H2 flooding on the development of surface roughness during time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling was studied to evaluate the different aspects of a H2 atmosphere in comparison to an ultrahigh vacuum (UHV) environment. Multilayer samples, consisting of different combinations of metal, metal oxide, and alloy layers of different elements, were bombarded with 1 and 2 keV Cs+ ion beams in UHV and a H2 atmosphere of 7 × 10-7 mbar. The surface roughness Sa was measured with atomic force microscopy (AFM) on the initial surface and in the craters formed while sputtering, either in the middle of the layers or at the interfaces. We found that the roughness after Cs+ sputtering depends on the chemical composition/structure of the individual layers, and it increases with the sputtering depth. However, the increase in the roughness was, in specific cases, approximately a few tens of percent lower when sputtering in the H2 atmosphere compared to the UHV. In the other cases, the average surface roughness was generally still lower when H2 flooding was applied, but the differences were statistically insignificant. Additionally, we observed that for the initially rough surfaces with an Sa of about 5 nm, sputtering with the 1 keV Cs+ beam might have a smoothing effect, thereby reducing the initial roughness. Our observations also indicate that Cs+ sputtering with ion energies of 1 and 2 keV has a similar effect on roughness development, except for the cases with initially very smooth samples. The results show the beneficial effect of H2 flooding on surface roughness development during the ToF-SIMS depth profiling in addition to a reduction of the matrix effect and an improved identification of thin layers.
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Affiliation(s)
- Jernej Ekar
- Jožef
Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
- Jožef
Stefan International Postgraduate School, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
| | - Janez Kovač
- Jožef
Stefan Institute, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia
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11
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Joshi R, Han SB, Cho WK, Kim DH. The role of cellular traction forces in deciphering nuclear mechanics. Biomater Res 2022; 26:43. [PMID: 36076274 PMCID: PMC9461125 DOI: 10.1186/s40824-022-00289-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2022] Open
Abstract
Cellular forces exerted on the extracellular matrix (ECM) during adhesion and migration under physiological and pathological conditions regulate not only the overall cell morphology but also nuclear deformation. Nuclear deformation can alter gene expression, integrity of the nuclear envelope, nucleus-cytoskeletal connection, chromatin architecture, and, in some cases, DNA damage responses. Although nuclear deformation is caused by the transfer of forces from the ECM to the nucleus, the role of intracellular organelles in force transfer remains unclear and a challenging area of study. To elucidate nuclear mechanics, various factors such as appropriate biomaterial properties, processing route, cellular force measurement technique, and micromanipulation of nuclear forces must be understood. In the initial phase of this review, we focused on various engineered biomaterials (natural and synthetic extracellular matrices) and their manufacturing routes along with the properties required to mimic the tumor microenvironment. Furthermore, we discussed the principle of tools used to measure the cellular traction force generated during cell adhesion and migration, followed by recently developed techniques to gauge nuclear mechanics. In the last phase of this review, we outlined the principle of traction force microscopy (TFM), challenges in the remodeling of traction forces, microbead displacement tracking algorithm, data transformation from bead movement, and extension of 2-dimensional TFM to multiscale TFM.
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Affiliation(s)
- Rakesh Joshi
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, South Korea
| | - Seong-Beom Han
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, South Korea
| | - Won-Ki Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Dong-Hwee Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, South Korea. .,Department of Integrative Energy Engineering, College of Engineering, Korea University, Seoul, South Korea.
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12
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Cisse A, Matsuo T, Plazanet M, Natali F, Koza MM, Ollivier J, Bicout DJ, Peters J. The dynamical Matryoshka model: 2. Modeling of local lipid dynamics at the sub-nanosecond timescale in phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183950. [PMID: 35525301 DOI: 10.1016/j.bbamem.2022.183950] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022]
Abstract
Biological membranes are generally formed by lipids and proteins. Often, the membrane properties are studied through model membranes formed by phospholipids only. They are molecules composed by a hydrophilic head group and hydrophobic tails, which can present a panoply of various motions, including small localized movements of a few atoms up to the diffusion of the whole lipid or collective motions of many of them. In the past, efforts were made to measure these motions experimentally by incoherent neutron scattering and to quantify them, but with upcoming modern neutron sources and instruments, such models can now be improved. In the present work, we expose a quantitative and exhaustive study of lipid dynamics on DMPC and DMPG membranes, using the Matryoshka model recently developed by our group. The model is confronted here to experimental data collected on two different membrane samples, at three temperatures and two instruments. Despite such complexity, the model describes reliably the data and permits to extract a series of parameters. The results compare also very well to other values found in the literature.
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Affiliation(s)
- Aline Cisse
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Marie Plazanet
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; CNR-IOM and INSIDE@ILL, c/o OGG, 38042 Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Jacques Ollivier
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Dominique J Bicout
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Univ. Grenoble Alpes, CNRS, Grenoble INP, VetAgro Sup, TIMC, 38000 Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Institut Universitaire de France, France.
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13
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Harris NJ, Pellowe GA, Blackholly LR, Gulaidi-Breen S, Findlay HE, Booth PJ. Methods to study folding of alpha-helical membrane proteins in lipids. Open Biol 2022; 12:220054. [PMID: 35855589 PMCID: PMC9297032 DOI: 10.1098/rsob.220054] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How alpha-helical membrane proteins fold correctly in the highly hydrophobic membrane interior is not well understood. Their folding is known to be highly influenced by the lipids within the surrounding bilayer, but the majority of folding studies have focused on detergent-solubilized protein rather than protein in a lipid environment. There are different ways to study folding in lipid bilayers, and each method has its own advantages and disadvantages. This review will discuss folding methods which can be used to study alpha-helical membrane proteins in bicelles, liposomes, nanodiscs or native membranes. These folding methods include in vitro folding methods in liposomes such as denaturant unfolding studies, and single-molecule force spectroscopy studies in bicelles, liposomes and native membranes. This review will also discuss recent advances in co-translational folding studies, which use cell-free expression with liposomes or nanodiscs or are performed in vivo with native membranes.
