1
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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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2
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Lekka M, Herman K, Zemła J, Bodek Ł, Pyka-Fościak G, Gil D, Dulińska-Litewka J, Ptak A, Laidler P. Probing the recognition specificity of α Vβ 1 integrin and syndecan-4 using force spectroscopy. Micron 2020; 137:102888. [PMID: 32554186 DOI: 10.1016/j.micron.2020.102888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/20/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022]
Abstract
The knowledge on how cells interact with microenvironment is particularly important in understanding the interaction of cancer cells with surrounding stroma, which affects cell migration, adhesion, and metastasis. The main cell surface receptors responsible for the interaction with extracellular matrix (ECM) are integrins, however, they are not the only ones. Integrins are accompanied to other molecules such as syndecans. The role of the latter has not yet been fully established. In our study, we would like to answer the question of whether integrins and syndecans, possessing similar functions, share also similar unbinding properties. By using single molecule force spectroscopy (SMFS), we conducted measurements of the unbinding properties of αVβ1 and syndecan-4 in the interaction with vitronectin (VN), which, as each ECM protein, possesses two binding sites specific to integrins and syndecans. The unbinding force and the kinetic off rate constant derived from SMFS describe the stability of single molecular complex. Obtained data show one barrier transition for each complex. The proposed model shows that the unbinding of αVβ1 from VN proceeds before the unbinding of SDC-4. However, despite different unbinding kinetics, the access to both receptors is needed for cell growth and proliferation.
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Affiliation(s)
- Małgorzata Lekka
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland.
| | - Katarzyna Herman
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznań, Poland
| | - Joanna Zemła
- Department of Biophysical Microstructures, Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - Łukasz Bodek
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Grażyna Pyka-Fościak
- Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034, Kraków, Poland
| | - Dorota Gil
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
| | - Joanna Dulińska-Litewka
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznań, Poland
| | - Piotr Laidler
- Chair of Medical Biochemistry Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
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3
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Koehler M, Lo Giudice C, Vogl P, Ebner A, Hinterdorfer P, Gruber HJ, Alsteens D. Control of Ligand-Binding Specificity Using Photocleavable Linkers in AFM Force Spectroscopy. NANO LETTERS 2020; 20:4038-4042. [PMID: 32320256 PMCID: PMC7252943 DOI: 10.1021/acs.nanolett.0c01426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/21/2020] [Indexed: 05/26/2023]
Abstract
In recent decades, atomic force microscopy (AFM), in particular the force spectroscopy mode, has become a method of choice to study biomolecular interactions at the single-molecule level. However, grafting procedures as well as determining binding specificity remain challenging. We report here an innovative approach based on a photocleavable group that enables in situ release of the ligands bound to the AFM tip and thus allows direct assessment of the binding specificity. Applicable to a wide variety of molecules, the strategy presented here provides new opportunities to study specific interactions and deliver single molecules with high spatiotemporal resolution in a wide range of applications, including AFM-based cell biology.
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Affiliation(s)
- Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Philipp Vogl
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - Andreas Ebner
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | | | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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4
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Deng Y, Wu T, Wang M, Shi S, Yuan G, Li X, Chong H, Wu B, Zheng P. Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level. Nat Commun 2019; 10:2775. [PMID: 31235796 PMCID: PMC6591319 DOI: 10.1038/s41467-019-10696-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
The recent development of chemical and bio-conjugation techniques allows for the engineering of various protein polymers. However, most of the polymerization process is difficult to control. To meet this challenge, we develop an enzymatic procedure to build polyprotein using the combination of a strict protein ligase OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases 1) and a protease TEV (tobacco etch virus). We firstly demonstrate the use of OaAEP1-alone to build a sequence-uncontrolled ubiquitin polyprotein and covalently immobilize the coupled protein on the surface. Then, we construct a poly-metalloprotein, rubredoxin, from the purified monomer. Lastly, we show the feasibility of synthesizing protein polymers with rationally-controlled sequences by the synergy of the ligase and protease, which are verified by protein unfolding using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides a strategy for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanchung Chong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
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5
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Ebner A, Wildling L, Gruber HJ. Functionalization of AFM Tips and Supports for Molecular Recognition Force Spectroscopy and Recognition Imaging. Methods Mol Biol 2019; 1886:117-151. [PMID: 30374865 DOI: 10.1007/978-1-4939-8894-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Linking of sensor molecules (e.g., antibodies) to an AFM tip converts it into a biosensor by which single target molecules (e.g., antigens) can be detected and localized on the sample surface. Moreover, the mechanism of interaction can be studied by force spectroscopy if purified target molecules are linked to an ultra-flat surface, such as mica or silicon (nitride). Rapid imaging of the binding sites and force spectroscopy studies are greatly facilitated if 6-10 nm long polyethylene glycol (PEG) chains are used as flexible tethers between the sensor molecule and the tip. Here, we describe a set of methods by which a variety of proteins, oligonucleotides, or small molecules can be tethered to silicon (nitride) tips or to mica. Methods are included which afford site-specific and oriented coupling of the sensor molecules.
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Affiliation(s)
- A Ebner
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - L Wildling
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - H J Gruber
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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6
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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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7
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8
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Leitner M, Poturnayova A, Lamprecht C, Weich S, Snejdarkova M, Karpisova I, Hianik T, Ebner A. Characterization of the specific interaction between the DNA aptamer sgc8c and protein tyrosine kinase-7 receptors at the surface of T-cells by biosensing AFM. Anal Bioanal Chem 2017; 409:2767-2776. [PMID: 28229174 PMCID: PMC5366180 DOI: 10.1007/s00216-017-0238-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 01/10/2023]
Abstract
We studied the interaction of the specific DNA aptamer sgc8c immobilized at the AFM tip with its corresponding receptor, the protein tyrosine kinase-7 (PTK7) embedded in the membrane of acute lymphoblastic leukemia (ALL) cells (Jurkat T-cells). Performing single molecule force spectroscopy (SMFS) experiments, we showed that the aptamer sgc8c bound with high probability (38.3 ± 7.48%) and high specificity to PTK7, as demonstrated by receptor blocking experiments and through comparison with the binding behavior of a nonspecific aptamer. The determined kinetic off-rate (koff = 5.16 s−1) indicates low dissociation of the sgc8c–PTK7 complex. In addition to the pulling force experiments, simultaneous topography and recognition imaging (TREC) experiments using AFM tips functionalized with sgc8c aptamers were realized on the outer regions surface of surface-immobilized Jurkat cells for the first time. This allowed determination of the distribution of PTK7 without any labeling and at near physiological conditions. As a result, we could show a homogeneous distribution of PTK7 molecules on the outer regions of ALL cells with a surface density of 325 ± 12 PTK7 receptors (or small receptor clusters) per μm2. The specific interaction of the DNA aptamer sgc8c and protein tyrosine kinase-7 (PTK7) on acute lymphoblastic leukemia (ALL) cells was characterized. AFM based single molecule force spectroscopy (SMFS) yielded a kinetic off-rate of 5.16 s−1 of the complex. Simultaneous topography and recognition imaging (TREC) revealed a PTK7 density of 325 ± 12 molecules or clusters per μm2 in the cell membrane ![]()
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Alexandra Poturnayova
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia.,Institute of Biochemistry and Animal Genetics, Slovak Academy of Sciences, Moyzesova 61, 900 28, Ivanka pri Dunaji, Slovakia
| | - Constanze Lamprecht
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Sabine Weich
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Maja Snejdarkova
- Institute of Biochemistry and Animal Genetics, Slovak Academy of Sciences, Moyzesova 61, 900 28, Ivanka pri Dunaji, Slovakia
| | - Ivana Karpisova
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia
| | - Tibor Hianik
- Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska dolina F1, 842 48, Bratislava, Slovakia
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.
