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Gan C, Wang K, Tang Q, Chen Y. Comparative investigation on the sizes and scavenger receptor binding of human native and modified lipoprotein particles with atomic force microscopy. J Nanobiotechnology 2018; 16:25. [PMID: 29592798 PMCID: PMC5872389 DOI: 10.1186/s12951-018-0352-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/13/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The size and receptor-binding abilities of plasma lipoproteins are closely related with their structure/functions. Presently, the sizes of native lipoproteins have been measured by various methods including atomic force microscopy (AFM) whereas the sizes of modified lipoproteins are poorly determined and the receptor-binding ability of lipoproteins is less detected and compared at the nanoscale. METHODS Here, AFM was utilized to detect/compare the size and scavenger receptor-binding properties of three native human lipoproteins including high-density lipoprotein, low-density lipoprotein (LDL), and very low-density lipoprotein, and two modified human lipoproteins including oxidized and acetylated LDL, as well as bovine serum albumin and their antibodies as negative and positive controls, respectively. RESULTS AFM detected that the sizes of these lipoproteins are close to the commonly known values and the previously-reported AFM-detected sizes and that native and modified LDL have different height/size. AFM also revealed that the CD36-binding abilities of the five lipoproteins are different from one another and from their SR-B1-binding abilities and that the anti-CD36/SR-B1 antibodies as positive controls have strong CD36/SR-B1-binding abilities. CONCLUSIONS The data provide important information on lipoproteins for better understanding their structures/functions. Moreover, the data certify that besides size measurement AFM also can visualize receptor-lipoprotein binding at the nanoscale, as well as antigen-antibody (scavenger receptors and their antibodies) binding.
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Affiliation(s)
- Chaoye Gan
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Kun Wang
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Qisheng Tang
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Yong Chen
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China. .,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China.
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2
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Stanley GJ, Fassati A, Hoogenboom BW. Biomechanics of the transport barrier in the nuclear pore complex. Semin Cell Dev Biol 2017; 68:42-51. [DOI: 10.1016/j.semcdb.2017.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/11/2017] [Indexed: 12/14/2022]
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3
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Ao M, Gan C, Shao W, Zhou X, Chen Y. Effects of cyclodextrins on the structure of LDL and its susceptibility to copper-induced oxidation. Eur J Pharm Sci 2016; 91:183-9. [PMID: 27140842 DOI: 10.1016/j.ejps.2016.04.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/19/2022]
Abstract
Cyclodextrins (CDs) have long been widely used as drug/food carriers and were recently developed as drugs for the treatment of diseases (e.g. Niemann-Pick C1 and cancers). It is unknown whether cyclodextrins may influence the structure of low-density lipoprotein (LDL), its susceptibility to oxidation, and atherogenesis. In this study, four widely used cyclodextrins including α-CD, γ-CD, and two derivatives of β-CD (HPβCD and MβCD) were recruited. Interestingly, agarose gel electrophoresis (staining lipid and protein components of LDL with Sudan Black B and Coomassie brilliant blue, respectively but simultaneously) shows that cyclodextrins at relatively high concentrations caused disappearance of the LDL band and/or appearance of an additional protein-free lipid band, implying that cyclodextrins at relatively high concentrations can induce significant electrophoresis-detectable lipid depletion of LDL. Atomic force microscopy (AFM) detected that MβCD (as a representative of cyclodextrins) induced size decrease of LDL particles in a dose-dependent manner, further confirming the lipid depletion effects of cyclodextrins. Moreover, the data from agarose gel electrophoresis, conjugated diene formation, MDA production, and amino group blockage of copper-oxidized LDL show that cyclodextrins can impair LDL susceptibility to oxidation. It implies that cyclodextrins probably help to inhibit atherogenesis by lowering LDL oxidation.
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Affiliation(s)
- Meiying Ao
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, PR China; Department of Pharmacy, Science and Technology College, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330025, PR China; College of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Chaoye Gan
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, PR China; College of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Wenxiang Shao
- School of Basic Medical Sciences, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330025, PR China
| | - Xing Zhou
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, PR China; College of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, PR China
| | - Yong Chen
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, Nanchang, Jiangxi 330031, PR China; College of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, PR China.