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Affiliation(s)
- Nicola J. Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A. Pellowe
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Laura R. Blackholly
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | | | - Heather E. Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paula J. Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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14
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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15
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Zhao G, Li H, Gao J, Cai M, Xu H, Shi Y, Wang H, Wang H. Insight into the Different Channel Proteins of Human Red Blood Cell Membranes Revealed by Combined dSTORM and AFM Techniques. Anal Chem 2021; 93:14113-14120. [PMID: 34657412 DOI: 10.1021/acs.analchem.1c02382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Membrane proteins tend to interact with each other in the cell membranes to form protein clusters and perform the corresponding physiological functions. However, because channel proteins are involved in many biological functions, their distribution and nano-organization in these protein clusters are unclear. To study the distribution patterns and relationships between the different channel proteins, we identified the locations of glucose transporter 1 (Glut1) and Band3 (anion transporter 1) precisely in the topography of the cytoplasmic side of the human red blood cell (hRBC) membranes using combined atomic force microscopy (AFM) and single-molecule localization microscopy (SMLM). The AFM results revealed that membrane proteins interacted with each other and aggregated into protein islands. The SMLM results showed that Glut1 and Band3 tended to form protein clusters in the hRBC membranes, and there was a strong colocalization between the two proteins. The results of the combined AFM and SMLM method indicated that the protein clusters of Glut1 and Band3 were mainly located in the protein islands of topography, and the protein islands in topography also interacted with each other to assemble into larger protein clusters or functional microdomains.
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Affiliation(s)
- Guanfang Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Hongru Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Mingjun Cai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Haijiao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Yan Shi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Huili Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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16
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On-site processing of single chromosomal DNA molecules using optically driven microtools on a microfluidic workbench. Sci Rep 2021; 11:7961. [PMID: 33846479 PMCID: PMC8042024 DOI: 10.1038/s41598-021-87238-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
We developed optically driven microtools for processing single biomolecules using a microfluidic workbench composed of a microfluidic platform that functions under an optical microscope. The optically driven microtools have enzymes immobilized on their surfaces, which catalyze chemical reactions for molecular processing in a confined space. Optical manipulation of the microtools enables them to be integrated with a microfluidic device for controlling the position, orientation, shape of the target sample. Here, we describe the immobilization of enzymes on the surface of microtools, the microfluidics workbench, including its microtool storage and sample positioning functions, and the use of this system for on-site cutting of single chromosomal DNA molecules. We fabricated microtools by UV lithography with SU-8 and selected ozone treatments for immobilizing enzymes. The microfluidic workbench has tool-stock chambers for tool storage and micropillars to trap and extend single chromosomal DNA molecules. The DNA cutting enzymes DNaseI and DNaseII were immobilized on microtools that were manipulated using optical tweezers. The DNaseI tool shows reliable cutting for on-site processing. This pinpoint processing provides an approach for analyzing chromosomal DNA at the single-molecule level. The flexibility of the microtool design allows for processing of various samples, including biomolecules and single cells.
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17
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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18
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Fuchs M, Sigmund AM, Waschke J, Vielmuth F. Desmosomal Hyperadhesion Is Accompanied with Enhanced Binding Strength of Desmoglein 3 Molecules. Biophys J 2020; 119:1489-1500. [PMID: 33031738 DOI: 10.1016/j.bpj.2020.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
Intercellular adhesion of keratinocytes depends critically on desmosomes that, during maturation, acquire a hyperadhesive and thus Ca2+ independent state. Here, we investigated the roles of desmoglein (Dsg) 3 and plakophilins (Pkps) in hyperadhesion. Atomic force microscopy single molecule force mappings revealed increased Dsg3 molecules but not Dsg1 molecules binding strength in murine keratinocytes. However, keratinocytes lacking Dsg3 or Pkp1 or 3 revealed reduced Ca2+ independency. In addition, Pkp1- or 3-deficient keratinocytes did not exhibit changes in Dsg3 binding on the molecular level. Further, wild-type keratinocytes showed increased levels of Dsg3 oligomers during acquisition of hyperadhesion, and Pkp1 deficiency abolished the formation of Ca2+ independent Dsg3 oligomers. In concordance, immunostaining for Dsg1 but not for Dsg3 was reduced after 24 h of Ca2+ chelation in an ex vivo human skin model, suggesting that desmosomal cadherins may have different roles during acquisition of hyperadhesion. Taken together, these data indicate that hyperadhesion may not be a state acquired by entire desmosomes but rather is paralleled by enhanced binding of specific Dsg isoforms such as Dsg3, a process for which plaque proteins including Pkp 1 and 3 are required as well.
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Affiliation(s)
- Michael Fuchs
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Anna Magdalena Sigmund
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Jens Waschke
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Franziska Vielmuth
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany.
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19
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Andersson J, Bilotto P, Mears LLE, Fossati S, Ramach U, Köper I, Valtiner M, Knoll W. Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins. Methods 2020; 180:56-68. [PMID: 32920130 DOI: 10.1016/j.ymeth.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.
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Affiliation(s)
| | - Pierluigi Bilotto
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Laura L E Mears
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Stefan Fossati
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Ulrich Ramach
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Markus Valtiner
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
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20
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Abstract
Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two types of intensively studied bacterial photosynthetic membranes: the chromatophore membranes of purple bacteria and the thylakoid membranes of cyanobacteria. Both systems are distinct from the plasma membrane, and both have a distinctive protein composition that reflects their specialized roles. Chromatophores are formed from plasma membrane invaginations, while thylakoid membranes appear to be an independent intracellular membrane system. We discuss the techniques that can be applied to study the organization and dynamics of these membrane systems, including electron microscopy techniques, atomic force microscopy, and many variants of fluorescence microscopy. We go on to discuss the insights that havebeen acquired from these techniques, and the role of membrane dynamics in the physiology of photosynthetic membranes. Membrane dynamics on multiple timescales are crucial for membrane function, from electron transport on timescales of microseconds to milliseconds to regulation and biogenesis on timescales of minutes to hours. We emphasize the open questions that remain in the field.
