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Okolo CA. A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences. Biochem Soc Trans 2022; 50:649-663. [PMID: 35257156 PMCID: PMC9162464 DOI: 10.1042/bst20210886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/27/2022]
Abstract
In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.
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Affiliation(s)
- Chidinma Adanna Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
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2
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Szeremeta WK, Harniman RL, Bermingham CR, Antognozzi M. Towards a Fully Automated Scanning Probe Microscope for Biomedical Applications. SENSORS 2021; 21:s21093027. [PMID: 33925843 PMCID: PMC8123492 DOI: 10.3390/s21093027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 01/27/2023]
Abstract
The increase in capabilities of Scanning Probe Microscopy (SPM) has resulted in a parallel increase in complexity that limits the use of this technique outside of specialised research laboratories. SPM automation could substantially expand its application domain, improve reproducibility and increase throughput. Here, we present a bottom-up design in which the combination of positioning stages, orientation, and detection of the probe produces an SPM design compatible with full automation. The resulting probe microscope achieves sub-femtonewton force sensitivity whilst preserving low mechanical drift (2.0±0.2 nm/min in-plane and 1.0±0.1 nm/min vertically). The additional integration of total internal reflection microscopy, and the straightforward operations in liquid, make this instrument configuration particularly attractive to future biomedical applications.
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Affiliation(s)
- Witold K. Szeremeta
- School of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK; (W.K.S.); (C.R.B.)
| | - Robert L. Harniman
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK;
| | - Charlotte R. Bermingham
- School of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK; (W.K.S.); (C.R.B.)
| | - Massimo Antognozzi
- School of Physics, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK; (W.K.S.); (C.R.B.)
- Correspondence: ; Tel.: +44-117-928-8749
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Hazime KS, Zhou Z, Joachimiak E, Bulgakova NA, Wloga D, Malicki JJ. STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena. Sci Rep 2021; 11:7899. [PMID: 33846423 PMCID: PMC8041816 DOI: 10.1038/s41598-021-86909-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
The base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.
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Affiliation(s)
- Khodor S Hazime
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Zhu Zhou
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Natalia A Bulgakova
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland.
| | - Jarema J Malicki
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Kulkarni T, Tam A, Mukhopadhyay D, Bhattacharya S. AFM study: Cell cycle and probe geometry influences nanomechanical characterization of Panc1 cells. Biochim Biophys Acta Gen Subj 2019; 1863:802-812. [PMID: 30763604 DOI: 10.1016/j.bbagen.2019.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/18/2022]
Abstract
Atomic force microscope (AFM) is emerging as an immensely promising tool to study the cellular morphology with a nanometer scale resolution and to analyze nanomechanical properties (NPs) at various physiological conditions. Advancement of AFM technology enables studying living cells and differentiating cancer cell from normal cells based on topography and NPs. Though the trend overlaps from different literature; numerical values of nanomechanical readouts depict variations over a wide range. These anomalies are associated with the experimental setup under study. In this manuscript, we have identified heterogeneity in cell culture system in addition to the selection of AFM probe with specific tip geometry as the major contributors to the above mentioned anomalies. To test our hypothesis, we have used Panc1 cells, which is a pancreatic ductal adenocarcinoma cell type. Our results suggest that the cellular morphology, membrane roughness and NPs calculated from AFM study are distinctly influenced by cell cycle. Furthermore, we found that the NPs readout is also significantly associated with AFM tip geometries. The cells were found to be softer in their early resting phase when indented with pyramidal probe and became increasingly stiffer as they progressed through the cell cycles. On the contrary, when indented with the spherical probe, cells in G0/G1 phase were observed to be the stiffest. Such an exhaustive study of the role of cell cycle in influencing the NPs in Panc1 cell line along with the impact of tip geometry on NPs is the first of its kind, to the best of our knowledge.
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Affiliation(s)
- Tanmay Kulkarni
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Alex Tam
- Electrical Engineering, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Pathology and Biomedical Engineering, Mayo Clinic, Jacksonville, FL, USA
| | - Santanu Bhattacharya
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Pathology and Biomedical Engineering, Mayo Clinic, Jacksonville, FL, USA.
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5
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Mapping the distribution of specific antibody interaction forces on individual red blood cells. Sci Rep 2017; 7:41956. [PMID: 28157207 PMCID: PMC5291206 DOI: 10.1038/srep41956] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Current blood typing methods rely on the agglutination of red blood cells (RBCs) to macroscopically indicate a positive result. An indirect agglutination mechanism is required when blood typing with IgG forms of antibodies. To date, the interaction forces between anti-IgG and IgG antibodies have been poorly quantified, and blood group related antigens have never been quantified with the atomic force microscope (AFM). Instead, the total intensity resulting from fluorescent-tagged antibodies adsorbed on RBC has been measured to calculate an average antigen density on a series of RBCs. In this study we mapped specific antibody interaction forces on the RBC surface. AFM cantilever tips functionalized with anti-IgG were used to probe RBCs incubated with specific IgG antibodies. This work provides unique insight into antibody-antigen interactions in their native cell-bound location, and crucially, on a per-cell basis rather than an ensemble average set of properties. Force profiles obtained from the AFM directly provide not only the anti-IgG – IgG antibody interaction force, but also the spatial distribution and density of antigens over a single cell. This new understanding might be translated into the development of very selective and quantitative interactions that underpin the action of drugs in the treatment of frontier illnesses.
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Godon C, Teulon JM, Odorico M, Basset C, Meillan M, Vellutini L, Chen SWW, Pellequer JL. Conditions to minimize soft single biomolecule deformation when imaging with atomic force microscopy. J Struct Biol 2016; 197:322-329. [PMID: 28017791 DOI: 10.1016/j.jsb.2016.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 12/06/2016] [Accepted: 12/21/2016] [Indexed: 11/24/2022]
Abstract
A recurrent interrogation when imaging soft biomolecules using atomic force microscopy (AFM) is the putative deformation of molecules leading to a bias in recording true topographical surfaces. Deformation of biomolecules comes from three sources: sample instability, adsorption to the imaging substrate, and crushing under tip pressure. To disentangle these causes, we measured the maximum height of a well-known biomolecule, the tobacco mosaic virus (TMV), under eight different experimental conditions positing that the maximum height value is a specific indicator of sample deformations. Six basic AFM experimental factors were tested: imaging in air (AIR) versus in liquid (LIQ), imaging with flat minerals (MICA) versus flat organic surfaces (self-assembled monolayers, SAM), and imaging forces with oscillating tapping mode (TAP) versus PeakForce tapping (PFT). The results show that the most critical parameter in accurately measuring the height of TMV in air is the substrate. In a liquid environment, regardless of the substrate, the most critical parameter is the imaging mode. Most importantly, the expected TMV height values were obtained with both imaging with the PeakForce tapping mode either in liquid or in air at the condition of using self-assembled monolayers as substrate. This study unambiguously explains previous poor results of imaging biomolecules on mica in air and suggests alternative methodologies for depositing soft biomolecules on well organized self-assembled monolayers.
