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Caggiano EG, Taniguchi CM. UCP2 and pancreatic cancer: conscious uncoupling for therapeutic effect. Cancer Metastasis Rev 2024; 43:777-794. [PMID: 38194152 PMCID: PMC11156755 DOI: 10.1007/s10555-023-10157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/13/2023] [Indexed: 01/10/2024]
Abstract
Pancreatic cancer has an exaggerated dependence on mitochondrial metabolism, but methods to specifically target the mitochondria without off target effects in normal tissues that rely on these organelles is a significant challenge. The mitochondrial uncoupling protein 2 (UCP2) has potential as a cancer-specific drug target, and thus, we will review the known biology of UCP2 and discuss its potential role in the pathobiology and future therapy of pancreatic cancer.
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Affiliation(s)
- Emily G Caggiano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Cullen M Taniguchi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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2
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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3
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Barreto P, Couñago RM, Arruda P. Mitochondrial uncoupling protein-dependent signaling in plant bioenergetics and stress response. Mitochondrion 2020; 53:109-120. [DOI: 10.1016/j.mito.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/06/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
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4
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Zhu R, Sandtner W, Ahiable JEA, Newman AH, Freissmuth M, Sitte HH, Hinterdorfer P. Allosterically Linked Binding Sites in Serotonin Transporter Revealed by Single Molecule Force Spectroscopy. Front Mol Biosci 2020; 7:99. [PMID: 32656227 PMCID: PMC7325972 DOI: 10.3389/fmolb.2020.00099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/01/2020] [Indexed: 01/24/2023] Open
Abstract
Crystal structures and experiments relying on the tools of molecular pharmacology reported conflicting results on ligand binding sites in neurotransmitter/sodium symporters (NSS). We explored the number and functionality of ligand binding sites of NSS in a physiological setting by designing novel tools for atomic force microscopy (AFM). These allow for directly measuring the interaction forces between the serotonin transporter (SERT) and the antidepressant S-citalopram (S-CIT) on the single molecule level: the AFM cantilever tips were functionalized with S-CIT via a flexible polyethylene glycol (PEG) linker. The tip chemistry was validated by specific force measurements and recognition imaging on CHO cells. Two distinct populations of characteristic binding strengths of S-CIT binding to SERT were revealed in Na+-containing buffer. In contrast, in Li+-containing buffer, SERT showed only low force interactions. Conversely, the vestibular mutant SERT-G402H merely displayed the high force population. These observations provide physical evidence for the existence of two binding sites in SERT. The dissociation rate constant of both binding sites was extracted by varying the dynamics of the force-probing experiments. Competition experiments revealed that the two sites are allosterically coupled and exert reciprocal modulation.
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Affiliation(s)
- Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Walter Sandtner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Joan E A Ahiable
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, Baltimore, MD, United States
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Harald H Sitte
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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5
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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Lu WH, Chang YM, Huang YS. Alternative Polyadenylation and Differential Regulation of Ucp1: Implications for Brown Adipose Tissue Thermogenesis Across Species. Front Pediatr 2020; 8:612279. [PMID: 33634052 PMCID: PMC7899972 DOI: 10.3389/fped.2020.612279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
Brown adipose tissue (BAT) is a thermogenic organ owing to its unique expression of uncoupling protein 1 (UCP1), which is a proton channel in the inner mitochondrial membrane used to dissipate the proton gradient and uncouple the electron transport chain to generate heat instead of adenosine triphosphate. The discovery of metabolically active BAT in human adults, especially in lean people after cold exposure, has provoked the "thermogenic anti-obesity" idea to battle weight gain. Because BAT can expend energy through UCP1-mediated thermogenesis, the molecular mechanisms regulating UCP1 expression have been extensively investigated at both transcriptional and posttranscriptional levels. Of note, the 3'-untranslated region (3'-UTR) of Ucp1 mRNA is differentially processed between mice and humans that quantitatively affects UCP1 synthesis and thermogenesis. Here, we summarize the regulatory mechanisms underlying UCP1 expression, report the number of poly(A) signals identified or predicted in Ucp1 genes across species, and discuss the potential and caution in targeting UCP1 for enhancing thermogenesis and metabolic fitness.