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Affiliation(s)
- Conrad W. Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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21
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Valizade M, Raesi Vanani A, Rezaei M, Khorsandi LS, Zeidooni L, Mahdavinia M. Mesobuthus eupeus venom induced injury in the colorectal carcinoma cell line (HT29) through altering the mitochondria membrane stability. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:760-767. [PMID: 32695292 PMCID: PMC7351445 DOI: 10.22038/ijbms.2020.40884.9659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Objective(s): The purpose of this study was to investigate cytotoxicity and membrane toxicity effects induced by Mesobuthus eupeus venom (MEV) on the HT-29 cell line. Materials and Methods: To determine the in vitro cytotoxicity via MTT assays, HT-29 (as cancer cell line) and Hek-293T (as normal cell) were treated through different concentrations of MEV, and cytotoxicity effects were then measured through assessment of mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) generation, and apoptosis induction. The colony formation assay was performed to measure the antiproliferative effect of MEV on HT-29 cells. Nuclei alterations were also observed during apoptosis following DAPI staining. Besides, atomic force microscopy (AFM) was used to detect alterations in morphology and ultrastructure of the cells at a nanoscale level. Results: According to MTT and clonogenic assays, MEV caused a significant decrease in cell viability and proliferation of HT-29 cells while it did not have any impact on normal cells and the IC50 value was found to be 10 µg/ml. Induction of apoptosis was also confirmed by flowcytometric analysis in HT-29 cells. Moreover, the results indicated that MEV had led to a suppression of proliferation and induction of apoptosis through increased ROS and depolarization of mitochondria. Furthermore, AFM imaging demonstrated apoptosis cell death after being treated with MEV in HT-29 cells. Conclusion: This study showed that MEV had an antiproliferative effect on HT-29 cells by inducing apoptosis through the mitochondria signaling pathway. These findings suggested that MEV could be used as a promising natural remedy for cancer treatment.
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Affiliation(s)
- Massood Valizade
- Cell & Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Atefeh Raesi Vanani
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Rezaei
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Laya Sadat Khorsandi
- Cell & Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Leila Zeidooni
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Masoud Mahdavinia
- Toxicology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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22
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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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23
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Clifton LA, Campbell RA, Sebastiani F, Campos-Terán J, Gonzalez-Martinez JF, Björklund S, Sotres J, Cárdenas M. Design and use of model membranes to study biomolecular interactions using complementary surface-sensitive techniques. Adv Colloid Interface Sci 2020; 277:102118. [PMID: 32044469 DOI: 10.1016/j.cis.2020.102118] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 01/07/2023]
Abstract
Cellular membranes are complex structures and simplified analogues in the form of model membranes or biomembranes are used as platforms to understand fundamental properties of the membrane itself as well as interactions with various biomolecules such as drugs, peptides and proteins. Model membranes at the air-liquid and solid-liquid interfaces can be studied using a range of complementary surface-sensitive techniques to give a detailed picture of both the structure and physicochemical properties of the membrane and its resulting interactions. In this review, we will present the main planar model membranes used in the field to date with a focus on monolayers at the air-liquid interface, supported lipid bilayers at the solid-liquid interface and advanced membrane models such as tethered and floating membranes. We will then briefly present the principles as well as the main type of information on molecular interactions at model membranes accessible using a Langmuir trough, quartz crystal microbalance with dissipation monitoring, ellipsometry, atomic force microscopy, Brewster angle microscopy, Infrared spectroscopy, and neutron and X-ray reflectometry. A consistent example for following biomolecular interactions at model membranes is used across many of the techniques in terms of the well-studied antimicrobial peptide Melittin. The overall objective is to establish an understanding of the information accessible from each technique, their respective advantages and limitations, and their complementarity.
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Affiliation(s)
- Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Richard A Campbell
- Division of Pharmacy and Optometry, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Federica Sebastiani
- Department of Biomedical Science and Biofilms - Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden
| | - José Campos-Terán
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe, Delegación Cuajimalpa de Morelos, 05348, Mexico; Lund Institute of advanced Neutron and X-ray Science, Lund University, Scheelevägen 19, 223 70 Lund, Sweden
| | - Juan F Gonzalez-Martinez
- Department of Biomedical Science and Biofilms - Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden
| | - Sebastian Björklund
- Department of Biomedical Science and Biofilms - Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden
| | - Javier Sotres
- Department of Biomedical Science and Biofilms - Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden
| | - Marité Cárdenas
- Department of Biomedical Science and Biofilms - Research Center for Biointerfaces, Malmö University, 20506 Malmö, Sweden.
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24
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Depond M, Henry B, Buffet P, Ndour PA. Methods to Investigate the Deformability of RBC During Malaria. Front Physiol 2020; 10:1613. [PMID: 32038293 PMCID: PMC6990122 DOI: 10.3389/fphys.2019.01613] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/23/2019] [Indexed: 12/25/2022] Open
Abstract
Despite a 30% decline in mortality since 2000, malaria still affected 219 million subjects and caused 435,000 deaths in 2017. Red blood cells (RBC) host Plasmodium parasites that cause malaria, of which Plasmodium falciparum is the most pathogenic. The deformability of RBC is markedly modified by invasion and development of P. falciparum. Surface membrane area is potentially impacted by parasite entry and development, the cytoskeleton is modified by parasite proteins and cytosol viscosity is altered by parasite metabolism. RBC hosting mature parasites (second half of the asexual erythrocytic cycle) are abnormally stiff but the main reason for their absence from the circulation is their adherence to endothelial cells, mediated by parasite proteins exposed at the infected-RBC surface. By contrast, the circulation of non-adherent rings and gametocytes, depends predominantly on deformability. Altered deformability of rings and of uninfected-RBC altered by malaria infection is an important determinant of malaria pathogenesis. It also impacts the response to antimalarial therapy. Unlike conventional antimalarials that target mature stages, currently recommended first-line artemisinin derivatives and the emerging spiroindolones act on circulating rings. Methods to investigate the deformability of RBC are therefore critical to understand the clearance of infected- and uninfected-RBC in malaria. Herein, we review the main methods to assess the deformability of P. falciparum infected-RBC, and their contribution to the understanding of how P. falciparum infection causes disease, how the parasite is transmitted and how antimalarial drugs induce parasite clearance.