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Affiliation(s)
| | - Jean-Marie Teulon
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France
| | - Michael Odorico
- ICSM-UMR5257 CEA/CNRS/UM2/ENSCM, F-30207 Bagnols sur Cèze, France
| | | | - Matthieu Meillan
- Univ. Bordeaux, ISM, UMR 5255, F-33400 Talence, France; CNRS, ISM, UMR 5255, F-33400 Talence, France
| | - Luc Vellutini
- Univ. Bordeaux, ISM, UMR 5255, F-33400 Talence, France; CNRS, ISM, UMR 5255, F-33400 Talence, France
| | | | - Jean-Luc Pellequer
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France.
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7
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Qin L, Zhang J, Sun J, Czajkowsky DM, Shao Z. Development of a low-noise cryogenic atomic force microscope for high resolution imaging of large biological complexes. Acta Biochim Biophys Sin (Shanghai) 2016; 48:859-61. [PMID: 27521793 DOI: 10.1093/abbs/gmw074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ling Qin
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjin Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Jiading Campus , Shanghai 201800, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Schein P, Kang P, O'Dell D, Erickson D. Nanophotonic force microscopy: characterizing particle-surface interactions using near-field photonics. NANO LETTERS 2015; 15:1414-20. [PMID: 25625877 PMCID: PMC4666516 DOI: 10.1021/nl504840b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Direct measurements of particle-surface interactions are important for characterizing the stability and behavior of colloidal and nanoparticle suspensions. Current techniques are limited in their ability to measure pico-Newton scale interaction forces on submicrometer particles due to signal detection limits and thermal noise. Here we present a new technique for making measurements in this regime, which we refer to as nanophotonic force microscopy. Using a photonic crystal resonator, we generate a strongly localized region of exponentially decaying, near-field light that allows us to confine small particles close to a surface. From the statistical distribution of the light intensity scattered by the particle we are able to map out the potential well of the trap and directly quantify the repulsive force between the nanoparticle and the surface. As shown in this Letter, our technique is not limited by thermal noise, and therefore, we are able to resolve interaction forces smaller than 1 pN on dielectric particles as small as 100 nm in diameter.
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Affiliation(s)
- Perry Schein
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Pilgyu Kang
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dakota O'Dell
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, United States
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9
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Czajkowsky DM, Li L, Sun J, Hu J, Shao Z. Heteroepitaxial streptavidin nanocrystals reveal critical role of proton "fingers" and subsurface atoms in determining adsorbed protein orientation. ACS NANO 2012; 6:190-198. [PMID: 22148246 DOI: 10.1021/nn203356p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Characterization of noncovalent interactions between nanometer-sized structures, such as proteins, and solid surfaces is a subject of intense interest of late owing to the rapid development of numerous solid materials for medical and technological applications. Yet the rational design of these surfaces to promote the adsorption of specific nanoscale complexes is hindered by a lack of an understanding of the noncovalent interactions between nanostructures and solid surfaces. Here we take advantage of the unexpected observation of two-dimensional nanocrystals of streptavidin on muscovite mica to provide details of the streptavidin-mica interface. Analysis of atomic force microscopic images together with structural modeling identifies six positively charged residues whose terminal amine locations match the positions of the single atom-sized anionic cavities in the basal mica surface to within 1 Å. Moreover, we find that the streptavidin crystallites are oriented only along a single direction on this surface and not in either of three different directions as they must be if the protein interacted solely with the 3-fold symmetric basal surface atoms. Hence, this broken symmetry indicates that the terminal amine protons must also interact directly with the subsurface hydroxide atoms that line the bottom of these anionic cavities and generate only a single axis of symmetry. Thus, in total, these results reveal that subsurface atoms can have a significant influence on protein adsorption and orientation and identify the insertion of proton "fingers" as a means by which proteins may generally interact with solid surfaces.
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Affiliation(s)
- Daniel M Czajkowsky
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
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10
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Csaki A, Schneider T, Wirth J, Jahr N, Steinbrück A, Stranik O, Garwe F, Müller R, Fritzsche W. Molecular plasmonics: light meets molecules at the nanoscale. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2011; 369:3483-3496. [PMID: 21807723 DOI: 10.1098/rsta.2011.0145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Certain metal nanoparticles exhibit the effect of localized surface plasmon resonance when interacting with light, based on collective oscillations of their conduction electrons. The interaction of this effect with molecules is of great interest for a variety of research disciplines, both in optics and in the life sciences. This paper attempts to describe and structure this emerging field of molecular plasmonics, situated between the molecular world and plasmonic effects in metal nanostructures, and demonstrates the potential of these developments for a variety of applications.
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Affiliation(s)
- Andrea Csaki
- Nano Biophotonics Department, Institute of Photonic Technology (IPHT), PO Box 100239, 07702 Jena, Germany
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11
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12
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Combs ZA, Chang S, Clark T, Singamaneni S, Anderson KD, Tsukruk VV. Label-free Raman mapping of surface distribution of protein a and IgG biomolecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:3198-3205. [PMID: 21294559 DOI: 10.1021/la104787w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have demonstrated a nanoengineered substrate composed of micropatterned silver nanoparticles to be used for the label-free mapping of adsorbed biomolecules. We utilized surface-enhanced Raman scattering (SERS) phenomenon to monitor the known bioanalytes, protein A and human immunoglobulin G (IgG). The SERS substrate was composed of a poly(alylamine hydrochloride) (PAH)/poly(styrenesulfonate) (PSS) layer-by-layer (LbL) nanocoating micropatterned with silver nanoparticles confined to microscopic stripes. Selective adsorption of biomacromolecules is facilitated by the amine-terminated LbL nanocoating, which prevents the surface adsorption of positively charged protein A across the surface except on the patterned regions containing negatively charged silver nanoparticles. Furthermore, adsorption of IgG on predetermined regions is facilitated by the selective binding of the Fc region of IgG to protein A. This label-free SERS approach provides accurate, selective, and fast detection of protein A and IgG solutions with a nanomolar concentration, down to below 1 nM for IgG in solution. This method could also be utilized for the facile detection of proteins in field conditions as well as in clinical, forensic, industrial, and environmental laboratories.