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9
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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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10
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Zhang Y, Zhang J, Xing C, Zhang M, Wang L, Zhao H. Protein Nanogels with Temperature-Induced Reversible Structures and Redox Responsiveness. ACS Biomater Sci Eng 2016; 2:2266-2275. [DOI: 10.1021/acsbiomaterials.6b00490] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yue Zhang
- Key
Laboratory of Functional Polymer Materials, Ministry of Education,
College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Jiamin Zhang
- The
Key Laboratory of Bioactive Materials, Ministry of Education, College
of Life Sciences, Nankai University, Tianjin 300071, China
| | - Cheng Xing
- The
Key Laboratory of Bioactive Materials, Ministry of Education, College
of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingming Zhang
- Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China
| | - Lianyong Wang
- The
Key Laboratory of Bioactive Materials, Ministry of Education, College
of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hanying Zhao
- Key
Laboratory of Functional Polymer Materials, Ministry of Education,
College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative
Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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11
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Atomic force microscopy for the investigation of molecular and cellular behavior. Micron 2016; 89:60-76. [DOI: 10.1016/j.micron.2016.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022]
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12
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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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13
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman A, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rong Zhu
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Doris Sinwel
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Peter S. Hasenhuetl
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Vivek Kumar
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Peng Zhang
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH; Mooslackengasse 17 1190 Vienna Austria
| | - Marion Holy
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Andreas Karner
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Hermann J. Gruber
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section; Molecular Targets and Medications Discovery Branch; Intramural Research Program; National Institute on Drug Abuse; Baltimore MD 21224 USA
| | - Harald H. Sitte
- Center of Physiology and Pharmacology; Medical University of Vienna; Waehringerstrasse 13a 1090 Vienna Austria
| | - Peter Hinterdorfer
- Institute for Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
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14
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Zhu R, Sinwel D, Hasenhuetl PS, Saha K, Kumar V, Zhang P, Rankl C, Holy M, Sucic S, Kudlacek O, Karner A, Sandtner W, Stockner T, Gruber HJ, Freissmuth M, Newman AH, Sitte HH, Hinterdorfer P. Nanopharmacological Force Sensing to Reveal Allosteric Coupling in Transporter Binding Sites. Angew Chem Int Ed Engl 2015; 55:1719-22. [PMID: 26695726 DOI: 10.1002/anie.201508755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/11/2015] [Indexed: 11/11/2022]
Abstract
Controversy regarding the number and function of ligand binding sites in neurotransmitter/sodium symporters arose from conflicting data in crystal structures and molecular pharmacology. Here, we have designed novel tools for atomic force microscopy that directly measure the interaction forces between the serotonin transporter (SERT) and the S- and R-enantiomers of citalopram on the single molecule level. This approach is based on force spectroscopy, which allows for the extraction of dynamic information under physiological conditions thus inaccessible via X-ray crystallography. Two distinct populations of characteristic binding strengths of citalopram 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 when accessed in a physiological context. Competition experiments revealed that these two sites are allosterically coupled and exert reciprocal modulation.
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Affiliation(s)
- Rong Zhu
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Doris Sinwel
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Peter S Hasenhuetl
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Kusumika Saha
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Vivek Kumar
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Peng Zhang
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Christian Rankl
- Keysight Technologies Austria GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Marion Holy
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Sonja Sucic
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Oliver Kudlacek
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Andreas Karner
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Thomas Stockner
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Hermann J Gruber
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, 21224, USA
| | - Harald H Sitte
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090, Vienna, Austria
| | - Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria. .,Center for Advanced Bioanalysis, Gruberstrasse 40, 4020, Linz, Austria.
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15
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Formosa C, Dague E. Imaging Living Yeast Cells and Quantifying Their Biophysical Properties by Atomic Force Microscopy. Fungal Biol 2015. [DOI: 10.1007/978-3-319-22437-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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16
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Xiao L, Chen Q, Wu Y, Qi X, Zhou A. Simultaneous topographic and recognition imaging of epidermal growth factor receptor (EGFR) on single human breast cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1988-95. [PMID: 26002322 DOI: 10.1016/j.bbamem.2015.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/27/2015] [Accepted: 05/13/2015] [Indexed: 12/31/2022]
Abstract
Epidermal growth factor receptor (EGFR) plays an important role in signaling pathway of the development of breast cancer cells. Since EGFR overexpresses in most breast cancer cells, it is regarded as a biomarker molecule of breast cancer cells. Here we demonstrated a new AFM technique-topography and recognition (TREC) imaging-to simultaneously obtain highly sensitive and specific molecular recognition images and high-resolution topographic images of EGFR on single breast cancer cells.
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Affiliation(s)
- Lifu Xiao
- Department of Biological Engineering, Utah State University, Logan , UT 84322-4105, USA
| | - Qian Chen
- Department of Biological Engineering, Utah State University, Logan , UT 84322-4105, USA
| | - Yangzhe Wu
- Department of Biological Engineering, Utah State University, Logan , UT 84322-4105, USA
| | - Xiaojun Qi
- Department of Computer Science, Utah State University, Logan, UT 84322-4205, USA
| | - Anhong Zhou
- Department of Biological Engineering, Utah State University, Logan , UT 84322-4105, USA.