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Affiliation(s)
- Wen-Hsin Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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7
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Pohl EE, Rupprecht A, Macher G, Hilse KE. Important Trends in UCP3 Investigation. Front Physiol 2019; 10:470. [PMID: 31133866 PMCID: PMC6524716 DOI: 10.3389/fphys.2019.00470] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/04/2019] [Indexed: 11/13/2022] Open
Abstract
Membrane uncoupling protein 3 (UCP3), a member of the mitochondrial uncoupling protein family, was discovered in 1997. UCP3's properties, such as its high homology to other mitochondrial carriers, especially to UCP2, its short lifetime and low specificity of UCP3 antibodies, have hindered progress in understanding its biological function and transport mechanism over decades. The abundance of UCP3 is highest in murine brown adipose tissue (BAT, 15.0 pmol/mg protein), compared to heart (2.7 pmol/mg protein) and the gastrocnemius muscle (1.7 pmol/mg protein), but it is still 400-fold lower than the abundance of UCP1, a biomarker for BAT. Investigation of UCP3 reconstituted in planar bilayer membranes revealed that it transports protons only when activated by fatty acids (FA). Although purine nucleotides (PN) inhibit UCP3-mediated transport, the molecular mechanism differs from that of UCP1. It remains a conundrum that two homologous proton-transporting proteins exist within the same tissue. Recently, we proposed that UCP3 abundance directly correlates with the degree of FA β-oxidation in cell metabolism. Further development in this field implies that UCP3 may have dual function in transporting substrates, which have yet to be identified, alongside protons. Evaluation of the literature with respect to UCP3 is a complex task because (i) UCP3 features are often extrapolated from its "twin" UCP2 without additional proof, and (ii) the specificity of antibodies against UCP3 used in studies is rarely evaluated. In this review, we primarily focus on recent findings obtained for UCP3 in biological and biomimetic systems.
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Affiliation(s)
- Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | - Anne Rupprecht
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
- Institute of Pharmacology and Toxicology, Rostock University Medical Center, Rostock, Germany
| | - Gabriel Macher
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | - Karolina E. Hilse
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
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8
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Ježek P, Jabůrek M, Porter RK. Uncoupling mechanism and redox regulation of mitochondrial uncoupling protein 1 (UCP1). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:259-269. [DOI: 10.1016/j.bbabio.2018.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023]
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9
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AFM-Based Force Spectroscopy Guided by Recognition Imaging: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density. Methods Protoc 2019; 2:mps2010006. [PMID: 31164590 PMCID: PMC6481044 DOI: 10.3390/mps2010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/07/2018] [Accepted: 01/03/2019] [Indexed: 11/17/2022] Open
Abstract
Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate receptor-ligand pairs leads to new insights into the molecular recognition involved in these processes. Here we present a detailed protocol about applying a technique, which combines atomic force microscopy (AFM)-based recognition imaging and force spectroscopy for studying the interaction between (membrane) receptors and ligands on the single molecule level. This method allows for the selection of a single receptor molecule reconstituted into a supported lipid membrane at low density, with the subsequent quantification of the receptor-ligand unbinding force. Based on AFM tapping mode, a cantilever tip carrying a ligand molecule is oscillated across a membrane. Topography and recognition images of reconstituted receptors are recorded simultaneously by analyzing the downward and upward parts of the oscillation, respectively. Functional receptor molecules are selected from the recognition image with nanometer resolution before the AFM is switched to the force spectroscopy mode, using positional feedback control. The combined mode allows for dynamic force probing on different pre-selected molecules. This strategy results in higher throughput when compared with force mapping. Applied to two different receptor-ligand pairs, we validated the presented new mode.
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10
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Wang N, Zhang M, Chen X, Ma X, Li C, Zhang Z, Tang J. Mapping the interaction sites of Mucin 1 and DNA aptamer by atomic force microscopy. Analyst 2018; 142:3800-3804. [PMID: 28930315 DOI: 10.1039/c7an01119a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mucin 1 (MUC1) is an attractive tumor marker for cancer diagnosis. An advanced atomic force microscopy (AFM) mode, peak-force tapping AFM with an aptamer functionalized tip, was introduced to map the specific interaction sites of an aptamer and MUC1. Single molecular force spectroscopy (SMFS) was used to investigate dynamic parameters of the aptamer-MUC1.
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Affiliation(s)
- Nan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.
