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Hou D, Cao W, Kim S, Cui X, Ziarnik M, Im W, Zhang XF. Biophysical investigation of interactions between SARS-CoV-2 spike protein and neuropilin-1. Protein Sci 2023; 32:e4773. [PMID: 37656811 PMCID: PMC10510470 DOI: 10.1002/pro.4773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Recent studies have suggested that neuropilin-1 (NRP1) may serve as a potential receptor in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the biophysical characteristics of interactions between NRP1 and SARS-CoV-2 remain unclear. In this study, we examined the interactions between NRP1 and various SARS-CoV-2 spike (S) fragments, including the receptor-binding domain (RBD) and the S protein trimer in a soluble form or expressed on pseudovirions, using atomic force microscopy and structural modeling. Our measurements shows that NRP1 interacts with the RBD and trimer at a higher binding frequency (BF) compared to ACE2. This NRP1-RBD interaction has also been predicted and simulated via AlphaFold2 and molecular dynamics simulations, and the results indicate that their binding patterns are very similar to RBD-ACE2 interactions. Additionally, under similar loading rates, the most probable unbinding forces between NRP1 and S trimer (both soluble form and on pseudovirions) are larger than the forces between NRP1 and RBD and between trimer and ACE2. Further analysis indicates that NRP1 has a stronger binding affinity to the SARS-CoV-2 S trimer with a dissociation rate of 0.87 s-1 , four times lower than the dissociation rate of 3.65 s-1 between NRP1 and RBD. Moreover, additional experiments show that RBD-neutralizing antibodies can significantly reduce the BF for both ACE2 and NRP1. Together, the study suggests that NRP1 can be an alternative receptor for SARS-CoV-2 attachment to human cells, and the neutralizing antibodies targeting SARS-CoV-2 RBD can reduce the binding between SARS-CoV-2 and NRP1.
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Affiliation(s)
- Decheng Hou
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Wenpeng Cao
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Xinyu Cui
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Matthew Ziarnik
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Departments of Biological Sciences, Chemistry, and Computer Science and EngineeringLehigh UniversityBethlehemUSA
| | - X. Frank Zhang
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
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2
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Serrano MP, Subramanian S, von Bilderling C, Rafti M, Vollmer F. "Grafting-To" Covalent Binding of Plasmonic Nanoparticles onto Silica WGM Microresonators: Mechanically Robust Single-Molecule Sensors and Determination of Activation Energies from Single-Particle Events. SENSORS (BASEL, SWITZERLAND) 2023; 23:3455. [PMID: 37050513 PMCID: PMC10098601 DOI: 10.3390/s23073455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/27/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
We hereby present a novel "grafting-to"-like approach for the covalent attachment of plasmonic nanoparticles (PNPs) onto whispering gallery mode (WGM) silica microresonators. Mechanically stable optoplasmonic microresonators were employed for sensing single-particle and single-molecule interactions in real time, allowing for the differentiation between binding and non-binding events. An approximated value of the activation energy for the silanization reaction occurring during the "grafting-to" approach was obtained using the Arrhenius equation; the results agree with available values from both bulk experiments and ab initio calculations. The "grafting-to" method combined with the functionalization of the plasmonic nanoparticle with appropriate receptors, such as single-stranded DNA, provides a robust platform for probing specific single-molecule interactions under biologically relevant conditions.
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Affiliation(s)
- Mariana P. Serrano
- INIFTA-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata B1900, Argentina
| | - Sivaraman Subramanian
- Living Systems Institute, Department of Physics & Astronomy, University of Exeter, Exeter EX4 4QD, UK
| | - Catalina von Bilderling
- INIFTA-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata B1900, Argentina
| | - Matías Rafti
- INIFTA-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata B1900, Argentina
| | - Frank Vollmer
- Living Systems Institute, Department of Physics & Astronomy, University of Exeter, Exeter EX4 4QD, UK
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3
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Thimm JC, Beketow E, Thiem J. Studies of carbohydrate-carbohydrate-interactions by atomic force microscopy employing functionalized 4-acetylthio-butyl glucopyranosides. Carbohydr Res 2022; 521:108649. [PMID: 36037650 DOI: 10.1016/j.carres.2022.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022]
Abstract
By Fischer glycosylation both anomers of 4-chlorobutyl gluco-as well as galactopyranosides were obtained and transformed into the corresponding 4-acetylthio-butyl glycopyranosides. Dependent on the precursors two straightforward routes were followed to obtain the appropriate 3-O-sulfated derivatives. Unsubstituted and sulfated glucopyranosides were attached to gold surfaces a gold tips. Their interactions were studied using atomic force microscopy for simulations of intercellular glycoside-based interactions and discussed in-depth.