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17
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Formosa C, Lachaize V, Galés C, Rols MP, Martin-Yken H, François JM, Duval RE, Dague E. Mapping HA-tagged protein at the surface of living cells by atomic force microscopy. J Mol Recognit 2014; 28:1-9. [DOI: 10.1002/jmr.2407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- C. Formosa
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; UMR 7565, SRSMC; Vandœuvre-lès-Nancy France
- Université de Lorraine; UMR 7565, Faculté de Pharmacie; Nancy France
| | - V. Lachaize
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale U1048; Université Toulouse III Paul Sabatier; 31432 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
| | - C. Galés
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale U1048; Université Toulouse III Paul Sabatier; 31432 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
| | - M. P. Rols
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; IPBS, UMR 5089; 205 route de Narbonne 31077 Toulouse France
| | - H. Martin-Yken
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- INRA; UMR 972 LISBP; Toulouse France
| | - J. M. François
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- INRA; UMR 972 LISBP; Toulouse France
| | - R. E. Duval
- CNRS; UMR 7565, SRSMC; Vandœuvre-lès-Nancy France
- Université de Lorraine; UMR 7565, Faculté de Pharmacie; Nancy France
- ABC Platform®; Nancy France
| | - E. Dague
- CNRS; LAAS; 7 avenue du Colonel Roche 31400 Toulouse France
- Université de Toulouse; LAAS, ITAV, IPBS; 31400 Toulouse France
- CNRS; ITAV; 1 Place Pierre Potier 31000 Toulouse France
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18
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Neundlinger I, Puntheeranurak T, Wildling L, Rankl C, Wang LX, Gruber HJ, Kinne RKH, Hinterdorfer P. Forces and dynamics of glucose and inhibitor binding to sodium glucose co-transporter SGLT1 studied by single molecule force spectroscopy. J Biol Chem 2014; 289:21673-83. [PMID: 24962566 DOI: 10.1074/jbc.m113.529875] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Single molecule force spectroscopy was employed to investigate the dynamics of the sodium glucose co-transporter (SGLT1) upon substrate and inhibitor binding on the single molecule level. CHO cells stably expressing rbSGLT1 were probed by using atomic force microscopy tips carrying either thioglucose, 2'-aminoethyl β-d-glucopyranoside, or aminophlorizin. Poly(ethylene glycol) (PEG) chains of different length and varying end groups were used as tether. Experiments were performed at 10, 25 and 37 °C to address different conformational states of SGLT1. Unbinding forces between ligands and SGLT1 were recorded at different loading rates by changing the retraction velocity, yielding binding probability, width of energy barrier of the binding pocket, and the kinetic off rate constant of the binding reaction. With increasing temperature, width of energy barrier and average life time increased for the interaction of SGLT1 with thioglucose (coupled via acrylamide to a long PEG) but decreased for aminophlorizin binding. The former indicates that in the membrane-bound SGLT1 the pathway to sugar translocation involves several steps with different temperature sensitivity. The latter suggests that also the aglucon binding sites for transport inhibitors have specific, temperature-sensitive conformations.
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Affiliation(s)
- Isabel Neundlinger
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Theeraporn Puntheeranurak
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria, Department of Biology, Faculty of Science, Mahidol University and Nanotec-MU Center of Excellence on Intelligent Materials and Systems, 272 Rama VI, Ratchathewi, Bangkok 10400, Thailand
| | - Linda Wildling
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | | | - Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, and
| | - Hermann J Gruber
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Rolf K H Kinne
- Max Planck Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Peter Hinterdorfer
- From the Institute for Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria,
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19
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Lamprecht C, Hinterdorfer P, Ebner A. Applications of biosensing atomic force microscopy in monitoring drug and nanoparticle delivery. Expert Opin Drug Deliv 2014; 11:1237-53. [PMID: 24809228 DOI: 10.1517/17425247.2014.917078] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The therapeutic effects of medicinal drugs not only depend on their properties, but also on effective transport to the target receptor. Here we highlight recent developments in this discipline and show applications of atomic force microscopy (AFM) that enable us to track the effects of drugs and the effectiveness of nanoparticle delivery at the single molecule level. AREAS COVERED Physiological AFM imaging enables visualization of topographical changes to cells as a result of drug exposure and allows observation of cellular responses that yield morphological changes. When we upgrade the regular measuring tip to a molecular biosensor, it enables investigation of functional changes at the molecular level via single molecule force spectroscopy. EXPERT OPINION Biosensing AFM techniques have generated powerful tools to monitor drug delivery in (living) cells. While technical developments in actual AFM methods have simplified measurements at relevant physiological conditions, understanding both the biological and technical background is still a crucial factor. However, due to its potential impact, we expect the number of application-based biosensing AFM techniques to further increase in the near future.
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Affiliation(s)
- Constanze Lamprecht
- University of Kiel, Institute of Materials Science Biocompatible Nanomaterials , Kaiserstr.2, 24143 Kiel , Germany
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20
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Senapati S, Manna S, Lindsay S, Zhang P. Application of catalyst-free click reactions in attaching affinity molecules to tips of atomic force microscopy for detection of protein biomarkers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14622-30. [PMID: 24180289 PMCID: PMC3886287 DOI: 10.1021/la4039667] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Atomic force microscopy (AFM) has been extensively used in studies of biological interactions. Particularly, AFM based force spectroscopy and recognition imaging can sense biomolecules on a single molecule level, having great potential to become a tool for molecular diagnostics in clinics. These techniques, however, require affinity molecules to be attached to AFM tips in order to specifically detect their targets. The attachment chemistry currently used on silicon tips involves multiple steps of reactions and moisture sensitive chemicals, such as (3-aminopropyl)triethoxysilane (APTES) and N-hydroxysuccinimide (NHS) ester, making the process difficult to operate in aqueous solutions. In the present study, we have developed a user-friendly protocol to functionalize the AFM tips with affinity molecules. A key feature of it is that all reactions are carried out in aqueous solutions. In summary, we first synthesized a molecular anchor composed of cyclooctyne and silatrane for introduction of a chemically reactive function to AFM tips and a bifunctional polyethylene glycol linker that harnesses two orthogonal click reactions, copper free alkyne-azide cycloaddition and thiol-vinylsulfone Michael addition, for attaching affinity molecules to AFM tips. The attachment chemistry was then validated by attaching antithrombin DNA aptamers and cyclo-RGD peptides to silicon nitride (SiN) tips, respectively, and measuring forces of unbinding these affinity molecules from their protein cognates human α-thrombin and human α5β1-integrin immobilized on mica surfaces. In turn, we used the same attachment chemistry to functionalize silicon tips with the same affinity molecules for AFM based recognition imaging, showing that the disease-relevant biomarkers such as α-thrombin and α5β1-integrin can be detected with high sensitivity and specificity by the single molecule technique. These studies demonstrate the feasibility of our attachment chemistry for the use in functionalization of AFM tips with affinity molecules.
