1
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Seeing the unseen: High-resolution AFM imaging captures antibiotic action in bacterial membranes. Nat Commun 2022; 13:6196. [PMID: 36271086 PMCID: PMC9587010 DOI: 10.1038/s41467-022-33839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
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2
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Shi C, He Y, Ding M, Wang Y, Zhong J. Nanoimaging of food proteins by atomic force microscopy. Part I: Components, imaging modes, observation ways, and research types. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2018.11.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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3
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Benaglia S, Gisbert VG, Perrino AP, Amo CA, Garcia R. Fast and high-resolution mapping of elastic properties of biomolecules and polymers with bimodal AFM. Nat Protoc 2018; 13:2890-2907. [DOI: 10.1038/s41596-018-0070-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Wang JY, Mullin N, Hobbs JK. High-speed large area atomic force microscopy using a quartz resonator. NANOTECHNOLOGY 2018; 29:335502. [PMID: 29794343 DOI: 10.1088/1361-6528/aac7a3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A high-speed atomic force microscope for scanning large areas, utilizing a quartz bar driven close to resonance to provide the motion in the fast scan axis is presented. Images up to 170 × 170 μm2 have been obtained on a polydimethylsiloxane (PDMS) grating in 1 s. This is provided through an average tip-sample velocity of 28 cm s-1 at a line rate of 830 Hz. Scan areas up to 80 × 80 μm2 have been obtained in 0.42 s with a line rate of 1410 Hz. To demonstrate the capability of the scanner the spherulitic crystallization of a semicrystalline polymer was imaged in situ at high speed.
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Affiliation(s)
- J-Y Wang
- Department of Physics and Astronomy, Hicks Building, University of Sheffield, S3 7RH, United Kingdom
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5
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Miyagi A, Scheuring S. A novel phase-shift-based amplitude detector for a high-speed atomic force microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:083704. [PMID: 30184715 DOI: 10.1063/1.5038095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
In any atomic force microscope operated in amplitude modulation mode, aka "tapping mode" or "oscillating mode," the most crucial operation is the detection of the cantilever oscillation amplitude. Indeed, it is the change in the cantilever oscillation amplitude that drives the feedback loop, and thus, the accuracy and speed of amplitude detection are of utmost importance for improved atomic force microscopy operation. This becomes even more crucial for the operation of a high-speed atomic force microscope (HS-AFM), where feedback operation on a single or a low number of cantilever oscillation cycles between 500 kHz and 1000 kHz oscillation frequency is desired. So far, the amplitude detection was performed by Fourier analysis of each oscillation, resulting in a single output amplitude value at the end of each oscillation cycle, i.e., 360° phase delay. Here, we present a novel analog amplitude detection circuit with theoretic continuous amplitude detection at 90° phase delay. In factual operation, when exposed to an abrupt amplitude change, our novel amplitude detector circuit reacted with a phase delay of ∼138° compared with the phase delay of ∼682° achieved by the Fourier analysis method. Integrated to a HS-AFM, the novel amplitude detector should allow faster image acquisition with lower invasiveness due to the faster and more accurate detection of cantilever oscillation amplitude change.
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Affiliation(s)
- Atsushi Miyagi
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, USA
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6
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刘 林, 魏 余, 刘 文, 孙 彤, 王 凯, 汪 颖, 李 宾. [Progress in the applications of high-speed atomic force microscopy in cell biology]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:931-937. [PMID: 30187879 PMCID: PMC6744042 DOI: 10.3969/j.issn.1673-4254.2018.08.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Indexed: 12/24/2022]
Abstract
Without losing its high resolution, high-speed atomic force microscope (HS-AFM) represents a perfect combinationof scanning speed and precision and allows real-time and in situ observation of the dynamic processes in a biological system atboth the cellular and molecular levels. By combining the extremely high temporal resolution with the spatial resolution andcoupling with other advanced technologies, HS-AFM shows promising prospects for applications in life sciences such as cellbiology. In this review, we summarize the latest progress of HS-AFM in the field of cell biology, and discuss the impact ofenvironmental factors on conformation dynamics of DNA, the binding processes between DNA and protein, the domainchanges of membrane proteins, motility of myosin, and surface structure changes of living cells.