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Affiliation(s)
- Zachary A Combs
- School of Materials Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia, United States
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Baykara MZ, Schwendemann TC, Altman EI, Schwarz UD. Three-dimensional atomic force microscopy - taking surface imaging to the next level. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:2838-2853. [PMID: 20379997 DOI: 10.1002/adma.200903909] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Materials properties are ultimately determined by the nature of the interactions between the atoms that form the material. On surfaces, the site-specific spatial distribution of force and energy fields governs the phenomena encountered. This article reviews recent progress in the development of a measurement mode called three-dimensional atomic force microscopy (3D-AFM) that allows the dense, three-dimensional mapping of these surface fields with atomic resolution. Based on noncontact atomic force microscopy, 3D-AFM is able to provide more detailed information on surface properties than ever before, thanks to the simultaneous multi-channel acquisition of complementary spatial data such as local energy dissipation and tunneling currents. By illustrating the results of experiments performed on graphite and pentacene, we explain how 3D-AFM data acquisition works, what challenges have to be addressed in its realization, and what type of data can be extracted from the experiments. Finally, a multitude of potential applications are discussed, with special emphasis on chemical imaging, heterogeneous catalysis, and nanotribology.
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Affiliation(s)
- Mehmet Z Baykara
- Department of Mechanical Engineering, Center for Research on Interface Structures and Phenomena, Yale University, New Haven, CT 06520-8284, USA
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14
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Czajkowsky DM, Shao Z. The human IgM pentamer is a mushroom-shaped molecule with a flexural bias. Proc Natl Acad Sci U S A 2009; 106:14960-5. [PMID: 19706439 PMCID: PMC2736442 DOI: 10.1073/pnas.0903805106] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Indexed: 01/08/2023] Open
Abstract
The textbook planar model of pentameric IgM, a potent activator of complement C1q, is based upon the crystallographic structure of IgG. Although widely accepted, key predictions of this model have not yet been directly confirmed, which is particularly important since IgG lacks a major Ig fold domain in its Fc region that is present in IgM. Here, we construct a homology-based structural model of the IgM pentamer using the recently obtained crystallographic structure of IgE Fc, which has this additional Ig domain, under the constraint that all of the cysteine residues known to form disulfide bridges both within each monomer and between monomers are bonded together. In contrast to the planar model, this model predicts a non-planar, mushroom-shaped complex, with the central portion formed by the C-terminal domains protruding out of the plane formed by the Fab domains. This unexpected conformation of IgM is, however, directly confirmed by cryo-atomic force microscopy of individual human IgM molecules. Further analysis of this model with free energy calculations of out-of-plane Fab domain rotations reveals a pronounced asymmetry favoring flexions toward the central protrusion. This bias, together with polyvalent attachment to cell surface antigen, would ensure that the IgM pentamer is oriented on the cell membrane with its C1q binding sites fully exposed to the solution, and thus provides a mechanistic explanation for the first steps of C1q activation by IgM.
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Affiliation(s)
- Daniel M. Czajkowsky
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, P.O. Box 800736, Charlottesville, VA 22908; and
| | - Zhifeng Shao
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, P.O. Box 800736, Charlottesville, VA 22908; and
- Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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Spyratou E, Mourelatou EA, Makropoulou M, Demetzos C. Atomic force microscopy: a tool to study the structure, dynamics and stability of liposomal drug delivery systems. Expert Opin Drug Deliv 2009; 6:305-17. [PMID: 19327046 DOI: 10.1517/17425240902828312] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Much work has been done during the past few decades to develop effective drug delivery systems (DDS), many of which are based on nanotechnology science. Liposomes are the most attractive lipid vesicles for drug delivery. The multifunctional properties of liposomes have a key role in modifying the bioavailability profile of a therapeutic agent. Different analytical techniques can be used to describe liposomes, not least applied scanning probe microscopy (SPM) techniques. Atomic force microscopy (AFM) seems to be one of the most effectively applied SPM techniques. This review article outlines the applications of AFM in evaluating the physical characteristics and stability of liposomal DDSs. Other well-known microscopy techniques used in evaluating liposome physical characteristics are also mentioned, and the contribution of AFM to evaluating liposomal stability is discussed. Among the advantages of AFM in examining the physicochemical properties of liposomal DDSs is its ability to provide morphological and metrology information on liposome properties. AFM thus appears to be a promising tool in technological characterization of liposomal DDSs.
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Affiliation(s)
- Ellas Spyratou
- National Technical University of Athens, School of Applied Mathematical and Physical Sciences, Zografou Campus, Athens, 15780, Greece
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16
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Wu J, Reading M, Craig DQM. Application of calorimetry, sub-ambient atomic force microscopy and dynamic mechanical analysis to the study of frozen aqueous trehalose solutions. Pharm Res 2008; 25:1396-404. [PMID: 18256792 DOI: 10.1007/s11095-007-9530-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
PURPOSE Disaccharides such as trehalose are widely used as cryo-protectants to maintain the activity of proteinaceous drugs during freezing. One unresolved issue is the double transition that is observed very commonly in DSC experiments on disaccharide solutions in the frozen state; the assignment of these transitions remains disputed. Here we use calorimetry and two new techniques to shed light on the true nature of these transitions. METHODS Modulated Temperature DSC (MTDSC), cryo atomic force microscopy (AFM) and a novel DMA technique were used to study these transitions. RESULTS MTDSC identified the two transitions Tr1 and Tr2 at -35.4 and -27.9 degrees C respectively in the reversing heat flow signal, an exotherm and endotherm were observed in the non-reversing signal at circa -32 and -29 degrees C respectively. It is shown for the first time that AFM images can be obtained of a softening and melting sample without damaging it. A force modulation imaging technique showed a softening at Tr1 and a loss of ice crystals at Tr2. These observations were supported by the DMA results. CONCLUSIONS The results indicate Tr1 is associated with a glass transition while Tr2 is associated with the onset of loss of crystallinity.
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Affiliation(s)
- Jiejun Wu
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
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17
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Past, present and future of atomic force microscopy in life sciences and medicine. J Mol Recognit 2008; 20:418-31. [PMID: 18080995 DOI: 10.1002/jmr.857] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To introduce this special issue of the Journal of Molecular Recognition dedicated to the applications of atomic force microscopy (AFM) in life sciences, this paper presents a short summary of the history of AFM in biology. Based on contributions from the first international conference of AFM in biological sciences and medicine (AFM BioMed Barcelona, 19-21 April 2007), we present and discuss recent progress made using AFM for studying cells and cellular interactions, probing single molecules, imaging biosurfaces at high resolution and investigating model membranes and their interactions. Future prospects in these different fields are also highlighted.