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Affiliation(s)
- Subhadip Senapati
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Saikat Manna
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Peiming Zhang
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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21
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Pollheimer P, Taskinen B, Scherfler A, Gusenkov S, Creus M, Wiesauer P, Zauner D, Schöfberger W, Schwarzinger C, Ebner A, Tampé R, Stutz H, Hytönen VP, Gruber HJ. Reversible biofunctionalization of surfaces with a switchable mutant of avidin. Bioconjug Chem 2013; 24:1656-68. [PMID: 23978112 DOI: 10.1021/bc400087e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Label-free biosensors detect binding of prey molecules (″analytes″) to immobile bait molecules on the sensing surface. Numerous methods are available for immobilization of bait molecules. A convenient option is binding of biotinylated bait molecules to streptavidin-functionalized surfaces, or to biotinylated surfaces via biotin-avidin-biotin bridges. The goal of this study was to find a rapid method for reversible immobilization of biotinylated bait molecules on biotinylated sensor chips. The task was to establish a biotin-avidin-biotin bridge which was easily cleaved when desired, yet perfectly stable under a wide range of measurement conditions. The problem was solved with the avidin mutant M96H which contains extra histidine residues at the subunit-subunit interfaces. This mutant was bound to a mixed self-assembled monolayer (SAM) containing biotin residues on 20% of the oligo(ethylene glycol)-terminated SAM components. Various biotinylated bait molecules were bound on top of the immobilized avidin mutant. The biotin-avidin-biotin bridge was stable at pH ≥3, and it was insensitive to sodium dodecyl sulfate (SDS) at neutral pH. Only the combination of citric acid (2.5%, pH 2) and SDS (0.25%) caused instantaneous cleavage of the biotin-avidin-biotin bridge. As a consequence, the biotinylated bait molecules could be immobilized and removed as often as desired, the only limit being the time span for reproducible chip function when kept in buffer (2-3 weeks at 25 °C). As expected, the high isolectric pH (pI) of the avidin mutant caused nonspecific adsorption of proteins. This problem was solved by acetylation of avidin (to pI < 5), or by optimization of SAM formation and passivation with biotin-BSA and BSA.
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Affiliation(s)
- Philipp Pollheimer
- Institute of Biophysics, Johannes Kepler University , Gruberstr. 40, 4020 Linz, Austria
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22
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Li Y, Qiao H, Yan W, Zhang J, Xing C, Wang H, Zhang B, Tang J. Molecular recognition force spectroscopy study of the dynamic interaction between aptamer GBI-10 and extracellular matrix protein tenascin-C on human glioblastoma cell. J Mol Recognit 2013; 26:46-50. [PMID: 23280617 DOI: 10.1002/jmr.2242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/04/2012] [Accepted: 09/16/2012] [Indexed: 11/09/2022]
Abstract
Molecular recognition force spectroscopy (MR-FS) was applied to investigate the dynamic interaction between aptamer GBI-10 and tenascin-C (TN-C) on human glioblastoma cell surface at single-molecule level. The unbinding force between aptamer GBI-10 and TN-C was 39 pN at the loading rate of 0.3 nN sec⁻¹. A series of kinetic parameters concerning interaction process such as the unbinding force f(u) , the association rate constant k(on) , dissociation rate constant at zero force k(off) , and dissociation constant K(D) for aptamer GBI-10/TN-C complexes were acquired. In addition, the interaction of aptamer GBI-10 with TN-C depended on the presence of Mg²⁺. This work demonstrates that MR-FS can be used as an attractive tool for exploring the interaction forces and dynamic process of aptamer and ligand at the single-molecule level. As a future perspective, MR-FS may be used as a potential diagnostic and therapeutic tool by combining with other techniques.
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Affiliation(s)
- Yongjun Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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23
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Scholl ZN, Marszalek PE. Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions. Ultramicroscopy 2013; 136:7-14. [PMID: 24001740 DOI: 10.1016/j.ultramic.2013.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 12/30/2022]
Abstract
The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.
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Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
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24
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Attwood SJ, Simpson AMC, Hamaia S, Bihan D, Roy D, Farndale R, Welland ME. Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy. Int J Mol Sci 2013; 14:2832-45. [PMID: 23434650 PMCID: PMC3588017 DOI: 10.3390/ijms14022832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/08/2013] [Accepted: 01/21/2013] [Indexed: 11/17/2022] Open
Abstract
The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.
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Affiliation(s)
- Simon J. Attwood
- Nanoscience Centre, Department of Engineering, Cambridge University, Cambridge, CB3 0FF, UK; E-Mail:
| | - Anna M. C. Simpson
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (S.W.H.); (D.B.)
| | - SamirW. Hamaia
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (S.W.H.); (D.B.)
| | - Dominique Bihan
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (S.W.H.); (D.B.)
| | - Debdulal Roy
- National Physical Laboratory, Teddington, TW11 0LW, UK; E-Mail:
| | - RichardW. Farndale
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (S.W.H.); (D.B.)
- Authors to whom correspondence should be addressed; E-Mails: (R.W.F.); (M.E.W.); Tel.: +44-1223-766111 (R.W.F.); +44-1223-760305 (M.E.W.); Fax: +44 -1223-760309 (M.E.W.)
| | - Mark E. Welland
- Nanoscience Centre, Department of Engineering, Cambridge University, Cambridge, CB3 0FF, UK; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (R.W.F.); (M.E.W.); Tel.: +44-1223-766111 (R.W.F.); +44-1223-760305 (M.E.W.); Fax: +44 -1223-760309 (M.E.W.)
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25
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Attwood SJ, Simpson AMC, Stone R, Hamaia S, Roy D, Farndale R, Ouberai M, Welland ME. A simple bioconjugate attachment protocol for use in single molecule force spectroscopy experiments based on mixed self-assembled monolayers. Int J Mol Sci 2012. [PMID: 23202965 PMCID: PMC3497339 DOI: 10.3390/ijms131013521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin.