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Affiliation(s)
- 林 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 余辉 魏
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 文静 刘
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 彤 孙
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 凯喆 王
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- 中国科学院大学,北京 100049University of Chinese Academy of Sciences, Beijing 100049, China
| | - 颖 汪
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - 宾 李
- 中国科学院上海应用物理研究所物理生物研究室,上海 201800Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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7
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Xiao J, Dufrêne YF. Optical and force nanoscopy in microbiology. Nat Microbiol 2016; 1:16186. [PMID: 27782138 PMCID: PMC5839876 DOI: 10.1038/nmicrobiol.2016.186] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
Microbial cells have developed sophisticated multicomponent structures and machineries to govern basic cellular processes, such as chromosome segregation, gene expression, cell division, mechanosensing, cell adhesion and biofilm formation. Because of the small cell sizes, subcellular structures have long been difficult to visualize using diffraction-limited light microscopy. During the last three decades, optical and force nanoscopy techniques have been developed to probe intracellular and extracellular structures with unprecedented resolutions, enabling researchers to study their organization, dynamics and interactions in individual cells, at the single-molecule level, from the inside out, and all the way up to cell-cell interactions in microbial communities. In this Review, we discuss the principles, advantages and limitations of the main optical and force nanoscopy techniques available in microbiology, and we highlight some outstanding questions that these new tools may help to answer.
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Affiliation(s)
- Jie Xiao
- Department of Biophysics &Biophysical Chemistry, The Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland 21212, USA
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Belgium
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8
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Bone quality assessment techniques: geometric, compositional, and mechanical characterization from macroscale to nanoscale. Clin Rev Bone Miner Metab 2016; 14:133-149. [PMID: 28936129 DOI: 10.1007/s12018-016-9222-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This review presents an overview of the characterization techniques available to experimentally evaluate bone quality, defined as the geometric and material factors that contribute to fracture resistance independently of areal bone mineral density (aBMD) assessed by dual energy x-ray absorptiometry. The methods available for characterization of the geometric, compositional, and mechanical properties of bone across multiple length scales are summarized, along with their outcomes and their advantages and disadvantages. Examples of how each technique is used are discussed, as well as practical concerns such as sample preparation and whether or not each testing method is destructive. Techniques that can be used in vivo and those that have been recently improved or developed are emphasized, including high resolution peripheral quantitative computed tomography to evaluate geometric properties and reference point indentation to evaluate material properties. Because no single method can completely characterize bone quality, we provide a framework for how multiple characterization methods can be used together to generate a more comprehensive analysis of bone quality to complement aBMD in fracture risk assessment.
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9
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Chen HM, Jheng KR, Yu AD, Hsu CC, Lin JH. Intercalating purple membranes into 2D β-alanine crystals to enhance photoelectric and nonlinear optical properties. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Zhong J, Yan J. Seeing is believing: atomic force microscopy imaging for nanomaterial research. RSC Adv 2016. [DOI: 10.1039/c5ra22186b] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Atomic force microscopy can image nanomaterial properties such as the topography, elasticity, adhesion, friction, electrical properties, and magnetism.