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Affiliation(s)
- Mallorie Depond
- UMR_S1134, BIGR, Inserm, Universit de Paris, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Benoit Henry
- UMR_S1134, BIGR, Inserm, Universit de Paris, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Pierre Buffet
- UMR_S1134, BIGR, Inserm, Universit de Paris, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Papa Alioune Ndour
- UMR_S1134, BIGR, Inserm, Universit de Paris, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
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25
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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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26
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Conjugates of Gold Nanoparticles and Antitumor Gold(III) Complexes as a Tool for Their AFM and SERS Detection in Biological Tissue. Int J Mol Sci 2019; 20:ijms20246306. [PMID: 31847177 PMCID: PMC6940825 DOI: 10.3390/ijms20246306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 11/17/2022] Open
Abstract
Citrate-capped gold nanoparticles (AuNPs) were functionalized with three distinct antitumor gold(III) complexes, e.g., [Au(N,N)(OH)2][PF6], where (N,N)=2,2'-bipyridine; [Au(C,N)(AcO)2], where (C,N)=deprotonated 6-(1,1-dimethylbenzyl)-pyridine; [Au(C,N,N)(OH)][PF6], where (C,N,N)=deprotonated 6-(1,1-dimethylbenzyl)-2,2'-bipyridine, to assess the chance of tracking their subcellular distribution by atomic force microscopy (AFM), and surface enhanced Raman spectroscopy (SERS) techniques. An extensive physicochemical characterization of the formed conjugates was, thus, carried out by applying a variety of methods (density functional theory-DFT, UV/Vis spectrophotometry, AFM, Raman spectroscopy, and SERS). The resulting gold(III) complexes/AuNPs conjugates turned out to be pretty stable. Interestingly, they exhibited a dramatically increased resonance intensity in the Raman spectra induced by AuNPs. For testing the use of the functionalized AuNPs for biosensing, their distribution in the nuclear, cytosolic, and membrane cell fractions obtained from human lymphocytes was investigated by AFM and SERS. The conjugates were detected in the membrane and nuclear cell fractions but not in the cytosol. The AFM method confirmed that conjugates induced changes in the morphology and nanostructure of the membrane and nuclear fractions. The obtained results point out that the conjugates formed between AuNPs and gold(III) complexes may be used as a tool for tracking metallodrug distribution in the different cell fractions.
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27
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Cao D, Song Y, Peng J, Ma R, Guo J, Chen J, Li X, Jiang Y, Wang E, Xu L. Advances in Atomic Force Microscopy: Weakly Perturbative Imaging of the Interfacial Water. Front Chem 2019; 7:626. [PMID: 31572715 PMCID: PMC6751248 DOI: 10.3389/fchem.2019.00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/30/2019] [Indexed: 11/17/2022] Open
Abstract
The structure and dynamics of interfacial water, determined by the water-interface interactions, are important for a wide range of applied fields and natural processes, such as water diffusion (Kim et al., 2013), electrochemistry (Markovic, 2013), heterogeneous catalysis (Over et al., 2000), and lubrication (Zilibotti et al., 2013). The precise understanding of water-interface interactions largely relies on the development of atomic-scale experimental techniques (Guo et al., 2014) and computational methods (Hapala et al., 2014b). Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields (Ichii et al., 2012; Shiotari and Sugimoto, 2017; Peng et al., 2018a). In this perspective, we review the recent progress in the noncontact atomic force microscopy (nc-AFM) imaging and AFM simulation techniques and discuss how the newly developed techniques are applied to study the properties of interfacial water. The nc-AFM with the quadrupole-like CO-terminated tip can achieve ultrahigh-resolution imaging of the interfacial water on different surfaces, trace the reconstruction of H-bonding network and determine the intrinsic structures of the weakly bonded water clusters and even their metastable states. In the end, we present an outlook on the directions of future AFM studies of interfacial water as well as the challenges faced by this field.
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Affiliation(s)
- Duanyun Cao
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Yizhi Song
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Jinbo Peng
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Institute of Experimental and Applied Physics, University of Regensburg, Regensburg, Germany
| | - Runze Ma
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China
| | - Jing Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Ji Chen
- School of Physics, Peking University, Beijing, China
| | - Xinzheng Li
- School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China
| | - Ying Jiang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China.,CAS Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Beijing, China
| | - Enge Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Ceramics Division, Songshan Lake Materials Lab, Institute of Physics, Chinese Academy of Sciences, Guangdong, China.,School of Physics, Liaoning University, Shenyang, China
| | - Limei Xu
- International Center for Quantum Materials, School of Physics, Peking University, Beijing, China.,Collaborative Innovation Center of Quantum Matter, Beijing, China
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28
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Chang Y, Andersson SB. OBSERVER-BASED CONTROL OF A DUAL-STAGE PIEZOELECTRIC SCANNER. PROCEEDINGS OF THE ASME DYNAMIC SYSTEMS AND CONTROL CONFERENCE. ASME DYNAMIC SYSTEMS AND CONTROL CONFERENCE 2019; 2019:V003T19A008. [PMID: 34504733 PMCID: PMC8424955 DOI: 10.1115/dscc2019-9163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite its proven success in a wide variety of applications, the atomic force microscope (AFM) remains limited by its slow imaging rate. One approach to overcome this challenge is to rely on algorithmic approaches that reduce the imaging time not by scanning faster but by scanning less. Such schemes are particularly useful on older instruments as they can provide significant gains despite the existing (slow) hardware. At the same time, algorithms for sub-sampling can yield even greater improvements in imaging rate when combined with advanced scanners that can be retrofitted into the system. In this work, we focus on the use of a dual-stage piezoelectric scanner coupled with a particular scanning algorithm known as Local Circular Scan (LCS). LCS drives the tip of the AFM along a circular trajectory while using feedback to center that circle on a sample edge and to move the circle along the feature, thus reducing imaging time by concentrating the samples to the region of interest. Dual-stage systems are well-suited to LCS as the algorithm is naturally described in terms of a high-frequency, short range path (the scanning circle) and a slower, long range path (the track along the sample). However, control of the scanner is not straightforward as the system is multi-input, single-output. Here we establish controllability and observability of the scanning stage, allowing us to develop individual controllers for the long-range and short-range actuators through the principle of separation. We then use an internal model controller for the short range actuator to track a sinusoidal input (to generate the circular motion) and a state-space set-point tracking controller for the long range actuator. The results are demonstrated through simulation.