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Affiliation(s)
- Simon J. Attwood
- Nanoscience Centre, Department of Engineering, Cambridge University, Cambridge, CB3 0FF, UK; E-Mails: (S.J.A.); (M.O.)
| | - Anna M. C. Simpson
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (R.S.); (S.W.H.); (R.W.F.)
| | - Rachael Stone
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (R.S.); (S.W.H.); (R.W.F.)
| | - SamirW. Hamaia
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (R.S.); (S.W.H.); (R.W.F.)
| | - Debdulal Roy
- National Physical Laboratory, Teddington, TW11 0LW, UK; E-Mail:
| | - RichardW. Farndale
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, UK; E-Mails: (A.M.C.S.); (R.S.); (S.W.H.); (R.W.F.)
| | - Myriam Ouberai
- Nanoscience Centre, Department of Engineering, Cambridge University, Cambridge, CB3 0FF, UK; E-Mails: (S.J.A.); (M.O.)
| | - Mark E. Welland
- Nanoscience Centre, Department of Engineering, Cambridge University, Cambridge, CB3 0FF, UK; E-Mails: (S.J.A.); (M.O.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-1223-760305; Fax: +44 -1223-760309
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26
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Moreau ALD, Janissen R, Santos CA, Peroni LA, Stach-Machado DR, de Souza AA, de Souza AP, Cotta MA. Highly-sensitive and label-free indium phosphide biosensor for early phytopathogen diagnosis. Biosens Bioelectron 2012; 36:62-8. [PMID: 22538056 DOI: 10.1016/j.bios.2012.03.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 03/23/2012] [Accepted: 03/26/2012] [Indexed: 11/30/2022]
Abstract
The development of highly-sensitive and label-free operating semiconductor-based, biomaterial detecting sensors has important applications in areas such as environmental science, biomedical research and medical diagnostics. In the present study, we developed an Indium Phosphide (InP) semiconductor-based resistive biosensor using the change of its electronic properties upon biomaterial adsorption as sensing element. To detect biomaterial at low concentrations, the procedure of functionalization and covalent biomolecule immobilization was also optimized to guarantee high molecule density and high reproducibility which are prerequisite for reliable results. The characterization, such as biomolecular conjugation efficiency, detection concentration limits, receptor:ligand specificity and concentration detection range was analyzed by using three different biological systems: i) synthetic dsDNA and two phytopathogenic diseases, ii) the severe CB-form of Citrus Tristeza Virus (CTV) and iii) Xylella fastidiosa, both causing great economic loss worldwide. The experimental results show a sensitivity of 1 pM for specific ssDNA detection and about 2 nM for the specific detection of surface proteins of CTV and X. fastidiosa phytopathogens. A brief comparison with other semiconductor based biosensors and other methodological approaches is discussed and confirms the high sensitivity and reproducibility of our InP based biosensor which could be suitable for reliable early infection diagnosis in environmental and life sciences.
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Affiliation(s)
- Alberto L D Moreau
- Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, 13083-859, Campinas, SP, Brazil.
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27
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Intracellular nucleic acid interactions facilitated by quantum dots: conceptualizing theranostics. Ther Deliv 2012; 3:479-99. [DOI: 10.4155/tde.12.15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The concept of theranostics arises from the unification of both diagnostic and therapeutic applications into a single package. The implementation of nanoparticles, such as semiconductor quantum dots (QDs), to achieve theranostic applications, offers great potential for development of methods that are suitable for personalized medicine. Researchers have taken advantage of the physiochemical properties of QDs to elicit novel bioconjugation techniques that enable the attachment of multifunctional moieties on the surface of QDs. In this review, the diagnostic and therapeutic applications of QDs that feature the use of nucleic acids are highlighted with a particular emphasis on the possibility of combinatorial applications. Nucleic acid research is of particular interest for gene therapy, and is relevant to the understanding of gene regulation pathways and gene expression dynamics. Recent toxicity studies featuring multifunctional QDs are also examined. Future perspectives discussing the expected development of this field conclude the article.
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28
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Wildling L, Rankl C, Haselgrübler T, Gruber HJ, Holy M, Newman AH, Zou MF, Zhu R, Freissmuth M, Sitte HH, Hinterdorfer P. Probing binding pocket of serotonin transporter by single molecular force spectroscopy on living cells. J Biol Chem 2011; 287:105-113. [PMID: 22033932 PMCID: PMC3249061 DOI: 10.1074/jbc.m111.304873] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The serotonin transporter (SERT) terminates neurotransmission by removing serotonin from the synaptic cleft. In addition, it is the site of action of antidepressants (which block the transporter) and of amphetamines (which induce substrate efflux). The interaction energies involved in binding of such compounds to the transporter are unknown. Here, we used atomic force microscopy (AFM) to probe single molecular interactions between the serotonin transporter and MFZ2-12 (a potent cocaine analog) in living CHOK1 cells. For the AFM measurements, MFZ2-12 was immobilized on AFM tips by using a heterobifunctional cross-linker. By varying the pulling velocity in force distance cycles drug-transporter complexes were ruptured at different force loadings allowing for mapping of the interaction energy landscape. We derived chemical rate constants from these recordings and compared them with those inferred from inhibition of transport and ligand binding: koff values were in good agreement with those derived from uptake experiments; in contrast, the kon values were scaled down when determined by AFM. Our observations generated new insights into the energy landscape of the interaction between SERT and inhibitors. They thus provide a useful framework for molecular dynamics simulations by exploring the range of forces and energies that operate during the binding reaction.
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Affiliation(s)
- Linda Wildling
- Institute for Biophysics, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
| | - Christian Rankl
- Agilent Technologies, Austria GmbH, Aubrunnerweg 11, 4040 Linz, Austria
| | | | - Hermann J Gruber
- Institute for Biophysics, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
| | - Marion Holy
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090 Vienna, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, Maryland 21224
| | - Mu-Fa Zou
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, Intramural Research Program, National Institute on Drug Abuse, Baltimore, Maryland 21224
| | - Rong Zhu
- Institute for Biophysics, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090 Vienna, Austria
| | - Harald H Sitte
- Center of Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse 13a, 1090 Vienna, Austria
| | - Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria; Center for Advanced Bioanalysis, Scharitzerstrasse 6-8, 4020 Linz, Austria.