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Affiliation(s)
- Jian Zhong
- College of Food Science & Technology
- Shanghai Ocean University
- Shanghai 201306
- People's Republic of China
| | - Juan Yan
- College of Food Science & Technology
- Shanghai Ocean University
- Shanghai 201306
- People's Republic of China
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11
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Assemblies of pore-forming toxins visualized by atomic force microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:500-11. [PMID: 26577274 DOI: 10.1016/j.bbamem.2015.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 10/23/2015] [Accepted: 11/09/2015] [Indexed: 02/05/2023]
Abstract
A number of pore-forming toxins (PFTs) can assemble on lipid membranes through their specific interactions with lipids. The oligomeric assemblies of some PFTs have been successfully revealed either by electron microscopy (EM) and/or atomic force microscopy (AFM). Unlike EM, AFM imaging can be performed under physiological conditions, enabling the real-time visualization of PFT assembly and the transition from the prepore state, in which the toxin does not span the membrane, to the pore state. In addition to characterizing PFT oligomers, AFM has also been used to examine toxin-induced alterations in membrane organization. In this review, we summarize the contributions of AFM to the understanding of both PFT assembly and PFT-induced membrane reorganization. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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12
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Cartagena-Rivera AX, Wang WH, Geahlen RL, Raman A. Fast, multi-frequency, and quantitative nanomechanical mapping of live cells using the atomic force microscope. Sci Rep 2015; 5:11692. [PMID: 26118423 PMCID: PMC4484408 DOI: 10.1038/srep11692] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/03/2015] [Indexed: 11/08/2022] Open
Abstract
A longstanding goal in cellular mechanobiology has been to link dynamic biomolecular processes underpinning disease or morphogenesis to spatio-temporal changes in nanoscale mechanical properties such as viscoelasticity, surface tension, and adhesion. This requires the development of quantitative mechanical microscopy methods with high spatio-temporal resolution within a single cell. The Atomic Force Microscope (AFM) can map the heterogeneous mechanical properties of cells with high spatial resolution, however, the image acquisition time is 1-2 orders of magnitude longer than that required to study dynamic cellular processes. We present a technique that allows commercial AFM systems to map quantitatively the dynamically changing viscoelastic properties of live eukaryotic cells at widely separated frequencies over large areas (several 10's of microns) with spatial resolution equal to amplitude-modulation (AM-AFM) and with image acquisition times (tens of seconds) approaching those of speckle fluorescence methods. This represents a ~20 fold improvement in nanomechanical imaging throughput compared to AM-AFM and is fully compatible with emerging high speed AFM systems. This method is used to study the spatio-temporal mechanical response of MDA-MB-231 breast carcinoma cells to the inhibition of Syk protein tyrosine kinase giving insight into the signaling pathways by which Syk negatively regulates motility of highly invasive cancer cells.
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Affiliation(s)
- Alexander X. Cartagena-Rivera
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana, USA
| | - Wen-Horng Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Robert L. Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Arvind Raman
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana, USA
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13
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Stoichev S, Krumova SB, Andreeva T, Busto JV, Todinova S, Balashev K, Busheva M, Goñi FM, Taneva SG. Low pH modulates the macroorganization and thermal stability of PSII supercomplexes in grana membranes. Biophys J 2015; 108:844-853. [PMID: 25692589 PMCID: PMC4336371 DOI: 10.1016/j.bpj.2014.12.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/08/2014] [Accepted: 12/22/2014] [Indexed: 11/25/2022] Open
Abstract
Protonation of the lumen-exposed residues of some photosynthetic complexes in the grana membranes occurs under conditions of high light intensity and triggers a major photoprotection mechanism known as energy dependent nonphotochemical quenching. We have studied the role of protonation in the structural reorganization and thermal stability of isolated grana membranes. The macroorganization of granal membrane fragments in protonated and partly deprotonated state has been mapped by means of atomic force microscopy. The protonation of the photosynthetic complexes has been found to induce large-scale structural remodeling of grana membranes-formation of extensive domains of the major light-harvesting complex of photosystem II and clustering of trimmed photosystem II supercomplexes, thinning of the membrane, and reduction of its size. These events are accompanied by pronounced thermal destabilization of the photosynthetic complexes, as evidenced by circular dichroism spectroscopy and differential scanning calorimetry. Our data reveal a detailed nanoscopic picture of the initial steps of nonphotochemical quenching.