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Girasole M, Pompeo G, Cricenti A, Congiu-Castellano A, Andreola F, Serafino A, Frazer BH, Boumis G, Amiconi G. Roughness of the plasma membrane as an independent morphological parameter to study RBCs: a quantitative atomic force microscopy investigation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1268-76. [PMID: 17320813 DOI: 10.1016/j.bbamem.2007.01.014] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/08/2007] [Accepted: 01/08/2007] [Indexed: 10/23/2022]
Abstract
A novel approach to the study of RBCs based on the collection of three-dimensional high-resolution AFM images and on the measure of the surface roughness of their plasma membrane is presented. The dependence of the roughness from several parameters of the imaging was investigated and a general rule for a trustful analysis and comparison has been suggested. The roughness of RBCs is a morphology-related parameter which has been shown to be characteristic of the single cells composing a sample, but independent of the overall geometric shape (discocyte or spherocyte) of the erythrocytes, thus providing extra-information with respect to a conventional morphology study. The use of the average roughness value as a label of a whole sample was tested on different kinds of samples. Analyzed data revealed that the quantitative roughness value does not change after treatment of RBCs with various commonly used fixation and staining methods while a drastic decrease occurs when studying cells with membrane-skeletal alteration both naturally occurring or artificially induced by chemical treatments. The present method provides a quantitative and powerful tool for a novel approach to the study of erythrocytes structure through an ultrastructural morphological analysis with the potential to give information, in a non-invasive way, on the RBCs function.
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Affiliation(s)
- M Girasole
- Istituto di Struttura della Materia-CNR, Via fosso del Cavaliere 100, 00133 Rome, Italy.
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19
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Gupta AK, Nair PR, Akin D, Ladisch MR, Broyles S, Alam MA, Bashir R. Anomalous resonance in a nanomechanical biosensor. Proc Natl Acad Sci U S A 2006; 103:13362-7. [PMID: 16938886 PMCID: PMC1569169 DOI: 10.1073/pnas.0602022103] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The decrease in resonant frequency (-Deltaomega(r)) of a classical cantilever provides a sensitive measure of the mass of entities attached on its surface. This elementary phenomenon has been the basis of a new class of bio-nanomechanical devices as sensing components of integrated microsystems that can perform rapid, sensitive, and selective detection of biological and biochemical entities. Based on classical analysis, there is a widespread perception that smaller sensors are more sensitive (sensitivity approximately -0.5omega(r)/m(C), where m(C) is the mass of the cantilever), and this notion has motivated scaling of biosensors to nanoscale dimensions. In this work, we show that the response of a nanomechanical biosensor is far more complex than previously anticipated. Indeed, in contrast to classical microscale sensors, the resonant frequencies of the nanosensor may actually decrease or increase after attachment of protein molecules. We demonstrate theoretically and experimentally that the direction of the frequency change arises from a size-specific modification of diffusion and attachment kinetics of biomolecules on the cantilevers. This work may have broad impact on microscale and nanoscale biosensor design, especially when predicting the characteristics of bio-nanoelectromechanical sensors functionalized with biological capture molecules.
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Affiliation(s)
- Amit K. Gupta
- *Birck Nanotechnology Center
- School of Electrical and Computer Engineering
| | - Pradeep R. Nair
- *Birck Nanotechnology Center
- School of Electrical and Computer Engineering
| | - Demir Akin
- *Birck Nanotechnology Center
- School of Electrical and Computer Engineering
- Weldon School of Biomedical Engineering, and
| | | | - Steve Broyles
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907
| | - Muhammad A. Alam
- *Birck Nanotechnology Center
- School of Electrical and Computer Engineering
| | - Rashid Bashir
- *Birck Nanotechnology Center
- School of Electrical and Computer Engineering
- Weldon School of Biomedical Engineering, and
- To whom correspondence should be addressed. E-mail:
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20
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Sheng S, Czajkowsky DM, Shao Z. Localization of linker histone in chromatosomes by cryo-atomic force microscopy. Biophys J 2006; 91:L35-7. [PMID: 16782797 PMCID: PMC1518653 DOI: 10.1529/biophysj.106.090423] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Linker histones play a fundamental role in determining higher order chromatin structure as a consequence of their association with nucelosomal DNA. Yet the locations and structural consequences of linker histone binding are still enigmatic. Here, using cryo-atomic force microscopy, we show that the linker histone H5 in native chromatin and in chromatosomes reconstituted on the 5S rDNA template is located at the dyad of the nucleosome core particle, within the "stem" structure. Direct measurement also indicates that the length of free linker DNA between chromatosomes in native chromatin is approximately 30 bp, slightly shorter than that estimated from nuclease digestion assays.
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Affiliation(s)
- Sitong Sheng
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908, USA
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21
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Thomson NH. The substructure of immunoglobulin G resolved to 25kDa using amplitude modulation AFM in air. Ultramicroscopy 2005; 105:103-10. [PMID: 16051439 DOI: 10.1016/j.ultramic.2005.06.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Revised: 03/21/2005] [Indexed: 11/18/2022]
Abstract
Amplitude modulation (or tapping-mode) atomic force microscopy (AM AFM or TM AFM) in air can reveal sub-molecular details of isolated multi-subunit proteins, such as immunoglobulin G (IgG) antibodies, on atomically flat support surfaces such as mica [A. San Paulo, R. Garcia, Biophys. J. 78(3) (2000) 1599]. This is achieved by controlling the microscope imaging parameters (e.g. cantilever drive frequency and set-point amplitude) to keep the AFM tip predominantly in the attractive force regime. Under these conditions, the 50 kDa F(c) and F(ab) subunits can be resolved when the molecule has the appropriate orientation on the surface. The presence of a water layer on hydrophilic mica is an important factor affecting imaging contrast, a consequence of capillary neck formation between tip and surface [L. Zitzler, S. Herminghaus, F. Mugele, Phys. Rev. B 66(15) (2002) 155436]. Desiccation of samples to remove surface bound water layers can yield reproducible imaging of the IgG substructure [N.H. Thomson, J. Microsc. (Oxford) 217(3) (2004) 193]. This approach has also given higher resolution than previously achieved, down to about 25 kDa, and these data are detailed here. These subdomains are formed as two immunoglobulin folds from the light and heavy peptide chains of the IgG crossover. This result has been validated by comparing the AFM images with X-ray crystallography data from the protein data bank. These data show that the AFM can obtain 25 kDa resolution on isolated protein molecules with commercially available silicon tips, but, as expected for a local probe technique, resolution is highly dependent on the macromolecular orientation on the support surface.