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Affiliation(s)
- Julian C Thimm
- Department of Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Eugen Beketow
- Department of Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Joachim Thiem
- Department of Chemistry, Faculty of Science, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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4
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Molecular Recognition of Surface Trans-Sialidases in Extracellular Vesicles of the Parasite Trypanosoma cruzi Using Atomic Force Microscopy (AFM). Int J Mol Sci 2022; 23:ijms23137193. [PMID: 35806197 PMCID: PMC9266976 DOI: 10.3390/ijms23137193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 02/06/2023] Open
Abstract
Trans-sialidases (TS) are important constitutive macromolecules of the secretome present on the surface of Trypanosoma cruzi (T. cruzi) that play a central role as a virulence factor in Chagas disease. These enzymes have been related to infectivity, escape from immune surveillance and pathogenesis exhibited by this protozoan parasite. In this work, atomic force microscopy (AFM)-based single molecule-force spectroscopy is implemented as a suitable technique for the detection and location of functional TS on the surface of extracellular vesicles (EVs) released by tissue-culture cell-derived trypomastigotes (Ex-TcT). For that purpose, AFM cantilevers with functionalized tips bearing the anti-TS monoclonal antibody mAb 39 as a sense biomolecule are engineered using a covalent chemical ligation based on vinyl sulfonate click chemistry; a reliable, simple and efficient methodology for the molecular recognition of TS using the antibody-antigen interaction. Measurements of the breakdown forces between anti-TS mAb 39 antibodies and EVs performed to elucidate adhesion and forces involved in the recognition events demonstrate that EVs isolated from tissue-culture cell-derived trypomastigotes of T. cruzi are enriched in TS. Additionally, a mapping of the TS binding sites with submicrometer-scale resolution is provided. This work represents the first AFM-based molecular recognition study of Ex-TcT using an antibody-tethered AFM probe.
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5
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Fekete T, Mészáros M, Szegletes Z, Vizsnyiczai G, Zimányi L, Deli MA, Veszelka S, Kelemen L. Optically Manipulated Microtools to Measure Adhesion of the Nanoparticle-Targeting Ligand Glutathione to Brain Endothelial Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:39018-39029. [PMID: 34397215 DOI: 10.1021/acsami.1c08454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Targeting nanoparticles as drug delivery platforms is crucial to facilitate their cellular entry. Docking of nanoparticles by targeting ligands on cell membranes is the first step for the initiation of cellular uptake. As a model system, we studied brain microvascular endothelial cells, which form the anatomical basis of the blood-brain barrier, and the tripeptide glutathione, one of the most effective targeting ligands of nanoparticles to cross the blood-brain barrier. To investigate this initial docking step between glutathione and the membrane of living brain endothelial cells, we applied our recently developed innovative optical method. We present a microtool, with a task-specific geometry used as a probe, actuated by multifocus optical tweezers to characterize the adhesion probability and strength of glutathione-coated surfaces to the cell membrane of endothelial cells. The binding probability of the glutathione-coated surface and the adhesion force between the microtool and cell membrane was measured in a novel arrangement: cells were cultured on a vertical polymer wall and the mechanical forces were generated laterally and at the same time, perpendicularly to the plasma membrane. The adhesion force values were also determined with more conventional atomic force microscopy (AFM) measurements using functionalized colloidal probes. The optical trapping-based method was found to be suitable to measure very low adhesion forces (≤ 20 pN) without a high level of noise, which is characteristic for AFM measurements in this range. The holographic optical tweezers-directed functionalized microtools may help characterize the adhesion step of nanoparticles initiating transcytosis and select ligands to target nanoparticles.