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Affiliation(s)
- Svetozar Stoichev
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sashka B Krumova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tonya Andreeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Jon V Busto
- Unidad de Biofísica (CSIC, UPV-EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Svetla Todinova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Konstantin Balashev
- Department of Physical Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Mira Busheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Félix M Goñi
- Unidad de Biofísica (CSIC, UPV-EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Stefka G Taneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria; Unidad de Biofísica (CSIC, UPV-EHU) and Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain.
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14
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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15
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Duneau JP, Sturgis JN. Lateral organization of biological membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:843-50. [DOI: 10.1007/s00249-013-0933-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/13/2013] [Accepted: 09/26/2013] [Indexed: 11/24/2022]
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16
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Brown BP, Picco L, Miles MJ, Faul CFJ. Opportunities in high-speed atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3201-3211. [PMID: 23609982 DOI: 10.1002/smll.201203223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Indexed: 06/02/2023]
Abstract
The atomic force microscope (AFM) has become integrated into standard characterisation procedures in many different areas of research. Nonetheless, typical imaging rates of commercial microscopes are still very slow, much to the frustration of the user. Developments in instrumentation for "high-speed AFM" (HSAFM) have been ongoing since the 1990s, and now nanometer resolution imaging at video rate is readily achievable. Despite thorough investigation of samples of a biological nature, use of HSAFM instruments to image samples of interest to materials scientists, or to carry out AFM lithography, has been minimal. This review gives a summary of different approaches to and advances in the development of high-speed AFMs, highlights important discoveries made with new instruments, and briefly discusses new possibilities for HSAFM in materials science.
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Affiliation(s)
- Benjamin P Brown
- Bristol Centre for Functional Nanomaterials, Centre for NSQI, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, UK
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17
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Abstract
Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.
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Affiliation(s)
- Toshio Ando
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan.
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18
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Bubner P, Plank H, Nidetzky B. Visualizing cellulase activity. Biotechnol Bioeng 2013; 110:1529-49. [DOI: 10.1002/bit.24884] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 01/08/2013] [Accepted: 02/22/2013] [Indexed: 11/08/2022]
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19
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Molecular machines directly observed by high-speed atomic force microscopy. FEBS Lett 2013; 587:997-1007. [PMID: 23318713 DOI: 10.1016/j.febslet.2012.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 11/22/2022]
Abstract
Molecular machines made of proteins are highly dynamic and carry out sophisticated biological functions. The direct and dynamic high-resolution visualization of molecular machines in action is considered to be the most straightforward approach to understanding how they function but this has long been infeasible until recently. High-speed atomic force microscopy has recently been realized, making such visualization possible. The captured images of myosin V, F1-ATPase, and bacteriorhodopsin have enabled their dynamic processes and structure dynamics to be revealed in great detail, giving unique and deep insights into their functional mechanisms.
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20
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Abstract
High-speed atomic force microscopy (HS-AFM) has been developed as a nano-dynamics visualization technique. This microscopy permits direct observation of structure dynamics and dynamic processes of biological molecules in physiological solutions, at a subsecond to sub-100 ms temporal resolution and an ∼2 nm lateral and a 0.1 nm vertical resolution. Importantly, tip-sample interactions do not disturb the biomolecules' functions. Various functioning proteins including myosin V walking on an actin filament and bacteriorhodopsin responding to light have been successfully visualized with HS-AFM. In the quest for understanding the functional mechanisms of proteins, inferences no longer have to be made from static snapshots of molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies obtained from HS-AFM observations reveal the details of molecules' dynamic behavior in action, without the need for intricate analyses and interpretations. In this review, I first describe the fundamentals behind the achieved high imaging rate and low invasiveness to samples, and then highlight recent imaging studies. Finally, future studies are briefly described.