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4
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Nautiyal A, Rani PS, Sharples GJ, Muniyappa K. Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain. Mol Microbiol 2016; 100:656-74. [PMID: 26817626 DOI: 10.1111/mmi.13338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The Mycobacterium tuberculosis genome possesses homologues of the ruvC and yqgF genes that encode putative Holliday junction (HJ) resolvases. However, their gene expression profiles and enzymatic properties have not been experimentally defined. Here we report that expression of ruvC and yqgF is induced in response to DNA damage. Protein-DNA interaction assays with purified M. tuberculosis RuvC (MtRuvC) and YqgF (MtRuvX) revealed that both associate preferentially with HJ DNA, albeit with differing affinities. Although both MtRuvC and MtRuvX cleaved HJ DNA in vitro, the latter displayed robust HJ resolution activity by symmetrically related, paired incisions. MtRuvX showed a higher binding affinity for the HJ structure over other branched recombination and replication intermediates. An MtRuvX(D28N) mutation, eliminating one of the highly conserved catalytic residues in this class of endonucleases, dramatically reduced its ability to cleave HJ DNA. Furthermore, a unique cysteine (C38) fulfils a crucial role in HJ cleavage, consistent with disulfide-bond mediated dimerization being essential for MtRuvX activity. In contrast, E. coli YqgF is monomeric and exhibits no branched DNA binding or cleavage activity. These results fit with a functional modification of YqgF in M. tuberculosis so that it can act as a dimeric HJ resolvase analogous to that of RuvC.
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Affiliation(s)
- Astha Nautiyal
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - P Sandhya Rani
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Gary J Sharples
- Department of Chemistry, School of Biological and Biomedical Sciences, Biophysical Sciences Institute, University of Durham, DH1 3LE, UK
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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5
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AFM volumetric methods for the characterization of proteins and nucleic acids. Methods 2013; 60:113-21. [DOI: 10.1016/j.ymeth.2013.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
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6
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Liu TH, Hsu SH, Huang YT, Lin SM, Huang TW, Chuang TH, Fan SK, Fu CC, Tseng FG, Pan RL. The proximity between C-termini of dimeric vacuolar H+-pyrophosphatase determined using atomic force microscopy and a gold nanoparticle technique. FEBS J 2009; 276:4381-94. [PMID: 19614743 DOI: 10.1111/j.1742-4658.2009.07146.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vacuolar H(+)-translocating inorganic pyrophosphatase [vacuolar H(+)-pyrophosphatase (V-PPase); EC 3.6.1.1] is a homodimeric proton translocase; it plays a pivotal role in electrogenic translocation of protons from the cytosol to the vacuolar lumen, at the expense of PP(i) hydrolysis, for the storage of ions, sugars, and other metabolites. Dimerization of V-PPase is necessary for full proton translocation function, although the structural details of V-PPase within the vacuolar membrane remain uncertain. The C-terminus presumably plays a crucial role in sustaining enzymatic and proton-translocating reactions. We used atomic force microscopy to visualize V-PPases embedded in an artificial lipid bilayer under physiological conditions. V-PPases were randomly distributed in reconstituted lipid bilayers; approximately 43.3% of the V-PPase protrusions faced the cytosol, and 56.7% faced the vacuolar lumen. The mean height and width of the cytosolic V-PPase protrusions were 2.8 +/- 0.3 nm and 26.3 +/- 4.7 nm, whereas those of the luminal protrusions were 1.2 +/- 0.1 nm and 21.7 +/- 3.6 nm, respectively. Moreover, both C-termini of dimeric subunits of V-PPase are on the same side of the membrane, and they are close to each other, as visualized with antibody and gold nanoparticles against 6xHis tags on C-terminal ends of the enzyme. The distance between the V-PPase C-terminal ends was determined to be approximately 2.2 +/- 1.4 nm. Thus, our study is the first to provide structural details of a membrane-bound V-PPase dimer, revealing its adjacent C-termini.