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Affiliation(s)
- Yuhe Chang
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215
| | - Sean B Andersson
- Department of Mechanical Engineering, Division of Systems Engineering, Boston University, Boston, Massachusetts 02215
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29
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Park PSH. Rhodopsin Oligomerization and Aggregation. J Membr Biol 2019; 252:413-423. [PMID: 31286171 DOI: 10.1007/s00232-019-00078-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022]
Abstract
Rhodopsin is the light receptor in photoreceptor cells of the retina and a prototypical G protein-coupled receptor. Two types of quaternary structures can be adopted by rhodopsin. If rhodopsin folds and attains a proper tertiary structure, it can then form oligomers and nanodomains within the photoreceptor cell membrane. In contrast, if rhodopsin misfolds, it cannot progress through the biosynthetic pathway and instead will form aggregates that can cause retinal degenerative disease. In this review, emerging views are highlighted on the supramolecular organization of rhodopsin within the membrane of photoreceptor cells and the aggregation of rhodopsin that can lead to retinal degeneration.
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Affiliation(s)
- Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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30
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Senapati S, Poma AB, Cieplak M, Filipek S, Park PSH. Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes. Anal Chem 2019; 91:7226-7235. [PMID: 31074606 DOI: 10.1021/acs.analchem.9b00546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force-distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young's modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Adolfo B Poma
- Institute of Fundamental Technological Research , Polish Academy of Sciences , Pawińskiego 5B , 02-106 Warsaw , Poland.,Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Marek Cieplak
- Institute of Physics , Polish Academy of Sciences , Aleja Lotników 32/46 , 02-668 Warsaw , Poland
| | - Sławomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre , University of Warsaw , 02-093 Warsaw , Poland
| | - Paul S H Park
- Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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31
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Giliberti V, Polito R, Ritter E, Broser M, Hegemann P, Puskar L, Schade U, Zanetti-Polzi L, Daidone I, Corni S, Rusconi F, Biagioni P, Baldassarre L, Ortolani M. Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches. NANO LETTERS 2019; 19:3104-3114. [PMID: 30950626 PMCID: PMC6745627 DOI: 10.1021/acs.nanolett.9b00512] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channelrhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450-1800 cm-1 range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy. We find clear spectroscopic evidence of a branching of the photocycle for BR molecules in direct contact with the gold surfaces, with equal amounts of proteins either following the standard proton-pump photocycle or being trapped in an intermediate state not directly contributing to light-induced proton transport. Our results are particularly relevant for BR-based optoelectronic and energy-harvesting devices, where BR molecular monolayers are put in contact with metal surfaces, and, more generally, for AFM-based IR spectroscopy studies of conformational changes of proteins embedded in intrinsically heterogeneous native cell membranes.
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Affiliation(s)
- Valeria Giliberti
- Istituto
Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161 Roma, Italy
- E-mail:
| | - Raffaella Polito
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
| | - Eglof Ritter
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Matthias Broser
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Humboldt-Universität
zu Berlin, Institut für
Biologie, Invalidenstraße
42, D-10115 Berlin, Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Ulrich Schade
- Helmholtz-Zentrum
Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Laura Zanetti-Polzi
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via Vetoio, I-67010 L’Aquila, Italy
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via Vetoio, I-67010 L’Aquila, Italy
| | - Stefano Corni
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
- CNR
Institute
of Nanoscience, Via Campi
213/A, I-41125 Modena, Italy
| | - Francesco Rusconi
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Paolo Biagioni
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Leonetta Baldassarre
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
| | - Michele Ortolani
- Istituto
Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161 Roma, Italy
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, I-00185 Roma, Italy
- E-mail:
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32
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Reus-Chavarría E, Martínez-Vieyra I, Salinas-Nolasco C, Chávez-Piña AE, Méndez-Méndez JV, López-Villegas EO, Sosa-Peinado A, Cerecedo D. Enhanced expression of the Epithelial Sodium Channel in neutrophils from hypertensive patients. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:387-402. [DOI: 10.1016/j.bbamem.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/29/2018] [Accepted: 11/08/2018] [Indexed: 12/17/2022]
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33
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Abstract
Atomic force microscopy (AFM) is a form of contact microscopy that uses a very sharp tip to scan the surface of a sample. It provides a 3D image of the surface structure and in the force mode it can also be used to test the mechanical properties of the sample. AFM has been successfully applied to study the molecular mechanism of pore-forming proteins on model membranes. It gives information about both the structural reorganization of the membrane surface and the changes in the force required for membrane piercing upon incubation with this special type of proteins. Here we describe robust protocols to investigate the effect of pore-forming proteins in supported lipid bilayers .
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Affiliation(s)
- Joseph D Unsay
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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34
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Nasrallah H, Vial A, Pocholle N, Soulier J, Costa L, Godefroy C, Bourillot E, Lesniewska E, Milhiet PE. Imaging Artificial Membranes Using High-Speed Atomic Force Microscopy. Methods Mol Biol 2019; 1886:45-59. [PMID: 30374861 DOI: 10.1007/978-1-4939-8894-5_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Supported lipid bilayers represent a very attractive way to mimic biological membranes, especially to investigate molecular mechanisms associated with the lateral segregation of membrane components. Observation of these model membranes with high-speed atomic force microscopy (HS-AFM) allows the capture of both topography and dynamics of membrane components, with a spatial resolution in the nanometer range and image capture time of less than 1 s. In this context, we have developed new protocols adapted for HS-AFM to form supported lipid bilayers on small mica disks using the vesicle fusion or Langmuir-Blodgett methods. In this chapter we describe in detail the protocols to fabricate supported artificial bilayers as well as the main guidelines for HS-AFM imaging of such samples.
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Affiliation(s)
- Hussein Nasrallah
- INSERM, U1054, Montpellier, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
| | - Anthony Vial
- INSERM, U1054, Montpellier, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
| | - Nicolas Pocholle
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Jérémy Soulier
- INSERM, U1054, Montpellier, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
| | - Luca Costa
- INSERM, U1054, Montpellier, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
| | - Cédric Godefroy
- INSERM, U1054, Montpellier, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France
| | - Eric Bourillot
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Pierre-Emmanuel Milhiet
- INSERM, U1054, Montpellier, France.
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, UMR 5048, Montpellier, France.