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Affiliation(s)
- Toshio Ando
- Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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21
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Yip CM. Correlative optical and scanning probe microscopies for mapping interactions at membranes. Methods Mol Biol 2013; 950:439-56. [PMID: 23086889 DOI: 10.1007/978-1-62703-137-0_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative approaches for real-time imaging on molecular-length scales are providing researchers with powerful strategies for characterizing molecular and cellular structures and dynamics. Combinatorial techniques that integrate two or more distinct imaging modalities are particularly compelling as they provide a means for overcoming the limitations of the individual modalities and, when applied simultaneously, enable the collection of rich multi-modal datasets. Almost since its inception, scanning probe microscopy has closely associated with optical microscopy. This is particularly evident in the fields of cellular and molecular biophysics where researchers are taking full advantage of these real-time, in situ, tools to acquire three-dimensional molecular-scale topographical images with nanometer resolution, while simultaneously characterizing their structure and interactions though conventional optical microscopy. The ability to apply mechanical or optical stimuli provides an additional experimental dimension that has shown tremendous promise for examining dynamic events on sub-cellular length scales. In this chapter, we describe recent efforts in developing these integrated platforms, the methodology for, and inherent challenges in, performing coupled imaging experiments, and the potential and future opportunities of these research tools for the fields of molecular and cellular biophysics with a specific emphasis on the application of these coupled approaches for the characterization of interactions occurring at membrane interfaces.
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Affiliation(s)
- Christopher M Yip
- Department of Chemical Engineering and Applied Chemistry, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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22
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Picas L, Milhiet PE, Hernández-Borrell J. Atomic force microscopy: a versatile tool to probe the physical and chemical properties of supported membranes at the nanoscale. Chem Phys Lipids 2012. [PMID: 23194897 DOI: 10.1016/j.chemphyslip.2012.10.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Atomic force microscopy (AFM) was developed in the 1980s following the invention of its precursor, scanning tunneling microscopy (STM), earlier in the decade. Several modes of operation have evolved, demonstrating the extreme versatility of this method for measuring the physicochemical properties of samples at the nanoscopic scale. AFM has proved an invaluable technique for visualizing the topographic characteristics of phospholipid monolayers and bilayers, such as roughness, height or laterally segregated domains. Implemented modes such as phase imaging have also provided criteria for discriminating the viscoelastic properties of different supported lipid bilayer (SLB) regions. In this review, we focus on the AFM force spectroscopy (FS) mode, which enables determination of the nanomechanical properties of membrane models. The interpretation of force curves is presented, together with newly emerging techniques that provide complementary information on physicochemical properties that may contribute to our understanding of the structure and function of biomembranes. Since AFM is an imaging technique, some basic indications on how real-time AFM imaging is evolving are also presented at the end of this paper.
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Affiliation(s)
- Laura Picas
- Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 Paris, France
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Erickson BW, Coquoz S, Adams JD, Burns DJ, Fantner GE. Large-scale analysis of high-speed atomic force microscopy data sets using adaptive image processing. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2012; 3:747-58. [PMID: 23213638 PMCID: PMC3512124 DOI: 10.3762/bjnano.3.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 10/08/2012] [Indexed: 05/27/2023]
Abstract
Modern high-speed atomic force microscopes generate significant quantities of data in a short amount of time. Each image in the sequence has to be processed quickly and accurately in order to obtain a true representation of the sample and its changes over time. This paper presents an automated, adaptive algorithm for the required processing of AFM images. The algorithm adaptively corrects for both common one-dimensional distortions as well as the most common two-dimensional distortions. This method uses an iterative thresholded processing algorithm for rapid and accurate separation of background and surface topography. This separation prevents artificial bias from topographic features and ensures the best possible coherence between the different images in a sequence. This method is equally applicable to all channels of AFM data, and can process images in seconds.