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11
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Ježek P, Holendová B, Garlid KD, Jabůrek M. Mitochondrial Uncoupling Proteins: Subtle Regulators of Cellular Redox Signaling. Antioxid Redox Signal 2018; 29:667-714. [PMID: 29351723 PMCID: PMC6071544 DOI: 10.1089/ars.2017.7225] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Mitochondria are the energetic, metabolic, redox, and information signaling centers of the cell. Substrate pressure, mitochondrial network dynamics, and cristae morphology state are integrated by the protonmotive force Δp or its potential component, ΔΨ, which are attenuated by proton backflux into the matrix, termed uncoupling. The mitochondrial uncoupling proteins (UCP1-5) play an eminent role in the regulation of each of the mentioned aspects, being involved in numerous physiological events including redox signaling. Recent Advances: UCP2 structure, including purine nucleotide and fatty acid (FA) binding sites, strongly support the FA cycling mechanism: UCP2 expels FA anions, whereas uncoupling is achieved by the membrane backflux of protonated FA. Nascent FAs, cleaved by phospholipases, are preferential. The resulting Δp dissipation decreases superoxide formation dependent on Δp. UCP-mediated antioxidant protection and its impairment are expected to play a major role in cell physiology and pathology. Moreover, UCP2-mediated aspartate, oxaloacetate, and malate antiport with phosphate is expected to alter metabolism of cancer cells. CRITICAL ISSUES A wide range of UCP antioxidant effects and participations in redox signaling have been reported; however, mechanisms of UCP activation are still debated. Switching off/on the UCP2 protonophoretic function might serve as redox signaling either by employing/releasing the extra capacity of cell antioxidant systems or by directly increasing/decreasing mitochondrial superoxide sources. Rapid UCP2 degradation, FA levels, elevation of purine nucleotides, decreased Mg2+, or increased pyruvate accumulation may initiate UCP-mediated redox signaling. FUTURE DIRECTIONS Issues such as UCP2 participation in glucose sensing, neuronal (synaptic) function, and immune cell activation should be elucidated. Antioxid. Redox Signal. 29, 667-714.
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Affiliation(s)
- Petr Ježek
- 1 Department of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences , Prague, Czech Republic
| | - Blanka Holendová
- 1 Department of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences , Prague, Czech Republic
| | - Keith D Garlid
- 2 UCLA Cardiovascular Research Laboratory, David Geffen School of Medicine at UCLA , Los Angeles, California
| | - Martin Jabůrek
- 1 Department of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences , Prague, Czech Republic
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12
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Zhang P, Chen YP, Qiu JH, Dai YZ, Feng B. Imaging the Microprocesses in Biofilm Matrices. Trends Biotechnol 2018; 37:214-226. [PMID: 30075862 DOI: 10.1016/j.tibtech.2018.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022]
Abstract
Biofilms, which are aggregates of microorganisms and extracellular matrices, widely colonize natural water bodies, wastewater treatment systems, and body tissues, and have vital roles in water purification, biofouling, and infectious diseases. Recently, multiple imaging modalities have been developed to visualize the morphological structure and material distribution within biofilms and to probe the microprocesses in biofilm matrices, including biofilm formation, transfer and metabolism of substrates, and cell-cell communication. These technologies have improved our understanding of biofilm control and the fates of substrates in biofilms. In this review, we describe the principles of various imaging techniques and discuss the advantages and limitations of each approach to characterizing microprocesses in biofilm matrices.
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Affiliation(s)
- Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
| | - Ju-Hui Qiu
- College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - You-Zhi Dai
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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Macher G, Koehler M, Rupprecht A, Kreiter J, Hinterdorfer P, Pohl EE. Inhibition of mitochondrial UCP1 and UCP3 by purine nucleotides and phosphate. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:664-672. [PMID: 29212043 PMCID: PMC6118327 DOI: 10.1016/j.bbamem.2017.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/04/2017] [Accepted: 12/01/2017] [Indexed: 11/26/2022]
Abstract
Mitochondrial membrane uncoupling protein 3 (UCP3) is not only expressed in skeletal muscle and heart, but also in brown adipose tissue (BAT) alongside UCP1, which facilitates a proton leak to support non-shivering thermogenesis. In contrast to UCP1, the transport function and molecular mechanism of UCP3 regulation are poorly investigated, although it is generally agreed upon that UCP3, analogous to UCP1, transports protons, is activated by free fatty acids (FFAs) and is inhibited by purine nucleotides (PNs). Because the presence of two similar uncoupling proteins in BAT is surprising, we hypothesized that UCP1 and UCP3 are differently regulated, which may lead to differences in their functions. By combining atomic force microscopy and electrophysiological measurements of recombinant proteins reconstituted in planar bilayer membranes, we compared the level of protein activity with the bond lifetimes between UCPs and PNs. Our data revealed that, in contrast to UCP1, UCP3 can be fully inhibited by all PNs and IC50 increases with a decrease in PN-phosphorylation. Experiments with mutant proteins demonstrated that the conserved arginines in the PN-binding pocket are involved in the inhibition of UCP1 and UCP3 to different extents. Fatty acids compete with all PNs bound to UCP1, but only with ATP bound to UCP3. We identified phosphate as a novel inhibitor of UCP3 and UCP1, which acts independently of PNs. The differences in molecular mechanisms of the inhibition between the highly homologous transporters UCP1 and UCP3 indicate that UCP3 has adapted to fulfill a different role and possibly another transport function in BAT.
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Affiliation(s)
- Gabriel Macher
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | - Melanie Koehler
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Anne Rupprecht
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | - Jürgen Kreiter
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria
| | | | - Elena E Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Vienna, Austria.