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Puntheeranurak T, Neundlinger I, Kinne RKH, Hinterdorfer P. Single-molecule recognition force spectroscopy of transmembrane transporters on living cells. Nat Protoc 2011; 6:1443-52. [PMID: 21886107 DOI: 10.1038/nprot.2011.370] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Atomic force microscopy (AFM) has proven to be a powerful tool in biological sciences. Its particular advantage over other high-resolution methods commonly used is that biomolecules can be investigated not only under physiological conditions but also while they perform their biological functions. Single-molecule force spectroscopy with AFM tip-modification techniques can provide insight into intermolecular forces between individual ligand-receptor pairs of biological systems. Here we present protocols for force spectroscopy of living cells, including cell sample preparation, tip chemistry, step-by-step AFM imaging, force spectroscopy and data analysis. We also delineate critical steps and describe limitations that we have experienced. The entire protocol can be completed in 12 h. The model studies discussed here demonstrate the power of AFM for studying transmembrane transporters at the single-molecule level.
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Wildling L, Unterauer B, Zhu R, Rupprecht A, Haselgrübler T, Rankl C, Ebner A, Vater D, Pollheimer P, Pohl EE, Hinterdorfer P, Gruber HJ. Linking of sensor molecules with amino groups to amino-functionalized AFM tips. Bioconjug Chem 2011; 22:1239-48. [PMID: 21542606 PMCID: PMC3115690 DOI: 10.1021/bc200099t] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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The measuring tip of an atomic force microscope (AFM) can be upgraded to a specific biosensor by attaching one or a few biomolecules to the apex of the tip. The biofunctionalized tip is then used to map cognate target molecules on a sample surface or to study biophysical parameters of interaction with the target molecules. The functionality of tip-bound sensor molecules is greatly enhanced if they are linked via a thin, flexible polymer chain. In a typical scheme of tip functionalization, reactive groups are first generated on the tip surface, a bifunctional cross-linker is then attached with one of its two reactive ends, and finally the probe molecule of interest is coupled to the free end of the cross-linker. Unfortunately, the most popular functional group generated on the tip surface is the amino group, while at the same time, the only useful coupling functions of many biomolecules (such as antibodies) are also NH2 groups. In the past, various tricks or detours were applied to minimize the undesired bivalent reaction of bifunctional linkers with adjacent NH2 groups on the tip surface. In the present study, an uncompromising solution to this problem was found with the help of a new cross-linker (“acetal-PEG-NHS”) which possesses one activated carboxyl group and one acetal-protected benzaldehyde function. The activated carboxyl ensures rapid unilateral attachment to the amino-functionalized tip, and only then is the terminal acetal group converted into the amino-reactive benzaldehyde function by mild treatment (1% citric acid, 1–10 min) which does not harm the AFM tip. As an exception, AFM tips with magnetic coating become demagnetized in 1% citric acid. This problem was solved by deprotecting the acetal group before coupling the PEG linker to the AFM tip. Bivalent binding of the corresponding linker (“aldehyde-PEG-NHS”) to adjacent NH2 groups on the tip was largely suppressed by high linker concentrations. In this way, magnetic AFM tips could be functionalized with an ethylene diamine derivative of ATP which showed specific interaction with mitochondrial uncoupling protein 1 (UCP1) that had been purified and reconstituted in a mica-supported planar lipid bilayer.
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Affiliation(s)
- Linda Wildling
- Institute of Biophysics, J. Kepler University, Altenberger Str. 69, A-4040 Linz, Austria
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31
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Rosso M, Nguyen AT, de Jong E, Baggerman J, Paulusse JMJ, Giesbers M, Fokkink RG, Norde W, Schroën K, van Rijn CJM, Zuilhof H. Protein-repellent silicon nitride surfaces: UV-induced formation of oligoethylene oxide monolayers. ACS APPLIED MATERIALS & INTERFACES 2011; 3:697-704. [PMID: 21309535 DOI: 10.1021/am100985c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The grafting of polymers and oligomers of ethylene oxide onto surfaces is widely used to prevent nonspecific adsorption of biological material on sensors and membrane surfaces. In this report, we show for the first time the robust covalent attachment of short oligoethylene oxide-terminated alkenes (CH(3)O(CH(2)CH(2)O)(3)(CH(2))(11)-(CH═CH(2)) [EO(3)] and CH(3)O(CH(2)CH(2)O)(6)(CH(2))(11)-(CH═CH(2)) [EO(6)]) from the reaction of alkenes onto silicon-rich silicon nitride surfaces at room temperature using UV light. Reflectometry is used to monitor in situ the nonspecific adsorption of bovine serum albumin (BSA) and fibrinogen (FIB) onto oligoethylene oxide coated silicon-rich silicon nitride surfaces (EO(n)-Si(x)N(4), x > 3) in comparison with plasma-oxidized silicon-rich silicon nitride surfaces (SiO(y)-Si(x)N(4)) and hexadecane-coated Si(x)N(4) surfaces (C(16)-Si(x)N(4)). A significant reduction in protein adsorption on EO(n)-Si(x)N(4) surfaces was achieved, adsorption onto EO(3)-Si(x)N(4) and EO(6)-Si(x)N(4) were 0.22 mg m(-2) and 0.08 mg m(-2), respectively. The performance of the obtained EO(3) and EO(6) layers is comparable to those of similar, highly protein-repellent monolayers formed on gold and silver surfaces. EO(6)-Si(x)N(4) surfaces prevented significantly the adsorption of BSA (0.08 mg m(-2)). Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), X-ray reflectivity and static water contact angle measurements were employed to characterize the modified surfaces. In addition, the stability of EO(6)-Si(x)N(4) surfaces in phosphate-buffered saline solution (PBS) and alkaline condition (pH 10) was studied. Prolonged exposure of the surfaces to PBS solution for 1 week or alkaline condition for 2 h resulted in only minor degradation of the ethylene oxide moieties and no oxidation of the Si(x)N(4) substrates was observed. Highly stable antifouling coatings on Si(x)N(4) surfaces significantly broaden the application potential of silicon nitride-coated microdevices, and in particular of microfabricated filtration membranes.
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Affiliation(s)
- Michel Rosso
- Laboratory of Organic Chemistry, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands
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32
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Li Y, Wang J, Xing C, Wang Z, Wang H, Zhang B, Tang J. Molecular Recognition Force Spectroscopy Study of the Specific Lectin and Carbohydrate Interaction in a Living Cell. Chemphyschem 2011; 12:909-12. [DOI: 10.1002/cphc.201001008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/29/2011] [Indexed: 01/06/2023]
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Boyle MM, Smaldone RA, Whalley AC, Ambrogio MW, Botros YY, Stoddart JF. Mechanised materials. Chem Sci 2011. [DOI: 10.1039/c0sc00453g] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Abstract
Atomic force microscopy (AFM) works by scanning a very tiny tip over a surface with great precision. The microscope tips can be chemically functionalized to improve the images obtained. Well-defined chemical functionalization of AFM tips is especially important for experiments, such as chemical force microscopy and single molecule recognition force microscopy, to examine specific interactions at the single molecular level. In this chapter, we present an overview of chemical modifications of tips that have been reported to date with regards to the proper fixation of probe molecules, focusing particularly on chemical procedures developed to anchor biological molecules on AFM tips.