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Affiliation(s)
- Tseng-Huang Liu
- Department of Life Sciences and Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsin Chu, Taiwan, ROC
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7
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Wagner M, Kaehler D, Anhenn O, Betz T, Awad S, Shamaa A, Theegarten D, Linder R. Nanostructural analysis by atomic force microscopy followed by light microscopy on the same archival slide. Microsc Res Tech 2009; 72:471-81. [PMID: 19208390 DOI: 10.1002/jemt.20691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Integrated information on ultrastructural surface texture and chemistry increasingly plays a role in the biomedical sciences. Light microscopy provides access to biochemical data by the application of dyes. Ultrastructural representation of the surface structure of tissues, cells, or macromolecules can be obtained by scanning electron microscopy (SEM). However, SEM often requires gold or coal coating of biological samples, which makes a combined examination by light microscopy and SEM difficult. Conventional histochemical staining methods are not easily applicable to biological material subsequent to such treatment. Atomic force microscopy (AFM) gives access to surface textures down to ultrastructural dimensions without previous coating of the sample. A combination of AFM with conventional histochemical staining protocols for light microscopy on a single slide is therefore presented. Unstained cores were examined using AFM (tapping mode) and subsequently stained histochemically. The images obtained by AFM were compared with the results of histochemistry. AFM technology did not interfere with any of the histochemical staining protocols. Ultrastructurally analyzed regions could be identified in light microscopy and histochemical properties of ultrastructurally determined regions could be seen. AFM-generated ultrastructural information with subsequent staining gives way to novel findings in the biomedical sciences.
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Affiliation(s)
- Mathias Wagner
- Institute of General and Special Pathology, University of Saarland Medical School, Homburg Saar, Germany.
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8
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Takahashi H, Hizume K, Kumeta M, H Yoshimura S, Takeyasu K. Single-molecule anatomy by atomic force microscopy and recognition imaging. ARCHIVES OF HISTOLOGY AND CYTOLOGY 2009; 72:217-25. [PMID: 21471656 DOI: 10.1679/aohc.72.217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Atomic force microscopy (AFM) has been a useful technique to visualize cellular and molecular structures at single-molecule resolution. The combination of imaging and force modes has also allowed the characterization of physical properties of biological macromolecules in relation to their structures. Furthermore, recognition imaging, which is obtained under the TREC(TM) (Topography and RECognition) mode of AFM, can map a specific protein of interest within an AFM image. In this study, we first demonstrated structural properties of purified α Actinin-4 by conventional AFM. Since this molecule is an actin binding protein that cross-bridges actin filaments and anchors it to integrin via tailin-vinculin-α actinin adaptor-interaction, we investigated their structural properties using the recognition mode of AFM. For this purpose, we attached an anti-α Actinin-4 monoclonal antibody to the AFM cantilever and performed recognition imaging against α Actinin-4. We finally succeeded in mapping the epitopic region within the α Actinin-4 molecule. Thus, recognition imaging using an antibody coupled AFM cantilever will be useful for single-molecule anatomy of biological macromolecules and structures.
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Affiliation(s)
- Hirohide Takahashi
- Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University Graduate School of Biostudies, Japan
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9
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An historical perspective on cell mechanics. Pflugers Arch 2007; 456:3-12. [DOI: 10.1007/s00424-007-0405-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 11/12/2007] [Accepted: 11/15/2007] [Indexed: 11/26/2022]
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10
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Meller K, Theiss C. Atomic force microscopy and confocal laser scanning microscopy on the cytoskeleton of permeabilised and embedded cells. Ultramicroscopy 2006; 106:320-5. [PMID: 16360280 DOI: 10.1016/j.ultramic.2005.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 10/07/2005] [Accepted: 10/19/2005] [Indexed: 11/23/2022]
Abstract
We describe a technical method of cell permeabilisation and embedding to study the organisation and distribution of intracellular proteins with aid of atomic force microscopy and confocal laser scanning microscopy in identical areas. While confocal laser scanning microscopy is useful for the identification of certain proteins subsequent labelling with markers or antibodies, atomic force microscopy allows the observation of macromolecular structures in fixed and living cells. To demonstrate the field of application of this preparatory technique, cells were permeabilised, fixed, and the actin cytoskeleton was stained with phalloidin-rhodamine. Confocal laser scanning microscopy was used to show the organisation of these microfilaments, e.g. geodesic dome structures. Thereafter, cells were embedded in Durcupan water-soluble resin, followed by UV-polymerisation of resin at 4 degrees C. This procedure allowed intracellular visualisation of the cell nucleus or cytoskeletal elements by atomic force microscopy, for instance to analyse the globular organisation of actin filaments. Therefore, this method offers a great potential to combine both microscopy techniques in order to understand and interpret intracellular protein relations, for example, the biochemical and morphological interaction of the cytoskeleton.