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14
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Danzberger J, Donovan M, Rankl C, Zhu R, Vicic S, Baltenneck C, Enea R, Hinterdorfer P, Luengo GS. Glycan distribution and density in native skin's stratum corneum. Skin Res Technol 2018; 24:450-458. [PMID: 29417655 PMCID: PMC6446803 DOI: 10.1111/srt.12453] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/01/2018] [Indexed: 01/01/2023]
Abstract
Background The glycosylation of proteins on the surface of corneocytes is believed to play an important role in cellular adhesion in the stratum corneum (SC) of human skin. Mapping with accuracy the localization of glycans on the surface of corneocytes through traditional methods of immunohistochemistry and electron microscopy remains a challenging task as both approaches lack enough resolution or need to be performed in high vacuum conditions. Materials and methods We used an advanced mode of atomic force microscope (AFM), with simultaneous topography and recognition imaging to investigate the distribution of glycans on native (no chemical preparation) stripped samples of human SC. The AFM cantilever tips were functionalized with anti‐heparan sulfate antibody and the lectin wheat germ agglutinin (WGA) which binds specifically to N‐acetyl glucosamine and sialic acid. Results From the recognition imaging, we observed the presence of the sulfated glycosaminoglycan, heparan sulfate, and the glycans recognized by WGA on the surface of SC corneocytes in their native state. These glycans were found associated with bead‐like domains which represent corneodesmosomes in the SC layers. Glycan density was calculated to be ~1200 molecules/μm2 in lower layers of SC compared to an important decrease, (~106 molecules/μm2) closer to the surface due probably to corneodesmosome degradation. Conclusion Glycan spatial distribution and degradation is first observed on the surface of SC in native conditions and at high resolution. The method used can be extended to precisely localize the presence of other macromolecules on the surface of skin or other tissues where the maintenance of its native state is required.
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Affiliation(s)
- J Danzberger
- Center for Advanced Bioanalysis GmbH, Linz, Austria
| | - M Donovan
- L'Oréal Research and Innovation, Aulnay sous Bois, France
| | - C Rankl
- RECENDT-Research Center for Non-Destructive Testing GmbH, Linz, Austria
| | - R Zhu
- Institute for Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - S Vicic
- L'Oréal Research and Innovation, Aulnay sous Bois, France
| | - C Baltenneck
- L'Oréal Research and Innovation, Aulnay sous Bois, France
| | - R Enea
- L'Oréal Research and Innovation, Aulnay sous Bois, France
| | - P Hinterdorfer
- Center for Advanced Bioanalysis GmbH, Linz, Austria.,Institute for Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - G S Luengo
- L'Oréal Research and Innovation, Aulnay sous Bois, France
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15
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Ozkan AD, Topal AE, Dikecoglu FB, Guler MO, Dana A, Tekinay AB. Probe microscopy methods and applications in imaging of biological materials. Semin Cell Dev Biol 2018; 73:153-164. [DOI: 10.1016/j.semcdb.2017.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 01/21/2023]
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16
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Chtcheglova LA, Hinterdorfer P. Simultaneous AFM topography and recognition imaging at the plasma membrane of mammalian cells. Semin Cell Dev Biol 2018; 73:45-56. [DOI: 10.1016/j.semcdb.2017.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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17
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Bae YI, Hwang I, Kim I, Kim K, Park JW. Force Measurement for the Interaction between Cucurbit[7]uril and Mica and Self-Assembled Monolayer in the Presence of Zn 2+ Studied with Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11884-11892. [PMID: 28946747 DOI: 10.1021/acs.langmuir.7b02168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force spectroscopy with atomic force microscopy (AFM) revealed that cucurbit[7]uril (CB[7]) strongly binds to a mica surface in the presence of cations. Indeed, Zn2+ was observed to facilitate the self-assembly of CB[7] on the mica surface, whereas monocations, such as Na+, were less effective. The progression of the process and the cation-mediated self-assembled monolayer were characterized using AFM, and the observed height of the layer agrees well with the calculated CB[7] value (9.1 Å). We utilized force-based AFM to further study the interaction of CB[7] with guest molecules. To this end, CB[7] was immobilized on a glass substrate, and aminomethylferrocene (am-Fc) was conjugated onto an AFM tip. The single-molecule interaction between CB[7] and am-Fc was monitored by collecting the unbinding force curves. The force histogram showed single ruptures and a unimodal distribution, and the most probable unbinding force value was 101 pN in deionized water and 86 pN in phosphate-buffered saline buffer. The results indicate that the unbinding force was larger than that of streptavidin-biotin measured under the same conditions, whereas the dissociation constant was smaller by 1 order of magnitude (0.012 s-1 vs 0.13 s-1). Furthermore, a high-resolution adhesion force map showed a part of the CB[7] cavities on the surface.