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Affiliation(s)
- Blake W Erickson
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Séverine Coquoz
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Jonathan D Adams
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
| | - Daniel J Burns
- Mechatronics Laboratory, Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, École Polytechnique Fédérale de Lausanne, Batiment BM 3109 Station 17, 1015 Lausanne, Switzerland
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24
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Abstract
Unraveling the structure of microbial cells is a major challenge in current microbiology and offers exciting prospects in biomedicine. Atomic force microscopy (AFM) appears as a powerful method to image the surface ultrastructure of live cells under physiological conditions and allows real-time imaging to follow dynamic processes such as cell growth, and division and effects of drugs and chemicals. The following chapter introduces different methods of sample preparation to gain insights into the microbial cell organization. Successful strategies to immobilize microorganisms, including physical entrapment and chemical attachment, are described. This step is a key step and a prerequisite of any analysis and persists as an important limitation to the application of AFM to microbiology due to the wide diversity of microorganisms. Finally, some applications are depicted which underlie the ability of AFM to explore living microbes with unprecedented resolution.
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25
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Colom A, Casuso I, Boudier T, Scheuring S. High-speed atomic force microscopy: cooperative adhesion and dynamic equilibrium of junctional microdomain membrane proteins. J Mol Biol 2012; 423:249-56. [PMID: 22796628 DOI: 10.1016/j.jmb.2012.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 06/29/2012] [Accepted: 07/03/2012] [Indexed: 11/29/2022]
Abstract
Junctional microdomains, paradigm for membrane protein segregation in functional assemblies, in eye lens fiber cell membranes are constituted of lens-specific aquaporin-0 tetramers (AQP0(4)) and connexin (Cx) hexamers, termed connexons. Both proteins have double function to assure nutrition and mediate adhesion of lens cells. Here we use high-speed atomic force microscopy to examine microdomain protein dynamics at the single-molecule level. We found that the adhesion function of head-to-head associated AQP0(4) and Cx is cooperative. This finding provides first experimental evidence for the mechanistic importance for junctional microdomain formation. From the observation of lateral association-dissociation events of AQP0(4), we determine that the enthalpic energy gain of a single AQP0(4)-AQP0(4) interaction in the membrane plane is -2.7 k(B)T, sufficient to drive formation of microdomains. Connexon association is stronger as dynamics are rarely observed, explaining their rim localization in junctional microdomains.
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Affiliation(s)
- Adai Colom
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique de Luminy, Marseille F-13009, France
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26
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Abstract
High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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27
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Casuso I, Rico F, Scheuring S. High-speed atomic force microscopy: Structure and dynamics of single proteins. Curr Opin Chem Biol 2011; 15:704-9. [PMID: 21632275 DOI: 10.1016/j.cbpa.2011.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 05/04/2011] [Accepted: 05/04/2011] [Indexed: 11/18/2022]
Abstract
For surface analysis of biological molecules, atomic force microscopy (AFM) is an appealing technique combining data acquisition under physiological conditions, for example buffer solution, room temperature and ambient pressure, and high resolution. However, a key feature of life, dynamics, could not be assessed until recently because of the slowness of conventional AFM setups. Thus, for observing bio-molecular processes, the gain of image acquisition speed signifies a key progress. Here, we review the development and recent achievements using high-speed atomic force microscopy (HS-AFM). The HS-AFM is now the only technique to assess structure and dynamics of single molecules, revealing molecular motor action and diffusion dynamics. From this imaging data, watching molecules at work, novel and direct insights could be gained concerning the structure, dynamics and function relationship at the single bio-molecule level.
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Affiliation(s)
- Ignacio Casuso
- INSERM U1006, Institut Curie, 26 rue d'Ulm, 75005 Paris, France
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28
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Humphris ADL, Zhao B, Catto D, Howard-Knight JP, Kohli P, Hobbs JK. High speed nano-metrology. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:043710. [PMID: 21529016 DOI: 10.1063/1.3584935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
For manufacturing at the nanometre scale a method for rapid and accurate measurement of the resultant functional devices is required. Although atomic force microscopy (AFM) has the requisite spatial resolution, it is severely limited in scan speed, the resolution and repeatability of vertical and lateral measurements being degraded when speed is increased. Here we present a new approach to AFM that makes a direct and feedback-independent measurement of surface height using a laser interferometer focused onto the back of the AFM tip. Combining this direct height measurement with a passive, feedback-free method for maintaining tip-sample contact removes the constraint on scan speed that comes from the bandwidth of the z-feedback loop. Conventional laser reflection detection is used for feedback control, which now plays the role of minimising tip-sample forces, rather than producing the sample topography. Using the system in conjunction with a rapid scanner, true height images are obtained with areas up to (36 × 36) μm(2) at 1 image/second, suitable for in-line applications.