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Affiliation(s)
- Régis Barattin
- Département de chimie, Université Laval, Quebec, QC, Canada
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35
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Abstract
Protein-protein interactions are the basis of both biochemical and biophysical signaling of living cells. In many cases, the receptor is present on the cell surface while the ligand is in solution or linked to another support (extracellular matrix or another cell). In the case of cellular adhesion, forces are continuously applied to receptor-ligand complexes and, as a consequence, the dissociation kinetics of the bonds may change. It is, thus, relevant to study the kinetics of protein-protein interactions in response to applied forces, as this is the most physiologically relevant situation. The atomic force microscope (AFM) was one of the first nanotools to be applied to this end. However, new approaches need to be developed to better understand the complex energy landscape of molecular interactions under applied stress. In this chapter, we described the use of the AFM to carry out force-clamp measurements on receptor-ligand bonds. Force-clamp measurements on bonds consist of applying a constant and controlled force to a receptor-ligand bond and measure the resulting dissociation lifetime. The described methods include the required materials, functionalization of tips and substrates, force-clamping measurements, and processing and interpretation of the results. An illustrative example is given with the well-studied streptavidin-biotin complex.
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Affiliation(s)
- Félix Rico
- Miller School of Medicine, University of Miami, Miami, FL, USA
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36
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Ghosh SK, Ostanin VP, Seshia AA. Anharmonic Surface Interactions for Biomolecular Screening and Characterization. Anal Chem 2010; 83:549-54. [DOI: 10.1021/ac102261q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sourav K. Ghosh
- University of Cambridge Nanoscience Centre, 11 J J Thomson Avenue, Cambridge, Cambridgeshire, United Kingdom, CB3 0FF
| | - Victor P. Ostanin
- University of Cambridge Nanoscience Centre, 11 J J Thomson Avenue, Cambridge, Cambridgeshire, United Kingdom, CB3 0FF
| | - Ashwin A. Seshia
- University of Cambridge Nanoscience Centre, 11 J J Thomson Avenue, Cambridge, Cambridgeshire, United Kingdom, CB3 0FF
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37
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Boyd RD, Winkless L, Cuenat A, Kazakova O. Mapping the placement of oligonucleotide molecules using scanning probe microscopy. Colloids Surf B Biointerfaces 2010; 83:10-5. [PMID: 21106351 DOI: 10.1016/j.colsurfb.2010.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/30/2010] [Accepted: 10/11/2010] [Indexed: 10/18/2022]
Abstract
The successful development of novel bio-inspired devices requires the ability to place specific biomolecules on a substrate with nanometre precision, in such a way so that their bioactivity is retained. A method is required that can verify this bio-modification. Scanning probe microscopy (SPM) can image and probe a surface in a liquid environment with nanometre resolution. Using short chain complementary oligonucleotides as the bioactive molecules we have modified continuous and patterned gold substrates and SPM probes. We demonstrated that the attached oligonucleotides retained their biological activity after surface attachment with a hybridization interaction force that varies between 50 and 400pN as measured by SPM force measurements. Finally, the position of the attached oligonucleotides was determined with nanometre resolution. Thus we have demonstrated the capabilities of SPM in the application of the development of substrates and templates suitable for forming the basis of novel and innovative devices.
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Affiliation(s)
- Robert D Boyd
- The National Physical Laboratory, Teddington, Middlesex, TW11 0LW, UK.
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38
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Byeon JY, Limpoco FT, Bailey RC. Efficient bioconjugation of protein capture agents to biosensor surfaces using aniline-catalyzed hydrazone ligation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15430-5. [PMID: 20809595 PMCID: PMC2947609 DOI: 10.1021/la1021824] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Aniline-catalyzed hydrazone ligation between surface-immobilized hydrazines and aldehyde-modified antibodies is shown to be an efficient method for attaching protein capture agents to model oxide-coated biosensor substrates. Silicon photonic microring resonators are used to directly evaluate the efficiency of this surface bioconjugate reaction at various pHs and in the presence or absence of aniline as a nucleophilic catalyst. It is found that aniline significantly increases the net antibody loading for surfaces functionalized over a pH range from 4.5 to 7.4, allowing derivatization of substrates with reduced incubation time and sample consumption. This increase in antibody loading directly results in more sensitive antigen detection when functionalized microrings are employed in a label-free immunoassay. Furthermore, these experiments also reveal an interesting pH-dependent noncovalent binding trend that plays an important role in dictating the amount of antibody attached onto the substrate, highlighting the competing contributions of the bioconjugate reaction rate and the dynamic interactions that control opportunities for a solution-phase biomolecule to react with a substrate-bound reagent.
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Affiliation(s)
- Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - F. T. Limpoco
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
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40
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Jung J, Solanki A, Memoli KA, Kamei KI, Kim H, Drahl MA, Williams LJ, Tseng HR, Lee K. Selective inhibition of human brain tumor cells through multifunctional quantum-dot-based siRNA delivery. Angew Chem Int Ed Engl 2010; 49:103-7. [PMID: 19950159 DOI: 10.1002/anie.200905126] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jongjin Jung
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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41
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Hofer M, Adamsmaier S, van Zanten TS, Chtcheglova LA, Manzo C, Duman M, Mayer B, Ebner A, Moertelmaier M, Kada G, Garcia-Parajo MF, Hinterdorfer P, Kienberger F. Molecular recognition imaging using tuning fork-based transverse dynamic force microscopy. Ultramicroscopy 2010; 110:605-11. [PMID: 20226591 DOI: 10.1016/j.ultramic.2010.02.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We demonstrate simultaneous transverse dynamic force microscopy and molecular recognition imaging using tuning forks as piezoelectric sensors. Tapered aluminum-coated glass fibers were chemically functionalized with biotin and anti-lysozyme molecules and attached to one of the prongs of a 32kHz tuning fork. The lateral oscillation amplitude of the tuning fork was used as feedback signal for topographical imaging of avidin aggregates and lysozyme molecules on mica substrate. The phase difference between the excitation and detection signals of the tuning fork provided molecular recognition between avidin/biotin or lysozyme/anti-lysozyme. Aggregates of avidin and lysozyme molecules appeared as features with heights of 1-4nm in the topographic images, consistent with single molecule atomic force microscopy imaging. Recognition events between avidin/biotin or lysozyme/anti-lysozyme were detected in the phase image at high signal-to-noise ratio with phase shifts of 1-2 degrees. Because tapered glass fibers and shear-force microscopy based on tuning forks are commonly used for near-field scanning optical microscopy (NSOM), these results open the door to the exciting possibility of combining optical, topographic and biochemical recognition at the nanometer scale in a single measurement and in liquid conditions.