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Affiliation(s)
- Karl Meller
- Abteilung für Cytologie, Ruhr-University Bochum, Bochum, Germany
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11
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Yoshimura SH, Maruyama H, Ishikawa F, Ohki R, Takeyasu K. Molecular mechanisms of DNA end-loop formation by TRF2. Genes Cells 2004; 9:205-18. [PMID: 15005708 DOI: 10.1111/j.1356-9597.2004.00719.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In the telomere region of human chromosomes, the (TTAGGG)n sequence stretches over several kilobases and forms a distinct higher-order structure with various proteins. Telomere repeat binding factors (TRFs) bind specifically to this sequence and play critical roles in the maintenance of telomere structure and function. Here, we prepared a series of linear DNA carrying a stretch of telomeric sequence ((TTAGGG)n, approximately 1.8 (kb) with different end-structures and observed their higher-order complexes with TRFs by atomic force microscopy. TRF2 molecules exclusively bound to the telomeric DNA region at several different places simultaneously mainly as a dimer, and often mediated DNA loop formation by forming a tetramer at the root. These multiple-binding, multimerization and DNA loop formation by TRF2 were observed regardless of the DNA-end structure (blunt, 3'-overhanging, telomeric, non-telomeric). However, when the DNA end carried the telomeric-3'-overhanging region, the loop was frequently formed at the end of the DNA. Namely, the TRF2-mediated DNA loop formation is independent of the end-structure and the 3'-overhanging TTAGGG sequence is responsible for the stabilization of the loop. TRF1 also bound to the telomeric DNA as a dimer, but did not mediate DNA loop formation by itself. These results provide a new insight into the molecular mechanism of DNA end-loop formation by TRFs.
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Affiliation(s)
- Shige H Yoshimura
- Department of Responses to Environmental Signals and Stresses, Graduate School of Biostudies, Kyoto University, Kitashirawkawa-oiwake-cho Sakyo-ku Kyoto, 606-8502, Japan.
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12
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Gruenbaum Y, Goldman RD, Meyuhas R, Mills E, Margalit A, Fridkin A, Dayani Y, Prokocimer M, Enosh A. The nuclear lamina and its functions in the nucleus. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 226:1-62. [PMID: 12921235 DOI: 10.1016/s0074-7696(03)01001-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The nuclear lamina is a structure near the inner nuclear membrane and the peripheral chromatin. It is composed of lamins, which are also present in the nuclear interior, and lamin-associated proteins. The increasing number of proteins that interact with lamins and the compound interactions between these proteins and chromatin-associated proteins make the nuclear lamina a highly complex but also a very exciting structure. The nuclear lamina is an essential component of metazoan cells. It is involved in most nuclear activities including DNA replication, RNA transcription, nuclear and chromatin organization, cell cycle regulation, cell development and differentiation, nuclear migration, and apoptosis. Specific mutations in nuclear lamina genes cause a wide range of heritable human diseases. These diseases include Emery-Dreifuss muscular dystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy (DCM) with conduction system disease, familial partial lipodystrophy (FPLD), autosomal recessive axonal neuropathy (Charcot-Marie-Tooth disorder type 2, CMT2), mandibuloacral dysplasia (MAD), Hutchison Gilford Progeria syndrome (HGS), Greenberg Skeletal Dysplasia, and Pelger-Huet anomaly (PHA). Genetic analyses in Caenorhabditis elegans, Drosophila, and mice show new insights into the functions of the nuclear lamina, and recent structural analyses have begun to unravel the molecular structure and assembly of lamins and their associated proteins.