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Affiliation(s)
- Andrew D L Humphris
- Infinitesima Ltd, Oxford Centre for Innovation, Mill St., Oxford OX2 0JX, United Kingdom
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29
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Unraveling lipid/protein interaction in model lipid bilayers by Atomic Force Microscopy. J Mol Recognit 2011; 24:387-96. [DOI: 10.1002/jmr.1083] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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30
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Allison DP, Mortensen NP, Sullivan CJ, Doktycz MJ. Atomic force microscopy of biological samples. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2011; 2:618-34. [PMID: 20672388 DOI: 10.1002/wnan.104] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate how this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).
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Affiliation(s)
- David P Allison
- Biosciences Division, Oak Ridge National Laboratory, TN 37831-6445, USA
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31
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Casuso I, Sens P, Rico F, Scheuring S. Experimental evidence for membrane-mediated protein-protein interaction. Biophys J 2011; 99:L47-9. [PMID: 20923630 DOI: 10.1016/j.bpj.2010.07.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 07/12/2010] [Accepted: 07/14/2010] [Indexed: 12/27/2022] Open
Abstract
Membrane proteins diffuse within the membrane, form oligomers and supramolecular assemblies. Using high-speed atomic force microscopy, we present direct experimental measure of an in-membrane-plane interaction potential between membrane proteins. In purple membranes, ATP-synthase c-rings formed dimers that temporarily dissociated. C-ring dimers revealed subdiffusive motion, while dissociated monomers diffused freely. C-rings center-to-center distance probability distribution allowed the calculation and modeling of an in-membrane-plane energy landscape that presented repulsion at 80 Å, most stable dimer association at 103 Å (-3.5 k(B)T strength), and dissociation at 125 Å (-1 k(B)T strength). This first experimental data of nonlabeled membrane protein diffusion and the corresponding in-membrane-plane interaction energy landscape characterized membrane protein interaction with an attractive range of several k(B)T that reaches to a radius of ∼50 Å within the membrane plane.
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32
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Heterogeneous diffusion of a membrane-bound pHLIP peptide. Biophys J 2010; 98:2914-22. [PMID: 20550904 DOI: 10.1016/j.bpj.2010.03.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 02/24/2010] [Accepted: 03/19/2010] [Indexed: 11/20/2022] Open
Abstract
Lateral diffusion of cell membrane constituents is a prerequisite for many biological functions. However, the diffusivity (or mobility) of a membrane-bound species can be influenced by many factors. To provide a better understanding of how the conformation and location of a membrane-bound biological molecule affect its mobility, herein we study the diffusion properties of a pH low insertion peptide (pHLIP) in model membranes using fluorescence correlation spectroscopy. It is found that when the pHLIP peptide is located on the membrane surface, its lateral diffusion is characterized by a distribution of diffusion times, the characteristic of which depends on the peptide/lipid ratio. Whereas, under conditions where pHLIP adopts a well-defined transmembrane alpha-helical conformation the peptide still exhibits heterogeneous diffusion, the distribution of diffusion times is found to be independent of the peptide/lipid ratio. Taken together, these results indicate that the mobility of a membrane-bound species is sensitive to its conformation and location and that diffusion measurement could provide useful information regarding the conformational distribution of membrane-bound peptides. Furthermore, the observation that the mobility of a membrane-bound species depends on its concentration may have important implications for diffusion-controlled reactions taking place in membranes.