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Affiliation(s)
- Young-In Bae
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ilha Hwang
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ikjin Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Kimoon Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joon Won Park
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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18
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Crichton PG, Lee Y, Kunji ERS. The molecular features of uncoupling protein 1 support a conventional mitochondrial carrier-like mechanism. Biochimie 2017; 134:35-50. [PMID: 28057583 PMCID: PMC5395090 DOI: 10.1016/j.biochi.2016.12.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/24/2016] [Indexed: 12/14/2022]
Abstract
Uncoupling protein 1 (UCP1) is an integral membrane protein found in the mitochondrial inner membrane of brown adipose tissue, and facilitates the process of non-shivering thermogenesis in mammals. Its activation by fatty acids, which overcomes its inhibition by purine nucleotides, leads to an increase in the proton conductance of the inner mitochondrial membrane, short-circuiting the mitochondrion to produce heat rather than ATP. Despite 40 years of intense research, the underlying molecular mechanism of UCP1 is still under debate. The protein belongs to the mitochondrial carrier family of transporters, which have recently been shown to utilise a domain-based alternating-access mechanism, cycling between a cytoplasmic and matrix state to transport metabolites across the inner membrane. Here, we review the protein properties of UCP1 and compare them to those of mitochondrial carriers. UCP1 has the same structural fold as other mitochondrial carriers and, in contrast to past claims, is a monomer, binding one purine nucleotide and three cardiolipin molecules tightly. The protein has a single substrate binding site, which is similar to those of the dicarboxylate and oxoglutarate carriers, but also contains a proton binding site and several hydrophobic residues. As found in other mitochondrial carriers, UCP1 has two conserved salt bridge networks on either side of the central cavity, which regulate access to the substrate binding site in an alternating way. The conserved domain structures and mobile inter-domain interfaces are consistent with an alternating access mechanism too. In conclusion, UCP1 has retained all of the key features of mitochondrial carriers, indicating that it operates by a conventional carrier-like mechanism.
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Affiliation(s)
- Paul G Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.
| | - Yang Lee
- Laboratory of Molecular Biology, Medical Research Council, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Edmund R S Kunji
- Mitochondrial Biology Unit, Medical Research Council, Cambridge Biomedical Campus, Wellcome Trust, MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom.
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19
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Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy. SENSORS 2017; 17:s17010200. [PMID: 28117741 PMCID: PMC5298773 DOI: 10.3390/s17010200] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/23/2022]
Abstract
The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.
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20
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Koehler M, Macher G, Rupprecht A, Zhu R, Gruber HJ, Pohl EE, Hinterdorfer P. Combined Recognition Imaging and Force Spectroscopy: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density. SCIENCE OF ADVANCED MATERIALS 2017; 9:128-134. [PMID: 29743989 PMCID: PMC5937678 DOI: 10.1166/sam.2017.3066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We combined recognition imaging and force spectroscopy to study the interactions between receptors and ligands on the single molecule level. This method allowed the selection of a single receptor molecule reconstituted in a supported lipid membrane at low density, with the subsequent quantification of the receptor-ligand unbinding force. Based on atomic force microscopy (AFM) tapping mode, a cantilever tip carrying a ligand molecule was oscillated across a membrane. Topography and recognition images of reconstituted receptors were recorded simultaneously by analyzing the downward and upward parts of the oscillation, respectively. Functional receptor molecules were selected from the recognition image with nanometer resolution before the AFM was switched to the force spectroscopy mode, using positional feedback control. The combined mode allowed for dynamic force probing on different pre-selected molecules, resulting in higher throughput when compared with force mapping. We applied this method for a quantitative characterization of the binding mechanism between mitochondrial uncoupling protein 1 (UCP1) and its inhibitor adenosine triphosphate (ATP). Moreover the dynamics of force loading was varied to elucidate the binding dynamics and map the interaction energy landscape.