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Affiliation(s)
- Yosef Gruenbaum
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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13
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Moore-Nichols D, Arnott A, Dunn RC. Regulation of nuclear pore complex conformation by IP(3) receptor activation. Biophys J 2002; 83:1421-8. [PMID: 12202368 PMCID: PMC1302241 DOI: 10.1016/s0006-3495(02)73913-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In recent years, both the molecular architecture and functional dynamics of nuclear pore complexes (NPCs) have been revealed with increasing detail. These large, supramolecular assemblages of proteins form channels that span the nuclear envelope of cells, acting as crucial regulators of nuclear import and export. From the cytoplasmic face of the nuclear envelope, nuclear pore complexes exhibit an eightfold symmetric ring structure encompassing a central lumen. The lumen often appears occupied by an additional structure alternatively referred to as the central granule, nuclear transport complex, or nuclear plug. Previous studies have suggested that the central granule may play a role in mediating calcium-dependent regulation of diffusion across the nuclear envelope for intermediate sized molecules (10-40 kDa). Using atomic force microscopy to measure the surface topography of chemically fixed Xenopus laevis oocyte nuclear envelopes, we present measurements of the relative position of the central granule within the NPC lumen under a variety of conditions known to modify nuclear Ca(2+) stores. These measurements reveal a large, approximately 9-nm displacement of the central granule toward the cytoplasmic face of the nuclear envelope under calcium depleting conditions. Additionally, activation of nuclear inositol triphosphate (IP(3)) receptors by the specific agonist, adenophostin A, results in a concentration-dependent displacement of central granule position with an EC(50) of ~1.2 nM. The displacement of the central granule within the NPC is observed on both the cytoplasmic and nucleoplasmic faces of the nuclear envelope. The displacement is blocked upon treatment with xestospongin C, a specific inhibitor of IP(3) receptor activation. These results extend previous models of NPC conformational dynamics linking central granule position to depletion of IP(3) sensitive nuclear envelope calcium stores.
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14
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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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15
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Berge T, Ellis DJ, Dryden DT, Edwardson JM, Henderson RM. Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy. Biophys J 2000; 79:479-84. [PMID: 10866973 PMCID: PMC1300951 DOI: 10.1016/s0006-3495(00)76309-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bacterial type I restriction/modification systems are capable of performing multiple actions in response to the methylation pattern on their DNA recognition sequences. The enzymes making up these systems serve to protect the bacterial cells against viral infection by binding to their recognition sequences on the invading DNA and degrading it after extensive ATP-driven translocation. DNA cleavage has been thought to occur as the result of a collision between two translocating enzyme complexes. Using atomic force microscopy (AFM), we show here that EcoKI dimerizes rapidly when bound to a plasmid containing two recognition sites for the enzyme. Dimerization proceeds in the absence of ATP and is also seen with an EcoKI mutant (K477R) that is unable to translocate DNA. Only monomers are seen when the enzyme complex binds to a plasmid containing a single recognition site. Based on our results, we propose that the binding of EcoKI to specific DNA target sequences is accompanied by a conformational change that leads rapidly to dimerization. This event is followed by ATP-dependent translocation and cleavage of the DNA.
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Affiliation(s)
- T Berge
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1QJ, England
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16
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Henderson RM, Oberleithner H. Pushing, pulling, dragging, and vibrating renal epithelia by using atomic force microscopy. Am J Physiol Renal Physiol 2000; 278:F689-701. [PMID: 10807580 DOI: 10.1152/ajprenal.2000.278.5.f689] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Renal physiologists focus on events that take place on and around the surfaces of cells. Various techniques have been developed that follow transport functions at the molecular level, but until recently none of these techniques has been capable of making the behavior of molecular structures visible under physiological conditions. This apparent gap may be filled in the future by the application of atomic force microscopy. This technique produces an image not by optical means, but by "feeling" its way across a surface. Atomic force microscopy can, however, be modified in a number of ways, which means that besides producing a high-resolution image, it is possible to obtain several types of data on the interactions between the ultrastructural components of cell membranes (such as proteins) and other biologically active molecules (such as ATP). In this review we describe the recent use of the atomic force microscope in renal physiology, ranging from experiments in intact cells to those in isolated renal transport protein molecules, include examples of these extended applications of the technique, and point to uses that the microscope has recently found in other areas of biology that should prove fruitful in renal physiology in the near future.
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Affiliation(s)
- R M Henderson
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1QJ, United Kingdom.