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35
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Ren J, Zou Q. Modeling of Soft Sample Deformation in Atomic Force Microscope Imaging: Live Mammalian Cell Example. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Juan Ren
- Department of Mechanical Engineering Iowa State University Ames IA 50011 USA
| | - Qingze Zou
- Department of Mechanical and Aerospace Engineering Rutgers University Piscataway NJ 08854 USA
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36
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Mathelié-Guinlet M, Grauby-Heywang C, Martin A, Février H, Moroté F, Vilquin A, Béven L, Delville MH, Cohen-Bouhacina T. Detrimental impact of silica nanoparticles on the nanomechanical properties of Escherichia coli, studied by AFM. J Colloid Interface Sci 2018; 529:53-64. [PMID: 29883930 DOI: 10.1016/j.jcis.2018.05.098] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 12/17/2022]
Abstract
Despite great innovative and technological promises, nanoparticles (NPs) can ultimately exert an antibacterial activity by affecting the cell envelope integrity. This envelope, by conferring the cell its rigidity and protection, is intimately related to the mechanical behavior of the bacterial surface. Depending on their size, surface chemistry, shape, NPs can induce damages to the cell morphology and structure among others, and are therefore expected to alter the overall mechanical properties of bacteria. Although Atomic Force Microscopy (AFM) stands as a powerful tool to study biological systems, with high resolution and in near physiological environment, it has rarely been applied to investigate at the same time both morphological and mechanical degradations of bacteria upon NPs treatment. Consequently, this study aims at quantifying the impact of the silica NPs (SiO2-NPs) on the mechanical properties of E. coli cells after their exposure, and relating it to their toxic activity under a critical diameter. Cell elasticity was calculated by fitting the force curves with the Hertz model, and was correlated with the morphological study. SiO2-NPs of 100 nm diameter did not trigger any significant change in the Young modulus of E. coli, in agreement with the bacterial intact morphology and membrane structure. On the opposite, the 4 nm diameter SiO2-NPs did induce a significant decrease in E. coli Young modulus, mainly associated with the disorganization of lipopolysaccharides in the outer membrane and the permeation of the underlying peptidoglycan layer. The subsequent toxic behavior of these NPs is finally confirmed by the presence of membrane residues, due to cell lysis, exhibiting typical adhesion features.
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Affiliation(s)
- Marion Mathelié-Guinlet
- Univ. Bordeaux, CNRS, LOMA, UMR5798, 351 cours de la Libération, 33400 Talence, France; Univ. Bordeaux, CNRS, ICMCB, UMR5026, 87 avenue du Dr Albert Schweitzer, 33608 Pessac, France
| | | | - Axel Martin
- Univ. Bordeaux, CNRS, LOMA, UMR5798, 351 cours de la Libération, 33400 Talence, France
| | - Hugo Février
- Univ. Bordeaux, CNRS, LOMA, UMR5798, 351 cours de la Libération, 33400 Talence, France
| | - Fabien Moroté
- Univ. Bordeaux, CNRS, LOMA, UMR5798, 351 cours de la Libération, 33400 Talence, France
| | - Alexandre Vilquin
- Univ. Bordeaux, CNRS, LOMA, UMR5798, 351 cours de la Libération, 33400 Talence, France
| | - Laure Béven
- Univ. Bordeaux, INRA, UMR 1332 Biologie du Fruit et Pathologie, 33882 Villenave-d'Ornon, France
| | - Marie-Hélène Delville
- Univ. Bordeaux, CNRS, ICMCB, UMR5026, 87 avenue du Dr Albert Schweitzer, 33608 Pessac, France.
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37
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Vielmuth F, Spindler V, Waschke J. Atomic Force Microscopy Provides New Mechanistic Insights into the Pathogenesis of Pemphigus. Front Immunol 2018; 9:485. [PMID: 29643851 PMCID: PMC5883869 DOI: 10.3389/fimmu.2018.00485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/23/2018] [Indexed: 12/19/2022] Open
Abstract
Autoantibodies binding to the extracellular domains of desmoglein (Dsg) 3 and 1 are critical in the pathogenesis of pemphigus by mechanisms leading to impaired function of desmosomes and blister formation in the epidermis and mucous membranes. Desmosomes are highly organized protein complexes which provide strong intercellular adhesion. Desmosomal cadherins such as Dsgs, proteins of the cadherin superfamily which interact via their extracellular domains in Ca2+-dependent manner, are the transmembrane adhesion molecules clustered within desmosomes. Investigations on pemphigus cover a wide range of experimental approaches including biophysical methods. Especially atomic force microscopy (AFM) has recently been applied increasingly because it allows the analysis of native materials such as cultured cells and tissues under near-physiological conditions. AFM provides information about the mechanical properties of the sample together with detailed interaction analyses of adhesion molecules. With AFM, it was recently demonstrated that autoantibodies directly inhibit Dsg interactions on the surface of living keratinocytes, a phenomenon which has long been considered the main mechanism causing loss of cell cohesion in pemphigus. In addition, AFM allows to study how signaling pathways altered in pemphigus control binding properties of Dsgs. More general, AFM and other biophysical studies recently revealed the importance of keratin filaments for regulation of Dsg binding and keratinocyte mechanical properties. In this mini-review, we reevaluate AFM studies in pemphigus and keratinocyte research, recapitulate what is known about the interaction mechanisms of desmosomal cadherins and discuss the advantages and limitations of AFM in these regards.
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Affiliation(s)
| | | | - Jens Waschke
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
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38
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Abstract
Atomic force microscopy (AFM)-based force spectroscopy is a powerful technique which has seen significant enhancements in both force and time resolution in recent years. This chapter details two AFM cantilever modification procedures that yield high force precision over different temporal bandwidths. Specifically, it explains a fairly straightforward method to achieve sub-pN force precision and stability at low frequencies (<50 Hz) by removing the metal coatings from a commercially available cantilever. A more involved procedure utilizing a focused ion beam milling machine is required to maintain high force precision at enhanced bandwidths. Both modification methods allow site-specific attachment of biomolecules onto the apex area of the tips for force spectroscopy. The chapter concludes with a comparative demonstration using the two cantilever modification methods to study a lipid-protein interaction.
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Affiliation(s)
- Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
| | - Anna E Pittman
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
| | - Tina R Matin
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, USA.