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Affiliation(s)
- Neil H Thomson
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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22
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Carbonaro A, Sohn LL. A resistive-pulse sensor chip for multianalyte immunoassays. LAB ON A CHIP 2005; 5:1155-60. [PMID: 16175273 DOI: 10.1039/b504827c] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
MultiAnalyte immunoassays are often required to diagnose a pathologic condition. Here, we show how resistive-pulse sensing and multiple artificial pores can be integrated together on a single chip to detect different antigens rapidly and simultaneously. We use multiple pores on a single chip to detect the size change of latex colloids upon specific antigen-antibody binding on the colloid surface. As a proof-of-principle, we demonstrate our ability to detect simultaneously human G-CSF and GM-CSF antigens on a single chip. Our novel technique is a scalable technology that can lead to the sensing of at least N2 antigens simultaneously with an N N array of pores on a single chip.
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Affiliation(s)
- A Carbonaro
- Department of Mechanical Engineering, University of California, Berkeley, CA 94720, USA
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23
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Thomson NH. Imaging the substructure of antibodies with tapping-mode AFM in air: the importance of a water layer on mica. J Microsc 2005; 217:193-9. [PMID: 15725122 DOI: 10.1111/j.1365-2818.2005.01399.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoclonal antibodies (immunoglobulin G; IgG) against the N-terminal domain of the A subunit of DNA gyrase have been imaged using tapping-mode atomic force microscopy under ambient conditions on hydrophilic mica surfaces. The familiar tri-nodal submolecular resolution of IgG (i.e. 50-kDa resolution) has been achieved when operating the microscope with the tip predominantly in the attractive force regime. Under common laboratory conditions of about 40% relative humidity, the resolution of this substructure was not achieved owing to motion of the antibodies on the surface and/or image distortion from tip-sample instabilities. Reproducible imaging of the tri-nodal antibody substructure was achieved by desiccating the samples for extended periods of time (1 week or more) before imaging. This effect is attributed to the presence of a humidity-dependent thin water layer (a few molecules or nanometres thick), which has been observed previously using the surface force apparatus and scanning polarization force microscopy. Desiccation of the mica surfaces allowed enough water to be removed from the mica surface to prevent this effect. Degradation in the image quality over the imaging period of an hour or two was observed, owing to re-adsorption of water under the ambient laboratory conditions.
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Affiliation(s)
- N H Thomson
- Department of Physics and Astronomy and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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24
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Bozec L, Horton M. Topography and mechanical properties of single molecules of type I collagen using atomic force microscopy. Biophys J 2005; 88:4223-31. [PMID: 15778444 PMCID: PMC1305652 DOI: 10.1529/biophysj.104.055228] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the mechanical behavior of tendon and bone has been studied for decades, there is still relatively little understanding of the molecular basis for their specific properties. Thus, despite consisting structurally of the same type I collagen, bones and tendons have evolved to fulfill quite different functions in living organisms. In an attempt to understand the links between the mechanical properties of these collageneous structures at the macro- and nanoscale, we studied trimeric type I tropocollagen molecules by atomic force microscopy, both topologically and by force spectroscopy. High-resolution imaging demonstrated a mean (+/- SD) contour length of (287 +/- 35) nm and height of (0.21 +/- 0.03) nm. Submolecular features, namely the coil-pitch of the molecule, were also observed, appearing as a repeat pattern along the length of the molecule, with a length of approximately 8 nm that is comparable to the theoretical value. Using force spectroscopy, we established the stretching pattern of the molecule, where both the mechanical response of the molecule and pull-off peak are convoluted in a single feature. By interpreting this response with a wormlike chain model, we extracted the value of the effective contour length of the molecule at (202 +/- 5) nm. This value was smaller than that given by direct measurement, suggesting that the entire molecule was not being stretched during the force measurements; this is likely to be related to the absence of covalent binding between probe, sample, and substrate in our experimental procedure.
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Affiliation(s)
- Laurent Bozec
- Bone and Mineral Centre, Department of Medicine, University College London, UK. l.bozec@ucl..ac.uk
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25
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O'Hagan BMG, Doyle P, Allen JM, Sutton K, McKerr G. The effects of atomic force microscopy upon nominated living cells. Ultramicroscopy 2004; 102:1-5. [PMID: 15556694 DOI: 10.1016/j.ultramic.2004.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Revised: 06/21/2004] [Accepted: 06/28/2004] [Indexed: 11/20/2022]
Abstract
This work describes a system for precise re-location of cells within a monolayer after atomic force imaging. As we know little about probe interaction with soft biological surfaces any corroborative evidence is of great importance. For example, it is of paramount importance in living cell force microscopy that interrogated cells can be re-located and imaged by other corroborative technologies. Methodologies expressed here have shown that non-invasive force parameters can be established for specific cell types. Additionally, we show that the same sample can be transferred reliably to an SEM. Results here indicate that further work with live cells should initially establish appropriate prevailing force parameters and that cell damage should be checked for before and after an imaging experiment.
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26
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Czajkowsky DM, Hotze EM, Shao Z, Tweten RK. Vertical collapse of a cytolysin prepore moves its transmembrane beta-hairpins to the membrane. EMBO J 2004; 23:3206-15. [PMID: 15297878 PMCID: PMC514522 DOI: 10.1038/sj.emboj.7600350] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 07/08/2004] [Indexed: 11/08/2022] Open
Abstract
Perfringolysin O (PFO) is a prototype of the large family of pore-forming cholesterol-dependent cytolysins (CDCs). A central enigma of the cytolytic mechanism of the CDCs is that their membrane-spanning beta-hairpins (the transmembrane amphipathic beta-hairpins (TMHs)) appear to be approximately 40 A too far above the membrane surface to cross the bilayer and form the pore. We now present evidence, using atomic force microscopy (AFM), of a significant difference in the height by which the prepore and pore protrude from the membrane surface: 113+/-5 A for the prepore but only 73+/-5 A for the pore. Time-lapse AFM micrographs show this change in height in real time. Moreover, the monomers in both complexes exhibit nearly identical surface features and these results in combination with those of spectrofluorimetric analyses indicate that the monomers remain in a perpendicular orientation to the bilayer plane during this transition. Therefore, the PFO undergoes a vertical collapse that brings its TMHs to the membrane surface so that they can extend across the bilayer to form the beta-barrel pore.