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Affiliation(s)
- Tamás Fekete
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
- Doctoral School in Multidisciplinary Medicine, University of Szeged, Szeged 6720, Hungary
| | - Mária Mészáros
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - Zsolt Szegletes
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - Gaszton Vizsnyiczai
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - Mária A Deli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - Szilvia Veszelka
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
| | - Lóránd Kelemen
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged 6726, Hungary
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6
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Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
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Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
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7
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Paananen A, Weich S, Szilvay GR, Leitner M, Tappura K, Ebner A. Quantifying biomolecular hydrophobicity: Single molecule force spectroscopy of class II hydrophobins. J Biol Chem 2021; 296:100728. [PMID: 33933454 PMCID: PMC8164047 DOI: 10.1016/j.jbc.2021.100728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/30/2022] Open
Abstract
Hydrophobins are surface-active proteins produced by filamentous fungi. The amphiphilic structure of hydrophobins is very compact, containing a distinct hydrophobic patch on one side of the molecule, locked by four intramolecular disulfide bridges. Hydrophobins form dimers and multimers in solution to shield these hydrophobic patches from water exposure. Multimer formation in solution is dynamic, and hydrophobin monomers can be exchanged between multimers. Unlike class I hydrophobins, class II hydrophobins assemble into highly ordered films at the air-water interface. In order to increase our understanding of the strength and nature of the interaction between hydrophobins, we used atomic force microscopy for single molecule force spectroscopy to explore the molecular interaction forces between class II hydrophobins from Trichoderma reesei under different environmental conditions. A genetically engineered hydrophobin variant, NCys-HFBI, enabled covalent attachment of proteins to the apex of the atomic force microscopy cantilever tip and sample surfaces in controlled orientation with sufficient freedom of movement to measure molecular forces between hydrophobic patches. The measured rupture force between two assembled hydrophobins was ∼31 pN, at a loading rate of 500 pN/s. The results indicated stronger interaction between hydrophobins and hydrophobic surfaces than between two assembling hydrophobin molecules. Furthermore, this interaction was stable under different environmental conditions, which demonstrates the dominance of hydrophobicity in hydrophobin-hydrophobin interactions. This is the first time that interaction forces between hydrophobin molecules, and also between naturally occurring hydrophobic surfaces, have been measured directly at a single-molecule level.
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Affiliation(s)
- Arja Paananen
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Sabine Weich
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Géza R Szilvay
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Michael Leitner
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Kirsi Tappura
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Andreas Ebner
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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8
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Strasser J, de Jong RN, Beurskens FJ, Schuurman J, Parren PWHI, Hinterdorfer P, Preiner J. Weak Fragment Crystallizable (Fc) Domain Interactions Drive the Dynamic Assembly of IgG Oligomers upon Antigen Recognition. ACS NANO 2020; 14:2739-2750. [PMID: 31887016 DOI: 10.1021/acsnano.9b08347] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Activation of membrane receptors through clustering is a common mechanism found in various biological systems. Spatial proximity of receptors may be transduced across the membrane to initiate signaling pathways or alternatively be recognized by peripheral proteins or immune cells to trigger external effector functions. Here we show how specific immunoglobulin G (IgG) binding induces clustering of monomeric target molecules in lipid membranes through Fc-Fc interactions. We visualize and characterize the dynamic IgG oligomerization process and the molecular interactions involved using high-speed atomic force microscopy, single-molecule force spectroscopy, and quartz crystal microbalance experiments. We found that the Fc-Fc interaction strength is precisely tuned to be weak enough to prevent IgG oligomerization in solution at physiological titers, but enabling IgG oligomerization when Fabs additionally bind to their cognate surface epitopes, a mechanism that ultimately targets IgG-mediated effector functions such as classical complement activation to antigenic membranes.
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Affiliation(s)
- Jürgen Strasser
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | | | | | | | - Paul W H I Parren
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Lava Therapeutics, 3584 CM Utrecht, The Netherlands
| | | | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
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9
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Beaussart A, El-Kirat-Chatel S. Microbial adhesion and ultrastructure from the single-molecule to the single-cell levels by Atomic Force Microscopy. Cell Surf 2019; 5:100031. [PMID: 32743147 PMCID: PMC7389263 DOI: 10.1016/j.tcsw.2019.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 12/29/2022] Open
Abstract
In the last decades, atomic force microscopy (AFM) has evolved towards an accurate and lasting tool to study the surface of living cells in physiological conditions. Through imaging, single-molecule force spectroscopy and single-cell force spectroscopy modes, AFM allows to decipher at multiple scales the morphology and the molecular interactions taking place at the cell surface. Applied to microbiology, these approaches have been used to elucidate biophysical properties of biomolecules and to directly link the molecular structures to their function. In this review, we describe the main methods developed for AFM-based microbial surface analysis that we illustrate with examples of molecular mechanisms unravelled with unprecedented resolution.