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
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39
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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40
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Vélez-Ortega AC, Frolenkov GI. Visualization of Live Cochlear Stereocilia at a Nanoscale Resolution Using Hopping Probe Ion Conductance Microscopy. Methods Mol Biol 2017; 1427:203-21. [PMID: 27259929 DOI: 10.1007/978-1-4939-3615-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The mechanosensory apparatus that detects sound-induced vibrations in the cochlea is located on the apex of the auditory sensory hair cells and it is made up of actin-filled projections, called stereocilia. In young rodents, stereocilia bundles of auditory hair cells consist of 3-4 rows of stereocilia of decreasing height and varying thickness. Morphological studies of the auditory stereocilia bundles in live hair cells have been challenging because the diameter of each stereocilium is near or below the resolution limit of optical microscopy. In theory, scanning probe microscopy techniques, such as atomic force microscopy, could visualize the surface of a living cell at a nanoscale resolution. However, their implementations for hair cell imaging have been largely unsuccessful because the probe usually damages the bundle and disrupts the bundle cohesiveness during imaging. We overcome these limitations by using hopping probe ion conductance microscopy (HPICM), a non-contact scanning probe technique that is ideally suited for the imaging of live cells with a complex topography. Organ of Corti explants are placed in a physiological solution and then a glass nanopipette-which is connected to a 3D-positioning piezoelectric system and to a patch clamp amplifier-is used to scan the surface of the live hair cells at nanometer resolution without ever touching the cell surface.Here, we provide a detailed protocol for the imaging of mouse or rat stereocilia bundles in live auditory hair cells using HPICM. We provide information about the fabrication of the nanopipettes, the calibration of the HPICM setup, the parameters we have optimized for the imaging of live stereocilia bundles and, lastly, a few basic image post-processing manipulations.
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Affiliation(s)
- A Catalina Vélez-Ortega
- Department of Physiology, College of Medicine, Chandler Medical Center, University of Kentucky, MS508, 800 Rose Street, Lexington, KY, 40536, USA
| | - Gregory I Frolenkov
- Department of Physiology, College of Medicine, Chandler Medical Center, University of Kentucky, MS508, 800 Rose Street, Lexington, KY, 40536, USA.
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41
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Yeow N, Tabor RF, Garnier G. Atomic force microscopy: From red blood cells to immunohaematology. Adv Colloid Interface Sci 2017; 249:149-162. [PMID: 28515013 DOI: 10.1016/j.cis.2017.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
Atomic force microscopy (AFM) offers complementary imaging modes that can provide morphological and structural details of red blood cells (RBCs), and characterize interactions between specific biomolecules and RBC surface antigen. This review describes the applications of AFM in determining RBC health by the observation of cell morphology, elasticity and surface roughness. Measurement of interaction forces between plasma proteins and antibodies against RBC surface antigen using the AFM also brought new information to the immunohaematology field. With constant improvisation of the AFM in resolution and imaging time, the reaction of RBC to changes in the physico-chemistry of its environment and the presence of RBC surface antigen specific-biomolecules is achievable.
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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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The structure and function of cell membranes studied by atomic force microscopy. Semin Cell Dev Biol 2017; 73:31-44. [PMID: 28723581 DOI: 10.1016/j.semcdb.2017.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/08/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022]
Abstract
The cell membrane, involved in almost all communications of cells and surrounding matrix, is one of the most complicated components of cells. Lack of suitable methods for the detection of cell membranes in vivo has sparked debates on the biochemical composition and structure of cell membranes over half a century. The development of single molecule techniques, such as AFM, SMFS, and TREC, provides a versatile platform for imaging and manipulating cell membranes in biological relevant environments. Here, we discuss the latest developments in AFM and the progress made in cell membrane research. In particular, we highlight novel structure models and dynamic processes, including the mechanical properties of the cell membranes.
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Probing the threshold of membrane damage and cytotoxicity effects induced by silica nanoparticles in Escherichia coli bacteria. Adv Colloid Interface Sci 2017; 245:81-91. [PMID: 28477864 DOI: 10.1016/j.cis.2017.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 10/19/2022]
Abstract
The engineering of nanomaterials, because of their specific properties, is increasingly being developed for commercial purposes over the past decades, to enhance diagnosis, cosmetics properties as well as sensing efficiency. However, the understanding of their fate and thus their interactions at the cellular level with bio-organisms remains elusive. Here, we investigate the size- and charge-dependence of the damages induced by silica nanoparticles (SiO2-NPs) on Gram-negative Escherichia coli bacteria. We show and quantify the existence of a NPs size threshold discriminating toxic and inert SiO2-NPs with a critical particle diameter (Φc) in the range 50nm-80nm. This particular threshold is identified at both the micrometer scale via viability tests through Colony Forming Units (CFU) counting, and the nanometer scale via atomic force microscopy (AFM). At this nanometer scale, AFM emphasizes the interaction between the cell membrane and SiO2-NPs from both topographic and mechanical points of view. For SiO2-NPs with Φ>Φc no change in E. coli morphology nor its outer membrane (OM) organization is observed unless the NPs are positively charged in which case reorganization and disruption of the OM are detected. Conversely, when Φ<Φc, E. coli exhibit unusual spherical shapes, partial collapse, even lysis, and OM reorganization.
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Role of silver/zinc oxide in affecting de-adhesion strength of Staphylococcus aureus on polymer biocomposites. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 75:1106-1114. [DOI: 10.1016/j.msec.2017.02.131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/17/2016] [Accepted: 02/24/2017] [Indexed: 01/10/2023]
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Effects of Streptococcus sanguinis Bacteriocin on Deformation, Adhesion Ability, and Young's Modulus of Candida albicans. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5291486. [PMID: 28612025 PMCID: PMC5458367 DOI: 10.1155/2017/5291486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 11/18/2022]
Abstract
In order to study the thallus changes on microscopic morphology and mechanical properties of Candida albicans antagonized by Streptococcus sanguinis bacteriocin, the adhesion ability and Young's modulus of thalli and hypha of Candida albicans were measured by the relative measurement method using atomic force microscope's (AFM) tapping model. The results showed that the average adhesion ability and Young's modulus of thalli were 7.35 ± 0.77 nN and 7.33 ± 1.29 Mpa, respectively; the average adhesion ability and Young's modulus of hypha were 9.82 ± 0.39 nN and 4.04 ± 0.76 Mpa, respectively. After being antagonized by Streptococcus sanguinis bacteriocin, the adhesion ability was decreased along with the increasing of deformation in reaction region and Young's modulus followed the same changes. It could be concluded that the adhesion ability of hypha was greater than thalli, Young's modulus of hypha was less than thalli, and adhesion ability and Young's modulus of Candida albicans were decreased significantly after being antagonized by Streptococcus sanguinis bacteriocin.