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Affiliation(s)
- Daniel M Czajkowsky
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA, USA
| | - Eileen M Hotze
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Zhifeng Shao
- Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA, USA
| | - Rodney K Tweten
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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27
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Kienberger F, Mueller H, Pastushenko V, Hinterdorfer P. Following single antibody binding to purple membranes in real time. EMBO Rep 2004; 5:579-83. [PMID: 15143343 PMCID: PMC1299069 DOI: 10.1038/sj.embor.7400149] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2003] [Revised: 03/17/2004] [Accepted: 03/17/2004] [Indexed: 11/08/2022] Open
Abstract
Antibody binding to surface antigens in membranes is the primary event in the specific immune defence of vertebrates. Here we used force microscopy to study the dynamics of antibody recognition of mutant purple membranes from Halobacterium salinarum containing a genetically appended anti-Sendai recognition epitope. Ligation of individual anti-Sendai antibodies to their antigenic epitopes was observed over time. Their increase in number within a small selected area revealed an apparent kinetic on-rate. The membrane-bound antibodies showed many different conformations that ranged from globular to V- and Y-like shapes. The maximum distance of two Fab fragments of the same antibody was observed to be approximately 18 nm, indicating an overall strong intrinsic flexibility of the antibody hinge region. Fab fragments of bound anti-Sendai antibodies were allocated to antigenic sites of the purple membrane, allowing the identification and localization of individual recognition epitopes on the surface of purple membranes.
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Affiliation(s)
- Ferry Kienberger
- Institute for Biophysics, J. Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz, Austria
| | - Harald Mueller
- Department of Microbiology, University of Kassel, Heinrich Plett Strasse 40, D-34132 Kassel, Germany
| | - Vassili Pastushenko
- Institute for Biophysics, J. Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz, Austria
| | - Peter Hinterdorfer
- Institute for Biophysics, J. Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz, Austria
- Tel: +43 732 2468 9265; Fax: +43 732 2468 9280; E-mail:
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28
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29
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Sheng S, Gao Y, Khromov AS, Somlyo AV, Somlyo AP, Shao Z. Cryo-atomic force microscopy of unphosphorylated and thiophosphorylated single smooth muscle myosin molecules. J Biol Chem 2003; 278:39892-6. [PMID: 12907680 DOI: 10.1074/jbc.m306094200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The purpose of this study was to determine whether steric blockage of one head by the second head of native two-headed myosin was responsible for the inactivity of nonphosphorylated two-headed myosin compared with the high activity of single-headed myosin, as suggested on the basis of electron microscopy of two-dimensional crystals of heavy meromyosin (Wendt, T., Taylor, D., Messier, T., Trybus, K. M., and Taylor, K. A. (1999) J. Cell Biol. 147, 1385-1390; and Wendt, T., Taylor, D., Trybus, K. M., and Taylor, K. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 4361-4366). Our earlier cryo-atomic force microscopy (cryo-AFM) (Zhang, Y., Shao, Z., Somlyo, A. P., and Somlyo, A. V. (1997) Biophys. J. 72, 1308-1318) indicates that thiophosphorylation of the regulatory light chain increases the separation of the two heads of a single myosin molecule, but the thermodynamic probability of steric hindrance by strong binding between the two heads was not determined. We now report this probability determined by cryo-AFM of single whole myosin molecules shown to have normal low ATPase activity (0.007 s-1). We found that the thermodynamic probability of the relative head positions of nonphosphorylated myosin was approximately equal between separated heads as compared with closely apposed heads (energy difference of 0.24 kT (where k is a Boltzman constant and T is the absolute temperature)), and thiophosphorylation increased the number of molecules having separated heads (energy advantage of -1.2 kT (where k is a Boltzman constant and I is the absolute temperature)). Our results do not support the suggestion that strong binding of one head to the other stabilizes the blocked conformation against thermal fluctuations resulting in steric blockage that can account for the low activity of nonphosphorylated two-headed myosin.
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Affiliation(s)
- Sitong Sheng
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908-0736, USA
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30
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Abstract
The advent of single-molecule biology has allowed unprecedented insight into the dynamic behavior of biological macromolecules and their complexes. Unexpected properties, masked by the asynchronous behavior of myriads of molecules in bulk experiments, can be revealed; equally importantly, individual members of a molecular population often exhibit distinct features in their properties. Finally, the single-molecule approaches allow us to study the behavior of biological macromolecules under applied tension or torsion: understanding the mechanical properties of these molecules helps us understand how they function in the cell. The aim of this chapter is to summarize and critically evaluate the properties of single DNA molecules and of single chromatin fibers. The use of the high-resolution imaging capabilities of the atomic force microscopy has been covered, together with manipulating techniques such as optical fibers, optical and magnetic tweezers, and flow fields. We have learned a lot about DNA and how it responds to applied forces. It is also clear that even though the study of the properties of individual chromatin fibers has just begun, the single-molecule approaches are expected to provide a wealth of information concerning the mechanical properties of chromatin and the way its structure changes during processes like transcription and replication.
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Affiliation(s)
- Jordanka Zlatanova
- Department of Chemistry and Chemical Engineering, Polytechnic University, Brooklyn, NY 11201, USA.
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31
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Rossell JP, Allen S, Davies MC, Roberts CJ, Tendler SJB, Williams PM. Electrostatic interactions observed when imaging proteins with the atomic force microscope. Ultramicroscopy 2003; 96:37-46. [PMID: 12623170 DOI: 10.1016/s0304-3991(02)00379-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The atomic force microscope (AFM) is now an established and valuable tool for the study of biological macromolecules in aqueous environments. In this paper we form a patterned boundary via the microcontact printing of individually isolated proteins, covalently attached to a solid support. We use this boundary to investigate electrostatic interactions that can occur between an AFM tip and a protein surface during imaging in solution. The observed height variations of the protein film are found to be a combination of not only structural considerations and thickness of the protein film, but also the repulsive contribution from electrostatic interactions between the AFM tip and the sample. These variations in measured heights of the protein surface can be described by Derjaguin, Landau, Verway, Overbeek (DLVO) theory. Our experimental results show that height measurements can be manipulated either negatively or positively by adjusting the pH and concentration of the electrolyte buffer that is utilised.
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Affiliation(s)
- J P Rossell
- Laboratory of Biophysics and Surface Analysis, School of Pharmaceutical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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32
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Yamamoto D, Tani K, Gotoh T, Kouyama T. Direct observations of freeze-etching processes of ice-embedded biomembranes by atomic force microscopy. Micron 2003; 34:9-18. [PMID: 12694853 DOI: 10.1016/s0968-4328(03)00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have fabricated a cryogenic atomic force microscope that is designed for structural investigation of freeze-fractured biological specimens. The apparatus is operated in liquid nitrogen gas at atmospheric pressure. Freeze-fracturing, freeze-etching and subsequent imaging are carried out in the same chamber, so that the surface topography of a fractured plane is easily visualized without ice contamination. A controlled superficial sublimation of volatile molecules allows us to obtain three-dimensional views of ultrastructures of biological membranes.