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Affiliation(s)
- Melanie Koehler
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Gabriel Macher
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Anne Rupprecht
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Rong Zhu
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Hermann J. Gruber
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
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21
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Kim Y, Kim W, Park JW. Principles and Applications of Force Spectroscopy Using Atomic Force Microscopy. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Youngkyu Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Woong Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Joon Won Park
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
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22
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The conserved regulation of mitochondrial uncoupling proteins: From unicellular eukaryotes to mammals. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:21-33. [PMID: 27751905 DOI: 10.1016/j.bbabio.2016.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/29/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022]
Abstract
Uncoupling proteins (UCPs) belong to the mitochondrial anion carrier protein family and mediate regulated proton leak across the inner mitochondrial membrane. Free fatty acids, aldehydes such as hydroxynonenal, and retinoids activate UCPs. However, there are some controversies about the effective action of retinoids and aldehydes alone; thus, only free fatty acids are commonly accepted positive effectors of UCPs. Purine nucleotides such as GTP inhibit UCP-mediated mitochondrial proton leak. In turn, membranous coenzyme Q may play a role as a redox state-dependent metabolic sensor that modulates the complete activation/inhibition of UCPs. Such regulation has been observed for UCPs in microorganisms, plant and animal UCP1 homologues, and UCP1 in mammalian brown adipose tissue. The origin of UCPs is still under debate, but UCP homologues have been identified in all systematic groups of eukaryotes. Despite the differing levels of amino acid/DNA sequence similarities, functional studies in unicellular and multicellular organisms, from amoebae to mammals, suggest that the mechanistic regulation of UCP activity is evolutionarily well conserved. This review focuses on the regulatory feedback loops of UCPs involving free fatty acids, aldehydes, retinoids, purine nucleotides, and coenzyme Q (particularly its reduction level), which may derive from the early stages of evolution as UCP first emerged.
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23
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Dong C, Hu X, Dinu CZ. Current status and perspectives in atomic force microscopy-based identification of cellular transformation. Int J Nanomedicine 2016; 11:2107-18. [PMID: 27274238 PMCID: PMC4876801 DOI: 10.2147/ijn.s103501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Understanding the complex interplay between cells and their biomechanics and how the interplay is influenced by the extracellular microenvironment, as well as how the transforming potential of a tissue from a benign to a cancerous one is related to the dynamics of both the cell and its surroundings, holds promise for the development of targeted translational therapies. This review provides a comprehensive overview of atomic force microscopy-based technology and its applications for identification of cellular progression to a cancerous phenotype. The review also offers insights into the advancements that are required for the next user-controlled tool to allow for the identification of early cell transformation and thus potentially lead to improved therapeutic outcomes.
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Affiliation(s)
- Chenbo Dong
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, WV, USA
| | - Xiao Hu
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, WV, USA
| | - Cerasela Zoica Dinu
- Department of Chemical and Biomedical Engineering, West Virginia University, Morgantown, WV, USA
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24
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Senapati S, Lindsay S. Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy. Acc Chem Res 2016; 49:503-10. [PMID: 26934674 DOI: 10.1021/acs.accounts.5b00533] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Atomic force microscopy (AFM) is an extremely powerful tool in the field of bionanotechnology because of its ability to image single molecules and make measurements of molecular interaction forces with piconewton sensitivity. It works in aqueous media, enabling studies of molecular phenomenon taking place under physiological conditions. Samples can be imaged in their near-native state without any further modifications such as staining or tagging. The combination of AFM imaging with the force measurement added a new feature to the AFM technique, that is, molecular recognition imaging. Molecular recognition imaging enables mapping of specific interactions between two molecules (one attached to the AFM tip and the other to the imaging substrate) by generating simultaneous topography and recognition images (TREC). Since its discovery, the recognition imaging technique has been successfully applied to different systems such as antibody-protein, aptamer-protein, peptide-protein, chromatin, antigen-antibody, cells, and so forth. Because the technique is based on specific binding between the ligand and receptor, it has the ability to detect a particular protein in a mixture of proteins or monitor a biological phenomenon in the native physiological state. One key step for recognition imaging technique is the functionalization of the AFM tips (generally, silicon, silicon nitrides, gold, etc.). Several different functionalization methods have been reported in the literature depending on the molecules of interest and the material of the tip. Polyethylene glycol is routinely used to provide flexibility needed for proper binding as a part of the linker that carries the affinity molecule. Recently, a heterofunctional triarm linker has been synthesized and successfully attached with two different affinity molecules. This novel linker, when attached to AFM tip, helped to detect two different proteins simultaneously from a mixture of proteins using a so-called "two-color" recognition image. Biological phenomena in nature often involve multimolecular interactions, and this new linker could be ideal for studying them using AFM recognition imaging. It also has the potential to be used extensively in the diagnostics technique. This Account includes fundamentals behind AFM recognition imaging, a brief discussion on tip functionalization, recent advancements, and future directions and possibilities.