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Li A, Chen J, Liang ZH, Cai J, Cai HH, Chen M. Comparison of ultrastructural and nanomechanical signature of platelets from acute myocardial infarction and platelet activation. Biochem Biophys Res Commun 2017; 486:245-251. [PMID: 28274875 DOI: 10.1016/j.bbrc.2017.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/03/2017] [Indexed: 12/12/2022]
Abstract
Acute myocardial infarction (AMI) initiation and progression follow complex molecular and structural changes in the nanoarchitecture of platelets. However, it remains poorly understood how the transformation from health to AMI alters the ultrastructural and biomechanical properties of platelets within the platelet activation microenvironment. Here, we show using an atomic force microscope (AFM) that platelet samples, including living human platelets from the healthy and AMI patient, activated platelets from collagen-stimulated model, show distinct ultrastructural imaging and stiffness profiles. Correlative morphology obtained on AMI platelets and collagen-activated platelets display distinct pseudopodia structure and nanoclusters on membrane. In contrast to normal platelets, AMI platelets have a stiffer distribution resulting from complicated pathogenesis, with a prominent high-stiffness peak representative of platelet activation using AFM-based force spectroscopy. Similar findings are seen in specific stages of platelet activation in collagen-stimulated model. Further evidence obtained from different force measurement region with activated platelets shows that platelet migration is correlated to the more elasticity of pseudopodia while high stiffness at the center region. Overall, ultrastructural and nanomechanical profiling by AFM provides quantitative indicators in the clinical diagnostics of AMI with mechanobiological significance.
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Affiliation(s)
- Aiqun Li
- Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Jianwei Chen
- Department of Cardiology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Zhi-Hong Liang
- Analytical and Testing Center, Jinan University, Guangzhou 510632, China
| | - Jiye Cai
- Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China; State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau 999078, China
| | - Huai-Hong Cai
- Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China.
| | - Min Chen
- Department of Respiratory Medicine, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China; Department of Respiratory Medicine, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China.
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Sumino A, Uchihashi T, Oiki S. Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging. J Phys Chem Lett 2017; 8:785-793. [PMID: 28139934 DOI: 10.1021/acs.jpclett.6b03058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Here, we have developed a method of oriented reconstitution of the KcsA potassium channel amenable to high-resolution AFM imaging. The solubilized full-length KcsA channels with histidine-tagged (His-tag) C-terminal ends were attached to a Ni2+-coated mica surface, and then detergent-destabilized liposomes were added to fill the interchannel space. AFM revealed that the membrane-embedded KcsA channels were oriented with their extracellular faces upward, seen as a tetrameric square shape. This orientation was corroborated by the visible binding of a peptide scorpion toxin, agitoxin-2. To observe the cytoplasmic side of the channel, a His-tag was inserted into the extracellular loop, and the oppositely oriented channels provided wholly different images. In either orientation, the channels were individually dispersed at acidic pH, whereas they were self-assembled at neutral pH, indicating that the oriented channels are allowed to diffuse in the membrane. This method is readily applicable to membrane proteins in general for AFM imaging.
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Affiliation(s)
- Ayumi Sumino
- PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , 23-3 Matsuokashimoaizuki, Yoshida-gun, Fukui 910-1193, Japan
| | - Takayuki Uchihashi
- Department of Physics, Kanazawa University , Kakuma-machi, Kanazawa 920-1192, Japan
- Bio-AFM Frontier Research Center , Kanazawa 920-1192, Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , 23-3 Matsuokashimoaizuki, Yoshida-gun, Fukui 910-1193, Japan
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The selective cytotoxicity of DSF-Cu attributes to the biomechanical properties and cytoskeleton rearrangements in the normal and cancerous nasopharyngeal epithelial cells. Int J Biochem Cell Biol 2017; 84:96-108. [PMID: 28111334 DOI: 10.1016/j.biocel.2017.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 12/15/2022]
Abstract
Cancer initiation and progression follow complex changes of cellular architecture and biomechanical property. Cancer cells with more submissive (or "softer") than their healthy counterparts attributed to the reorganization of the complex cytoskeleton structure, may be considered as a potential anti-tumor therapeutic target. In this study, atomic force microscopy (AFM) was carried out to detect the topographical and biophysical changes of nasopharyngeal carcinoma CNE-2Z cells and normal nasopharyngeal epithelial cells NP69-SV40T by treating the Disulfiram chelated with Cu2+ (DSF-Cu). DSF-Cu induced the apoptotic population, ROS production and decreased the NF-κB-p65 expression of CNE-2Z cells, which was much higher than those of NP69-SV40T cells. DSF-Cu caused the obvious changes of cell morphology and membrane ultrastructure in CNE-2Z cells. The roughness decreased and stiffness increased significantly in CNE-2Z cells, which correlated with the rearrangement of intracellular F-actin, FLNa and α-tubulin structures in CNE-2Z cells. And the adhesion force of CNE-2Z cells was also increased accompanied with the increased E-cadherin expression. However, these results could not be observed in the NP69-SV40T cells even the concentration of DSF reached up to 400nM. Finally, the detection of cell wound scratch assay confirmed DSF-Cu could inhibit the migration of CNE-2Z cells, but no effect on NP69-SV40T cells. These findings demonstrated the selective cytotoxicity of DSF-Cu in CNE-2Z cells may attribute to the different mechanical properties and cytoskeleton rearrangement from the normal nasopharyngeal epithelial cells.
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50
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Single-molecule force spectroscopy on polyproteins and receptor–ligand complexes: The current toolbox. J Struct Biol 2017; 197:3-12. [DOI: 10.1016/j.jsb.2016.02.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/21/2022]
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