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10
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Dissecting the cytochrome c 2-reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy. Biochem J 2019; 476:2173-2190. [PMID: 31320503 PMCID: PMC6688529 DOI: 10.1042/bcj20170519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/17/2022]
Abstract
The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c 2 and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC-LH1-PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c 2 molecules. Microscale patterns of cytochrome c 2 and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c 2 Following the transient association of photo-oxidised RC and reduced cytochrome c 2 molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC-c 2 complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c 2 molecules decreased 5-fold. Thus, the redox states of the cytochrome c 2 haem cofactor and RC 'special pair' bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c 2[oxidised]-RC[reduced] 'product' state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.
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11
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Hu KH, Bruce MA, Liu J, Butte MJ. Biochemical Stimulation of Immune Cells and Measurement of Mechanical Responses Using Atomic Force Microscopy. ACTA ACUST UNITED AC 2019; 11:e63. [PMID: 30707509 DOI: 10.1002/cpch.63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This manuscript details methods to ligate cell-surface receptors on live cells with precise spatiotemporal control using an atomic force microscope (AFM) to deliver ligands. This approach can be used to image cellular responses upon activating T cell receptors when the AFM is mounted on an optical microscope. Moreover, the AFM measures forces generated by the cell during the contact. Using AFM to trigger cellular responses adds an important capability to the field of mechanobiology. We describe how to incorporate anti-CD3 antibodies or other molecules onto an AFM cantilever and how to use AFM to activate T cells. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kenneth H Hu
- Department of Pathology, University of California San Francisco, San Francisco, California
| | | | - Jianwei Liu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, and Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California
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12
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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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13
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Yang# Y, Yu# J, Esfahani AM, Seiffert-Sinha K, Xi N, Lee I, Sinha AA, Chen L, Sun Z, Yang R, Dong L. Single-cell membrane drug delivery using porous pen nanodeposition. NANOSCALE 2018; 10:12704-12712. [PMID: 29946596 PMCID: PMC6528655 DOI: 10.1039/c8nr02600a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Delivering molecules onto the plasma membrane of single cells is still a challenging task in profiling cell signaling pathways with single cell resolution. We demonstrated that a large quantity of molecules could be targeted and released onto the membrane of individual cells to trigger signaling responses. This is achieved by a porous pen nanodeposition (PPN) method, in which a multilayer porous structure, serving as a reservoir for a large amount of molecules, is formed on an atomic force microscope (AFM) tip using layer-by-layer assembly and post processing. To demonstrate its capability for single cell membrane drug delivery, PPN was employed to induce a calcium flux triggered by the binding of released antibodies to membrane antigens in an autoimmune skin disease model. This calcium signal propagates from the target cell to its neighbors in a matter of seconds, proving the theory of intercellular communication through cell-cell junctions. Collectively, these results demonstrated the effectiveness of PPN in membrane drug delivery for single cells; to the best of our knowledge, this is the first technique that can perform the targeted transport and delivery in single cell resolution, paving the way for probing complex signaling interactions in multicellular settings.
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Affiliation(s)
- Yongliang Yang#
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
| | - Jing Yu#
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Amir Monemian Esfahani
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA
| | | | - Ning Xi
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ilsoon Lee
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Animesh A. Sinha
- Department of Dermatology, University at Buffalo, Buffalo, New York 14203, USA
| | - Liangliang Chen
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Sun
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ruiguo Yang
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA,
| | - Lixin Dong
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
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14
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Permiakov NV, Spivak YM, Moshnikov VA, Shishov MA, Sapurina IY. New Opportunities of Atomic Force Microscopy Probes upon Polyaniline Functionalization. POLYMER SCIENCE SERIES A 2018. [DOI: 10.1134/s0965545x18030082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Formosa-Dague C, Castelain M, Martin-Yken H, Dunker K, Dague E, Sletmoen M. The Role of Glycans in Bacterial Adhesion to Mucosal Surfaces: How Can Single-Molecule Techniques Advance Our Understanding? Microorganisms 2018; 6:E39. [PMID: 29734645 PMCID: PMC6027152 DOI: 10.3390/microorganisms6020039] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
Bacterial adhesion is currently the subject of increased interest from the research community, leading to fast progress in our understanding of this complex phenomenon. Resent research within this field has documented the important roles played by glycans for bacterial surface adhesion, either through interaction with lectins or with other glycans. In parallel with this increased interest for and understanding of bacterial adhesion, there has been a growth in the sophistication and use of sensitive force probes for single-molecule and single cell studies. In this review, we highlight how the sensitive force probes atomic force microscopy (AFM) and optical tweezers (OT) have contributed to clarifying the mechanisms underlying bacterial adhesion to glycosylated surfaces in general and mucosal surfaces in particular. We also describe research areas where these techniques have not yet been applied, but where their capabilities appear appropriate to advance our understanding.