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Affiliation(s)
- Daisuke Yamamoto
- Department of Physics, Graduate School of Science, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya, Japan
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33
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Affiliation(s)
- Sitong Sheng
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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34
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35
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Mat-Arip Y, Garver K, Chen C, Sheng S, Shao Z, Guo P. Three-dimensional interaction of Phi29 pRNA dimer probed by chemical modification interference, cryo-AFM, and cross-linking. J Biol Chem 2001; 276:32575-84. [PMID: 11371551 DOI: 10.1074/jbc.m100045200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Six pRNAs (p for packaging) of bacterial virus phi29 form a hexamer complex that is an essential component of the viral DNA translocating motor. Dimers, the building block of pRNA hexamer, assemble in the order of dimer --> tetramer --> hexamer. The two-dimensional structure of the pRNA monomer has been investigated extensively; however, the three-dimensional structure concerning the distance constraints of the three stems and loops are unknown. In this report, we probed the three-dimensional structure of pRNA monomer and dimer by photo affinity cross-linking with azidophenacyl. Bases 75-81 of the left stem were found to be oriented toward the head loop and proximate to bases 26-31 in a parallel orientation. Chemical modification interference indicates the involvement of bases 45-71 and 82-91 in dimer formation. Dimer was formed via hand-in-hand contact, a novel RNA dimerization that in some aspects is similar to the kissing loops of the human immunodeficiency virus. The covalently linked dimers were found to be biologically active. Both the native dimer and the covalently linked dimer were found by cryo-atomic force microscopy to be similar in global conformation and size.
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Affiliation(s)
- Y Mat-Arip
- Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
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36
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Sakaue M, Taniguchi K. Imaging of the lectin-labeled cell surface of human lymphocytes by the use of atomic force microscope. J Vet Med Sci 2001; 63:223-5. [PMID: 11258467 DOI: 10.1292/jvms.63.223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The atomic force microscope (AFM) is a new useful tool to examine the surface structure of specimens with a higher resolution than the conventional scanning electron microscope. In the present study, we used the AFM to observe the surface of paraformaldehyde-fixed human lymphocytes processed for histochemistry using a biotinylated lectin, wheat germ agglutinin, followed by colloidal gold and silver-enhancement method. Before the treatment, no particles were attached to the cell surface. After treatment, many particles about 100 to 150 nm in diameter were visualized on it. Since we could observe the same cells on the slide glass before and after treatment, the AFM has the advantage to enable us the repeated imaging of samples treated with various kinds of histochemistries.
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Affiliation(s)
- M Sakaue
- Department of Veterinary Anatomy, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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37
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Reviakine I, Bergsma-Schutter W, Mazères-Dubut C, Govorukhina N, Brisson A. Surface topography of the p3 and p6 annexin V crystal forms determined by atomic force microscopy. J Struct Biol 2000; 131:234-9. [PMID: 11052896 DOI: 10.1006/jsbi.2000.4286] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Annexin V is a member of a family of structurally homologous proteins sharing the ability to bind to negatively charged phospholipid membranes in a Ca(2+)-dependent manner. The structure of the soluble form of annexin V has been solved by X-ray crystallography, while electron crystallography of two-dimensional (2D) crystals has been used to reveal the structure of its membrane-bound form. Two 2D crystal forms of annexin V have been reported to date, with either p6 or p3 symmetry. Atomic force microscopy has previously been used to investigate the growth and the topography of the p6 crystal form on supported phospholipid bilayers (Reviakine et al., 1998). The surface structure of the second crystal form, p3, is presented in this study, along with an improved topographic map of the p6 crystal form. The observed topography is correlated with the structure determined by X-ray crystallography.
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Affiliation(s)
- I Reviakine
- Department of Biophysical Chemistry, GBB, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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38
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Chen C, Sheng S, Shao Z, Guo P. A dimer as a building block in assembling RNA. A hexamer that gears bacterial virus phi29 DNA-translocating machinery. J Biol Chem 2000; 275:17510-6. [PMID: 10748150 DOI: 10.1074/jbc.m909662199] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Six RNA (pRNA) molecules form a hexamer, via hand-in-hand interaction, to gear bacterial virus phi29 DNA translocation machinery. Here we report the pathway and the conditions for the hexamer formation. Stable pRNA dimers and trimers were assembled in solution, isolated from native gels, and separated by sedimentation, providing a model system for the study of RNA dimers and trimers in a protein-free environment. Cryo-atomic force microscopy revealed that monomers displayed a check mark outline, dimers exhibited an elongated shape, and trimers formed a triangle. Dimerization of pRNA was promoted by a variety of cations including spermidine, whereas procapsid binding and DNA packaging required specific divalent cations, including Mg(2+), Ca(2+), and Mn(2+). Both the tandem and fused pRNA dimers with complementary loops designed to form even-numbered rings were active in DNA packaging, whereas those without complementary loops were inactive. We conclude that dimers are the building blocks of the hexamer, and the pathway of building a hexamer is: dimer --> tetramer --> hexamer. The Hill coefficient of 2.5 suggests that there are three binding sites with cooperative binding on the surface of the procapsid. The two interacting loops played a key role in recruiting the incoming dimer, whereas the procapsid served as the foundation for hexamer assembly.
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Affiliation(s)
- C Chen
- Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
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39
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San Paulo A, García R. High-resolution imaging of antibodies by tapping-mode atomic force microscopy: attractive and repulsive tip-sample interaction regimes. Biophys J 2000; 78:1599-605. [PMID: 10692344 PMCID: PMC1300757 DOI: 10.1016/s0006-3495(00)76712-9] [Citation(s) in RCA: 230] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A force microscope operated with an amplitude modulation feedback (usually known as tapping-mode atomic force microscope) has two tip-sample interaction regimes, attractive and repulsive. We have studied the performance of those regimes to imaging single antibody molecules. The attractive interaction regime allows determination of the basic morphologies of the antibodies on the support. More importantly, this regime is able to resolve the characteristic Y-shaped domain structure of antibodies and the hinge region between domains. Imaging in the repulsive interaction regime is associated with the irreversible deformation of the molecules. This causes a significant loss in resolution and contrast. Two major physical differences distinguish the repulsive interaction regime from the attractive interaction regime: the existence of tip-sample contact and the strength of the forces involved.