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Affiliation(s)
- Subhadip Senapati
- Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of
Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stuart Lindsay
- Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of
Physics, Arizona State University, Tempe, Arizona 85287, United States
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25
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Liu H, Krajcikova D, Wang N, Zhang Z, Wang H, Barak I, Tang J. Forces and Kinetics of the Bacillus subtilis Spore Coat Proteins CotY and CotX Binding to CotE Inspected by Single Molecule Force Spectroscopy. J Phys Chem B 2016; 120:1041-7. [DOI: 10.1021/acs.jpcb.5b11344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huiqing Liu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Daniela Krajcikova
- Institute
of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta
21, Bratislava 845 51, Slovakia
| | - Nan Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhe Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Hongda Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Imrich Barak
- Institute
of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta
21, Bratislava 845 51, Slovakia
| | - Jilin Tang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
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26
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Kulik AJ, Lekka M, Lee K, Pyka-Fościak G, Nowak W. Probing fibronectin-antibody interactions using AFM force spectroscopy and lateral force microscopy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1164-1175. [PMID: 26114080 PMCID: PMC4462853 DOI: 10.3762/bjnano.6.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
The first experiment showing the effects of specific interaction forces using lateral force microscopy (LFM) was demonstrated for lectin-carbohydrate interactions some years ago. Such measurements are possible under the assumption that specific forces strongly dominate over the non-specific ones. However, obtaining quantitative results requires the complex and tedious calibration of a torsional force. Here, a new and relatively simple method for the calibration of the torsional force is presented. The proposed calibration method is validated through the measurement of the interaction forces between human fibronectin and its monoclonal antibody. The results obtained using LFM and AFM-based classical force spectroscopies showed similar unbinding forces recorded at similar loading rates. Our studies verify that the proposed lateral force calibration method can be applied to study single molecule interactions.
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Affiliation(s)
- Andrzej J Kulik
- Laboratoire de la Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Małgorzata Lekka
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
| | - Kyumin Lee
- Laboratoire de la Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Grazyna Pyka-Fościak
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5/7, 87-100 Toruń, Poland
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27
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Kim Y, Kim ES, Lee Y, Kim JH, Shim BC, Cho SM, Lee JS, Park JW. Reading single DNA with DNA polymerase followed by atomic force microscopy. J Am Chem Soc 2014; 136:13754-60. [PMID: 25203438 DOI: 10.1021/ja5063983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The importance of DNA sequencing in the life sciences and personalized medicine is continually increasing. Single-molecule sequencing methods have been developed to analyze DNA directly without the need for amplification. Here, we present a new approach to sequencing single DNA molecules using atomic force microscopy (AFM). In our approach, four surface-conjugated nucleotides were examined sequentially with a DNA polymerase-immobilized AFM tip. By observing the specific rupture events upon examination of a matching nucleotide, we could determine the template base bound in the polymerase's active site. The subsequent incorporation of the complementary base in solution enabled the next base to be read. Additionally, we observed that the DNA polymerase could incorporate the surface-conjugated dGTP when the applied force was controlled by employing the force-clamp mode.
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Affiliation(s)
- Youngkyu Kim
- School of Interdisciplinary Bioscience and Bioengineering, ‡Department of Chemistry, and §Department of Life Sciences, Pohang University of Science and Technology , San 31 Hyoja-dong, Pohang, 790-784, Korea
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28
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Berardi MJ, Chou JJ. Fatty acid flippase activity of UCP2 is essential for its proton transport in mitochondria. Cell Metab 2014; 20:541-52. [PMID: 25127353 PMCID: PMC4156518 DOI: 10.1016/j.cmet.2014.07.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 01/11/2023]
Abstract
Modulation of cellular energy expenditure is fundamental to normal and pathological cell growth and differentiation. Mitochondria stores energy as a proton gradient across their inner membrane. Uncoupling proteins (UCPs) can dissipate the gradient to produce heat or regulate metabolite fluxes. UCP-mediated proton currents require fatty acids (FAs) and are blocked by nucleotides, but the molecular basis of these processes is unknown. We find, by nuclear magnetic resonance and functional mutagenesis, that UCP2 can bind FAs laterally through its peripheral site, and this intramembrane molecular recognition is essential for UCP2-catalyzed FA flipping across the membrane, which in turn is essential for proton translocation. The antagonist GDP binds inside the UCP2 cavity and perturbs its conformation, which can displace FA from the peripheral site as a mean of inhibiting proton currents. Our data provide a biophysical perspective of the intricate interplay of UCPs, FA, and nucleotides in determining proton fluxes in mitochondria.
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Affiliation(s)
- Marcelo J Berardi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.