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17
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Danker T, Schillers H, Storck J, Shahin V, Krämer B, Wilhelmi M, Oberleithner H. Nuclear hourglass technique: an approach that detects electrically open nuclear pores in Xenopus laevis oocyte. Proc Natl Acad Sci U S A 1999; 96:13530-5. [PMID: 10557355 PMCID: PMC23982 DOI: 10.1073/pnas.96.23.13530] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate both active transport and passive diffusion across the nuclear envelope (NE). Determination of NE electrical conductance, however, has been confounded by the lack of an appropriate technical approach. The nuclear patch clamp technique is restricted to preparations with electrically closed NPCs, and microelectrode techniques fail to resolve the extremely low input resistance of large oocyte nuclei. To address the problem, we have developed an approach for measuring the NE electrical conductance of Xenopus laevis oocyte nuclei. The method uses a tapered glass tube, which narrows in its middle part to 2/3 of the diameter of the nucleus. The isolated nucleus is sucked into the narrow part of the capillary by gentle fluid movement, while the resulting change in electrical resistance is monitored. NE electrical conductance was unexpectedly large (7.9 +/- 0.34 S/cm(2)). Evaluation of NPC density by atomic force microscopy showed that this conductance corresponded to 3.7 x 10(6) NPCs. In contrast to earlier conclusions drawn from nuclear patch clamp experiments, NPCs were in an electrically "open" state with a mean single NPC electrical conductance of 1.7 +/- 0.07 nS. Enabling or blocking of active NPC transport (accomplished by the addition of cytosolic extracts or gp62-directed antibodies) revealed this large NPC conductance to be independent of the activation state of the transport machinery located in the center of NPCs. We conclude that peripheral channels, which are presumed to reside in the NPC subunits, establish a high ionic permeability that is virtually independent of the active protein transport mechanism.
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Affiliation(s)
- T Danker
- Department of Physiology, University of Münster, Robert-Koch Str. 27a, D-48149 Münster, Germany.
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18
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Abstract
The origin of contrast in atomic force microscopy (AFM) lies in the probe's response to forces between itself and the sample. These forces most commonly result from changes in height as the tip is scanned over the surface, but can also originate in properties inherent in the sample. These have been exploited as further means of contrast and have spawned an array of similar imaging techniques, such as chemical force microscopy, magnetic force microscopy, and frictional force microscopy. All of these techniques use AFM as an extremely sensitive gauge to map forces at discrete sites on the surface. A natural extension of this approach is to map forces in an array, in order to create a force map. AFM can be used in aqueous or fluid environments, thus allowing the exploration of forces in biological systems under physiologically relevant conditions. By immobilizing one half of an interacting pair of proteins onto the tip and the other half onto the substrate, it is possible to investigate the electrostatic and hydrophobic interactions between them. We employed these techniques to examine the interaction between a pair of proteins of known affinity that are involved in exocytosis (NSF and alpha-SNAP) and separately to demonstrate how two-dimensional force mapping can be applied to the nuclear envelope to identify nuclear pore complexes.
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Affiliation(s)
- D J Ellis
- Department of Pharmacology, University of Cambridge, United Kingdom
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19
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Abstract
Nuclear lamins are intermediate filament-type proteins that are the major building blocks of the nuclear lamina, a fibrous proteinaceous meshwork underlying the inner nuclear membrane. Lamins can also be localized in the nuclear interior, in a diffuse or spotted pattern. Nuclei assembled in vitro in the absence of lamins are fragile, indicating that lamins mechanically stabilize the cell nucleus. Available evidence also indicates a role for lamins in DNA replication, chromatin organization, spatial arrangement of nuclear pore complexes, nuclear growth, and anchorage of nuclear envelope proteins. In this review we summarize the current state of knowledge on the structure, assembly, and possible functional roles of nuclear lamins, emphasizing the information concerning the ability of nuclear lamins to self-assemble into distinct oligomers and polymers.
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Affiliation(s)
- N Stuurman
- M. E. Müller-Institute for Microscopy at the Biozentrum, University of Basel, Basel, CH-4056, Switzerland
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Oberleithner H, Schneider SW, Henderson RM. Structural activity of a cloned potassium channel (ROMK1) monitored with the atomic force microscope: the "molecular-sandwich" technique. Proc Natl Acad Sci U S A 1997; 94:14144-9. [PMID: 9391167 PMCID: PMC28447 DOI: 10.1073/pnas.94.25.14144] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The atomic force microscope (AFM) was used to continuously follow height changes of individual protein molecules exposed to physiological stimuli. A AFM tip was coated with ROMK1 (a cloned renal epithelial potassium channel known to be highly pH sensitive) and lowered onto atomically flat mica surface until the protein was sandwiched between AFM tip and mica. Because the AFM tip was an integral part of a highly flexible cantilever, any structural alterations of the sandwiched molecule were transmitted to the cantilever. This resulted in a distortion of the cantilever that was monitored by means of a laser beam. With this system it was possible to resolve vertical height changes in the ROMK1 protein of >/=0.2 nm (approximately 5% of the molecule's height) with a time resolution of >/=1 msec. When bathed in electrolyte solution that contained the catalytic subunit of protein kinase A and 0.1 mM ATP (conditions that activate the native ion channel), we found stochastically occurring height fluctuations in the ROMK1 molecule. These changes in height were pH-dependent, being greatest at pH 7.6, and lowering the pH (either by titration or by the application of CO2) reduced their magnitude. The data show that overall changes in shape of proteins occur stochastically and increase in size and frequency when the proteins are active. This AFM "molecular-sandwich" technique, called MOST, measures structural activity of proteins in real time and could prove useful for studies on the relationship between structure and function of proteins at the molecular level.