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Affiliation(s)
- A San Paulo
- Instituto de Microelectrónica de Madrid, Consejo Superior de Investigaciones Científicas, 28760 Tres Cantos, Madrid, Spain
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40
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Abstract
Cryoatomic force microscopy (cryo-AFM) was used to image phalloidin-stabilized actin filaments adsorbed to mica. The single filaments are clearly shown to be right-handed helical structures with a periodicity of approximately 38 nm. Even at a moderate concentration ( approximately 10 microg/ml), narrow, branched rafts of actin filaments and larger aggregates have been observed. The resolution achieved is sufficient to resolve actin monomers within the filaments. A closer examination of the images shows that the branched rafts are composed of up to three individual filaments with a highly regular lateral registration with a fixed axial shift of approximately 13 nm. The implications of these higher-order structures are discussed in terms of x-ray fiber diffraction and rheology of actin gels. The cryo-AFM images also indicate that the recently proposed model of left-handed F-actin is likely to be an artifact of preparation and/or low-resolution AFM imaging.
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Affiliation(s)
- Z Shao
- Department of Molecular Physiology and Biological Physics, Health Sciences Center, University of Virginia, Charlottesville, Virginia 22908-0011 USA
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41
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Affiliation(s)
- H G Hansma
- Department of Physics, University of California, Santa Barbara, CA 93106, USA.
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42
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Takano H, Kenseth JR, Wong SS, O'Brien JC, Porter MD. Chemical and biochemical analysis using scanning force microscopy. Chem Rev 1999; 99:2845-90. [PMID: 11749504 DOI: 10.1021/cr9801317] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H Takano
- Ames Laboratory-USDOE, Microanalytical Instrumentation Center, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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43
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Shao Z. Probing Nanometer Structures with Atomic Force Microscopy. NEWS IN PHYSIOLOGICAL SCIENCES : AN INTERNATIONAL JOURNAL OF PHYSIOLOGY PRODUCED JOINTLY BY THE INTERNATIONAL UNION OF PHYSIOLOGICAL SCIENCES AND THE AMERICAN PHYSIOLOGICAL SOCIETY 1999; 14:142-149. [PMID: 11390840 DOI: 10.1152/physiologyonline.1999.14.4.142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic force microscopy (AFM) can generate high-resolution images of the surface of biological specimens and can also probe the interactions between and within single macromolecules. Thus isolated heterogeneous biological structures can be studied in submolecular detail with AFM.
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Affiliation(s)
- Zhifeng Shao
- Department of Molecular Physiology and Biological Physics of the University of Virginia, PO Box 10011, Charlottesville, VA 22906-0011, USA
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44
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Lemkadem B, Saulnier P, Boury F, Proust J. Interfacial behavior of HDL3 spread at air/water interface. II. Structural analysis by AFM. Colloids Surf B Biointerfaces 1999. [DOI: 10.1016/s0927-7765(99)00016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Linder A, Weiland U, Apell HJ. Novel polymer substrates for SFM investigations of living cells, biological membranes, and proteins. J Struct Biol 1999; 126:16-26. [PMID: 10329485 DOI: 10.1006/jsbi.1999.4104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Extended studies were performed to prepare substrates for scanning force microscopy of biological samples with a surface roughness below 1 nm rms over an area of 500 x 500 nm2. The substrate smoothness and the lack of tip obscuring material are indispensable in order to visualize detailed structures of membrane surfaces, particularly when scanning the lamellipodia of mechanically sensitive goldfish glial cells where peripheral lamellipodia are only 20-30 nm in thickness. Appropriate substrates are poly(vinyl phenyl ketone) or furan polymers with corrugations of 0.3 and 0.15 nm rms, respectively, to which the growth-promoting protein laminin adsorbs directly with an acceptably increased roughness. Cells show normal growth behavior on these substrates and stick to the substrates in a stable fashion during several scans. Thus details of the membrane's surface may be resolved and are not obscured by the substrate texture. The uncoated furan polymer substrates are suitable for immobilization of membrane preparations such as purified membrane fragments containing bacteriorhodopsin or Na, K-ATPase and protein preparations such as antibodies.
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Affiliation(s)
- A Linder
- Department of Biology, University of Konstanz, Konstanz, D-78457, Germany
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46
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Abstract
The intrinsically high signal-to-noise ratio of atomic force microscopy (AFM) permits structural determination of individual macromolecules to, at times, subnanometer resolution directly from unprocessed images, avoiding the conditions and possible consequences of averaging over an ensemble of molecules. In this article, we will review some of the most recent achievements in imaging single macromolecules with AFM.
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Affiliation(s)
- D M Czajkowsky
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville 22908, USA
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47
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Abstract
Biological atomic force microscopy (AFM) is now established as a method for studying the structure and function of biomolecular objects at the solid-liquid interface. Major progress in this field is linked to new developments in instrumentation, a better understanding of tip-sample interactions, and improved sample preparation techniques. In this review, the most common strategies for biomolecular immobilization with respect to biological AFM applications are summarized.
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Affiliation(s)
- P Wagner
- Department of Biochemistry, Stanford University Medical Center, CA 94305-5307, USA.
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48
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Atomic Force Microscopy of a Hydrophobin Protein from the Edible MushroomAgaricus bisporus. J Colloid Interface Sci 1998. [DOI: 10.1006/jcis.1998.5405] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Takeuchi M, Miyamoto H, Sako Y, Komizu H, Kusumi A. Structure of the erythrocyte membrane skeleton as observed by atomic force microscopy. Biophys J 1998; 74:2171-83. [PMID: 9591644 PMCID: PMC1299560 DOI: 10.1016/s0006-3495(98)77926-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The structure of the membrane skeleton on the cytoplasmic surface of the erythrocyte plasma membrane was observed in dried human erythrocyte ghosts by atomic force microscopy (AFM), taking advantage of its high sensitivity to small height variations in surfaces. The majority of the membrane skeleton can be imaged, even on the extracellular surface of the membrane. Various fixation and drying methods were examined for preparation of ghost membrane samples for AFM observation, and it was found that freeze-drying (freezing by rapid immersion in a cryogen) of unfixed specimens was a fast and simple way to obtain consistently good results for observation without removing the membrane or extending the membrane skeleton. Observation of the membrane skeleton at the external surface of the cell was possible mainly because the bilayer portion of the membrane sank into the cell during the drying process. The average mesh size of the spectrin network observed at the extracellular and cytoplasmic surfaces of the plasma membrane was 4800 and 3000 nm2, respectively, which indicates that spectrin forms a three-dimensionally folded meshwork, and that 80% of spectrin can be observed at the extracellular surface of the plasma membrane.
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Affiliation(s)
- M Takeuchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
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50
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Harada A, Yamaguchi H, Kamachi M. Imaging Antibody Molecules at Room Temperature by Contact Mode Atomic Force Microscope. CHEM LETT 1997. [DOI: 10.1246/cl.1997.1141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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