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33
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Baclayon M, Roos WH, Wuite GJL. Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 2010; 9:1678-88. [PMID: 20562411 PMCID: PMC2938060 DOI: 10.1074/mcp.r110.001461] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 12/17/2022] Open
Abstract
To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.
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Affiliation(s)
- Marian Baclayon
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Gijs J. L. Wuite
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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34
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Quinn PJ. A lipid matrix model of membrane raft structure. Prog Lipid Res 2010; 49:390-406. [PMID: 20478335 DOI: 10.1016/j.plipres.2010.05.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 05/06/2010] [Indexed: 12/12/2022]
Abstract
Domains in cell membranes are created by lipid-lipid interactions and are referred to as membrane rafts. Reliable isolation methods have been developed which have shown that rafts from the same membranes have different proteins and can be sub-fractionated by immunoaffinity methods. Analysis of these raft subfractions shows that they are also comprised of different molecular species of lipids. The major lipid classes present are phospholipids, glycosphingolipids and cholesterol. Model studies show that mixtures of phospholipids, particularly sphingomyelin, and cholesterol form liquid-ordered phase with properties intermediate between a gel and fluid phase. This type of liquid-ordered phase dominates theories of domain formation and raft structure in biological membranes. Recently it has been shown that sphingolipids with long (22-26C) N-acyl fatty acids form quasi-crystalline bilayer structures with diacylphospholipids that have well-defined stoichiometries. A two tier heuristic model of membrane raft structure is proposed in which liquid-ordered phase created by a molecular complex between sphingolipids with hydrocarbon chains of approximately equal length and cholesterol acts as a primary staging area for selecting raft proteins. Tailoring of the lipid anchors of raft proteins takes place at this site. Assembly of lipid-anchored proteins on a scaffold of sphingolipids with asymmetric hydrocarbon chains and phospholipids arranged in a quasi-crystalline bilayer structure serves to concentrate and orient the proteins in a manner that couples them functionally within the membrane. Specificity is inherent in the quasi-crystalline lipid structure of liquid-ordered matrices formed by both types of complex into which protein lipid anchors are interpolated. An interaction between the sugar residues of the glycolipids and the raft proteins provides an additional level of specificity that distinguishes one raft from another.
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Affiliation(s)
- Peter J Quinn
- Biochemistry Department, King's College London, 150 Stamford Street, London, UK.
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35
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Scheuring S, Dufrêne YF. Atomic force microscopy: probing the spatial organization, interactions and elasticity of microbial cell envelopes at molecular resolution. Mol Microbiol 2010; 75:1327-36. [DOI: 10.1111/j.1365-2958.2010.07064.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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36
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Casuso I, Scheuring S. Automated setpoint adjustment for biological contact mode atomic force microscopy imaging. NANOTECHNOLOGY 2010; 21:035104. [PMID: 19966388 DOI: 10.1088/0957-4484/21/3/035104] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Contact mode atomic force microscopy (AFM) is the most frequently used AFM imaging mode in biology. It is about 5-10 times faster than oscillating mode imaging (in conventional AFM setups), and provides topographs of biological samples with sub-molecular resolution and at a high signal-to-noise ratio. Unfortunately, contact mode imaging is sensitive to the applied force and intrinsic force drift: inappropriate force applied by the AFM tip damages the soft biological samples. We present a methodology that automatically searches for and maintains high resolution imaging forces. We found that the vertical and lateral vibrations of the probe during scanning are valuable signals for the characterization of the actual applied force by the tip. This allows automated adjustment and correction of the setpoint force during an experiment. A system that permanently performs this methodology steered the AFM towards high resolution imaging forces and imaged purple membrane at molecular resolution and live cells at high signal-to-noise ratio for hours without an operator.
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Affiliation(s)
- Ignacio Casuso
- Institut Curie, Equipe INSERM Avenir, UMR168-CNRS, Paris, France
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