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29
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Zhang S, Aslan H, Besenbacher F, Dong M. Quantitative biomolecular imaging by dynamic nanomechanical mapping. Chem Soc Rev 2014; 43:7412-29. [DOI: 10.1039/c4cs00176a] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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30
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Li M, Xiao X, Zhang W, Liu L, Xi N, Wang Y. AFM analysis of the multiple types of molecular interactions involved in rituximab lymphoma therapy on patient tumor cells and NK cells. Cell Immunol 2014; 290:233-44. [PMID: 25117605 DOI: 10.1016/j.cellimm.2014.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/12/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Rituximab is a monoclonal antibody drug approved for the treatment of patients with lymphomas. Rituximab's main killing mechanism is antibody-dependent cellular cytotoxicity (ADCC). During ADCC, rituximab's fragment antigen binding (Fab) region binds to the CD20 antigen on the tumor cell and its fragment crystallizable (Fc) region binds to the Fc receptor (FcR) on the natural killer (NK) cells. In this study, two types of molecular interactions (CD20-rituximab, FcR-rituximab) involved in ADCC were measured simultaneously on cells prepared from biopsy specimens of lymphoma patients by utilizing atomic force microscopy (AFM) with functionalized tips carrying rituximab. NK cells were detected by specific NKp46 fluorescent labeling and tumor cells were detected by specific ROR1 fluorescent labeling. Based on the fluorescence recognition, the binding affinity and distribution of FcRs on NK cells, and CD20 on tumor cells, were quantitatively measured and mapped. The binding affinity and distribution of FcRs (on NK cells) and CD20 (on tumor cells) were associated with rituximab clinical efficacy. The experimental results provide a new approach to simultaneously quantify the multiple types of molecular interactions involved in rituximab ADCC mechanism on patient biopsy cells, which is of potential clinical significance to predict rituximab efficacy for personalized medicine.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiubin Xiao
- Department of Lymphoma, Affiliated Hospital of Military Medical Academy of Sciences, Beijing 100071, China
| | - Weijing Zhang
- Department of Lymphoma, Affiliated Hospital of Military Medical Academy of Sciences, Beijing 100071, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Ning Xi
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China; Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.
| | - Yuechao Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
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31
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ZHANG J, ZHANG BL, TANG JL. Effect of Cancer Drug LHRH-PE40 on the Elasticity of Living HeLa Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(14)60747-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. A single-molecule approach to explore binding, uptake and transport of cancer cell targeting nanotubes. NANOTECHNOLOGY 2014; 25:125704. [PMID: 24577143 DOI: 10.1088/0957-4484/25/12/125704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity.
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Affiliation(s)
- C Lamprecht
- Institute of Biophysics, Johannes Kepler University, A-4020 Linz, Austria. Institute of Materials Science, Christian-Albrechts-University of Kiel, D-24114 Kiel, Germany
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33
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Zhang J, Chtcheglova LA, Zhu R, Hinterdorfer P, Zhang B, Tang J. Nanoscale Organization of Human GnRH-R on Human Bladder Cancer Cells. Anal Chem 2014; 86:2458-64. [DOI: 10.1021/ac403304g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Science, Changchun 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lilia A. Chtcheglova
- Center
for Advanced
Bioanalysis GmbH (CBL), Gruberstrasse
40-42, Linz 4020, Austria
| | - Rong Zhu
- Institute
for Biophysics, Kepler Johannes University of Linz, Gruberstrasse
40-42, Linz 4020, Austria
| | - Peter Hinterdorfer
- Center
for Advanced
Bioanalysis GmbH (CBL), Gruberstrasse
40-42, Linz 4020, Austria
- Institute
for Biophysics, Kepler Johannes University of Linz, Gruberstrasse
40-42, Linz 4020, Austria
| | - Bailin Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Science, Changchun 130022, P.R. China
| | - Jilin Tang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Science, Changchun 130022, P.R. China
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34
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Zoonens M, Comer J, Masscheleyn S, Pebay-Peyroula E, Chipot C, Miroux B, Dehez F. Dangerous liaisons between detergents and membrane proteins. The case of mitochondrial uncoupling protein 2. J Am Chem Soc 2013; 135:15174-82. [PMID: 24021091 DOI: 10.1021/ja407424v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The extraction of membrane proteins from their native environment by detergents is central to their biophysical characterization. Recent studies have emphasized that detergents may perturb the structure locally and modify the dynamics of membrane proteins. However, it remains challenging to determine whether these perturbations are negligible or could be responsible for misfolded conformations, altering the protein's function. In this work, we propose an original strategy combining functional studies and molecular simulations to address the physiological relevance of membrane protein structures obtained in the presence of detergents. We apply our strategy to a structure of isoform 2 of an uncoupling protein (UCP2) binding an inhibitor recently obtained in dodecylphosphocholine detergent micelles. Although this structure shares common traits with the ADP/ATP carrier, a member of the same protein family, its functional and biological significance remains to be addressed. In the present investigation, we demonstrate how dodecylphosphocholine severely alters the structure as well as the function of UCPs. The proposed original strategy opens new vistas for probing the physiological relevance of three-dimensional structures of membrane proteins obtained in non-native environments.
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Affiliation(s)
- Manuela Zoonens
- CNRS UMR 7099, Institut de Biologie Physico Chimique (IBPC), 75005 Paris, France
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