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Affiliation(s)
- Manuel Hofer
- University of Linz, Institute for Biophysics, Altenbergerstr. 69, Linz, Austria
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42
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43
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Jung J, Solanki A, Memoli K, Kamei KI, Kim H, Drahl M, Williams L, Tseng HR, Lee K. Selective Inhibition of Human Brain Tumor Cells through Multifunctional Quantum-Dot-Based siRNA Delivery. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905126] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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44
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Lamprecht C, Liashkovich I, Neves V, Danzberger J, Heister E, Rangl M, Coley HM, McFadden J, Flahaut E, Gruber HJ, Hinterdorfer P, Kienberger F, Ebner A. AFM imaging of functionalized carbon nanotubes on biological membranes. NANOTECHNOLOGY 2009; 20:434001. [PMID: 19801758 DOI: 10.1088/0957-4484/20/43/434001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging.
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Affiliation(s)
- C Lamprecht
- Institute of Biophysics, J Kepler University, Linz, Austria
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45
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Tang J, Ebner A, Kraxberger B, Leitner M, Hykollari A, Kepplinger C, Grunwald C, Gruber HJ, Tampé R, Sleytr UB, Ilk N, Hinterdorfer P. Detection of metal binding sites on functional S-layer nanoarrays using single molecule force spectroscopy. J Struct Biol 2009; 168:217-22. [DOI: 10.1016/j.jsb.2009.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/02/2009] [Accepted: 02/05/2009] [Indexed: 11/25/2022]
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46
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Lamprecht C, Danzberger J, Lukanov P, Tîlmaciu CM, Galibert AM, Soula B, Flahaut E, Gruber H, Hinterdorfer P, Ebner A, Kienberger F. AFM imaging of functionalized double-walled carbon nanotubes. Ultramicroscopy 2009; 109:899-906. [DOI: 10.1016/j.ultramic.2009.03.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Preiner J, Ebner A, Chtcheglova L, Zhu R, Hinterdorfer P. Simultaneous topography and recognition imaging: physical aspects and optimal imaging conditions. NANOTECHNOLOGY 2009; 20:215103. [PMID: 19423924 DOI: 10.1088/0957-4484/20/21/215103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Simultaneous topography and recognition imaging (TREC) allows for the investigation of receptor distributions on natural biological surfaces under physiological conditions. Based on atomic force microscopy (AFM) in combination with a cantilever tip carrying a ligand molecule, it enables us to sense topography and recognition of receptor molecules simultaneously with nanometre accuracy. In this study we introduce optimized handling conditions and investigate the physical properties of the cantilever-tip-sample ensemble, which is essential for the interpretation of the experimental data gained from this technique. In contrast to conventional AFM methods, TREC is based on a more sophisticated feedback loop, which enables us to discriminate topographical contributions from recognition events in the AFM cantilever motion. The features of this feedback loop were investigated through a detailed analysis of the topography and recognition data obtained on a model protein system. Single avidin molecules immobilized on a mica substrate were imaged with an AFM tip functionalized with a biotinylated IgG. A simple procedure for adjusting the optimal amplitude for TREC imaging is described by exploiting the sharp localization of the TREC signal within a small range of oscillation amplitudes. This procedure can also be used for proving the specificity of the detected receptor-ligand interactions. For understanding and eliminating topographical crosstalk in the recognition images we developed a simple theoretical model, which nicely explains its origin and its dependence on the excitation frequency.
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Affiliation(s)
- Johannes Preiner
- Christian Doppler Laboratory for Nanoscopic Methods in Biophysics, Johannes Kepler University of Linz, Linz, Austria
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48
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Optimized straight forward procedure for covalent surface immobilization of different biomolecules for single molecule applications. Colloids Surf B Biointerfaces 2009; 71:200-7. [PMID: 19329289 DOI: 10.1016/j.colsurfb.2009.02.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/05/2009] [Accepted: 02/10/2009] [Indexed: 11/20/2022]
Abstract
Covalent chemisorption of biomolecules to surfaces with high density and low unspecific background is prerequisite for most optical and mechanical single molecule experiments and accordingly, many recipes have been developed. However, new establishment of the surface functionalization process in the lab usually is still difficult and time consuming due to the complex procedures containing many pitfalls. Therefore, based on the known recipes, we developed and optimized a simple straight forward protocol. We demonstrated it resulting in a high density of the coupled biomolecules, homogeneous surfaces and a low unspecific background when binding nucleic acids, peptides and proteins. The protocol was optimized for borosilicate cover glasses and silicon nitride atomic force microscope cantilevers commonly used in single molecule experiments and takes advantage of commonly used chemicals. It consists of only four steps, silanol group generation, amination, grafting of poly(ethylene glycol) to the surface and biomolecule coupling. All individual steps were optimized comparing different variations partially described in the literature. Finally, a detailed description is provided which allows avoiding most sources of contamination, often being a main hurdle on the way to single molecule experiments.
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49
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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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50
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Tang J, Ebner A, Badelt-Lichtblau H, Völlenkle C, Rankl C, Kraxberger B, Leitner M, Wildling L, Gruber HJ, Sleytr UB, Ilk N, Hinterdorfer P. Recognition imaging and highly ordered molecular templating of bacterial S-layer nanoarrays containing affinity-tags. NANO LETTERS 2008; 8:4312-4319. [PMID: 19367846 DOI: 10.1021/nl802092c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Functional nanoarrays were fabricated using the chimeric bacterial cell surface layer (S-layer) protein rSbpA fused with the affinity tag Strep-tagII and characterized using various atomic force microscopy (AFM) techniques in aqueous environment. The accessibility of Strep-tagII was verified by single-molecule force spectroscopy studies employing Strep-Tactin as specific ligand. Simultaneous topography and recognition imaging (TREC) of the nanoarray yielded high resolution maps of the Strep-tagll binding sites with a positional accuracy of 1.5 nm. The nanoarrays were used as template for constructing highly ordered molecular binding blocks.
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Affiliation(s)
- Jilin Tang
- Institute of Biophysics, Johannes Kepler University of Linz, 4040 Linz, Austria
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