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Affiliation(s)
- H Oberleithner
- Department of Physiology, University of Münster, Robert-Koch-Strasse 27a Innenhof, D-48149 Münster, Germany.
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21
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Folprecht G, Schneider S, Oberleithner H. Aldosterone activates the nuclear pore transporter in cultured kidney cells imaged with atomic force microscopy. Pflugers Arch 1996; 432:831-8. [PMID: 8772133 DOI: 10.1007/s004240050205] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nuclear pore complexes (NPC), located in the nuclear envelope, functionally connect the cell nucleus with the cytoplasm and serve as a crucial pathway for macromolecule exchange. A Madin-Darby canine kidney (MDCK) clone that resembles principal cells of the collecting duct was shown recently to respond to sustained aldosterone exposure with a significant increase in the NPC number per nucleus. The present study elucidates the molecular nature of the NPC pathway and its regulation by aldosterone applying atomic force microscopy. We imaged individual NPC in situ and searched for a putative so-called transporter in the NPC centre. In aldosterone-depleted cells we found numerous macromolecules docked to individual NPC waiting for translocation into the nucleoplasm (standby mode=inactive pore). In contrast, in aldosterone-treated cells NPC were frequently found free of macromolecules, indicating that the translocation process kept pace with docking under hormone-stimulated conditions (transport mode=active pore). In the NPC centre we detected a ring-like structure with a central invagination. We assume that the ring is the putative transporter and that the invagination is the channel entrance used for translocation of macromolecules. Transporters were found in open and closed configurations. In conclusion, the results provide evidence for the existence of a nuclear transporter as part of the translocation machinery of an individual NPC. Aldosterone increases the activity of the nuclear transporter and thus facilitates steroid-mediated gene expression.
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Affiliation(s)
- G Folprecht
- Department of Physiology, University of Würzburg, Röntgenring 9, D-97070 Würzburg, Germany
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Henderson RM, Schneider S, Li Q, Hornby D, White SJ, Oberleithner H. Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy. Proc Natl Acad Sci U S A 1996; 93:8756-60. [PMID: 8710944 PMCID: PMC38746 DOI: 10.1073/pnas.93.16.8756] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The inwardly rectifying K+ channel ROMK1 has been implicated as being significant in K+ secretion in the distal nephron. ROMK1 has been shown by immunocytochemistry to be expressed in relevant nephron segments. The development of the atomic force microscope has made possible the production of high resolution images of small particles, including a variety of biological macromolecules. Recently, a fusion protein of glutathione S-transferase (GST) and ROMK1 (ROMK1-GST) has been used to produce a polyclonal antibody for immunolocalization of ROMK1. We have used atomic force microscopy to examine ROMK1-GST and the native ROMK1 polypeptide cleaved from GST. Imaging was conducted with the proteins in physiological solutions attached to mica. ROMK1-GST appears in images as a particle composed of two units of similar size. Analyses of images indicate that the two units have volumes of approximately 118 nm3, which is close to the theoretical volume of a globular protein of approximately 65 kDa (the molecular mass of ROMK1-GST). Native GST exists as a dimer, and the images obtained here are consistent with the ROMK1-GST fusion protein's existence as a heterodimer. In experiments on ROMK1 in aqueous solution, single molecules appear to aggregate, but contact to the mica was maintained. Addition of ATP to the solution produced a change in height of the aggregates. This change (which was reversible) suggests that ATP induces a structural change in the ROMK1 protein. The data show that atomic force microscopy is a useful tool for examination of purified protein molecules under near-physiological conditions, and furthermore, that structural alterations in the proteins may be continuously investigated.
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Affiliation(s)
- R M Henderson
- Department of Pharmacology, University of Cambridge, United Kingdom
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