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Affiliation(s)
| | - Mickaël Castelain
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France.
| | - Hélène Martin-Yken
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France.
| | - Karen Dunker
- Department of Biotechnology and Food Science, NTNU the Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
| | - Etienne Dague
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France.
| | - Marit Sletmoen
- Department of Biotechnology and Food Science, NTNU the Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
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16
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Chtcheglova LA, Hinterdorfer P. Simultaneous AFM topography and recognition imaging at the plasma membrane of mammalian cells. Semin Cell Dev Biol 2018; 73:45-56. [DOI: 10.1016/j.semcdb.2017.08.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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17
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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18
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Endothelial Glycocalyx-Mediated Nitric Oxide Production in Response to Selective AFM Pulling. Biophys J 2017; 113:101-108. [PMID: 28700908 DOI: 10.1016/j.bpj.2017.05.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 05/05/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023] Open
Abstract
Nitric oxide (NO) is a regulatory molecule in the vascular system and its inhibition due to endothelial injury contributes to cardiovascular disease. The glycocalyx is a thin layer of glycolipids, glycoproteins, and proteoglycans on the surface of mammalian epithelial cells. Extracellular forces are transmitted through the glycocalyx to initiate intracellular signaling pathways. In endothelial cells (ECs), previous studies have shown the glycocalyx to be a significant mediator of NO production; degradation of the endothelial glycocalyx layer (EGL) drastically reduces EC production of NO in response to fluid shear stress. However, the specific EGL components involved in this process are not well established. Recent work using short-hairpin RNA approaches in vitro suggest that the proteoglycan glypican-1, not syndecan-1, is the dominant core protein mediating shear-induced NO production. We utilized atomic force microscopy (AFM) to apply force selectively to components of the EGL of confluent rat fat pad ECs (RFPECs), including proteoglycans and glycosaminoglycans, to observe how each component individually contributes to force-induced production of NO. 4,5-diaminofluorescein diacetate, a cell-permeable fluorescent molecule, was used to detect changes in intracellular NO production. Antibody-coated AFM probes exhibited strong surface binding to RFPEC monolayers, with 100-300 pN mean adhesion forces. AFM pulling on glypican-1 and heparan sulfate for 10 min caused significantly increased NO production, whereas pulling on syndecan-1, CD44, hyaluronic acid, and with control probes did not. We conclude that AFM pulling can be used to activate EGL-mediated NO production and that the heparan sulfate proteoglycan glypican-1 is a primary mechanosensor for shear-induced NO production.
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19
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Baclayon M, Ulsen PV, Mouhib H, Shabestari MH, Verzijden T, Abeln S, Roos WH, Wuite GJL. Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates. ACS NANO 2016; 10:5710-9. [PMID: 27219538 DOI: 10.1021/acsnano.5b07072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The backbone of secreted autotransporter passenger proteins generally attains a stable β-helical structure. The secretion of passengers across the outer membrane was proposed to be driven by sequential folding of this structure at the cell surface. This mechanism would require a relatively stable intermediate as starting point. Here, we investigated the mechanics of secreted truncated versions of the autotransporter hemoglobin protease (Hbp) of Escherichia coli using atomic force microscopy. The data obtained reveal a β-helical structure at the C terminus that is very stable. In addition, several other distinct metastable intermediates are found which are connected during unfolding by multiroute pathways. Computational analysis indicates that these intermediates correlate to the β-helical rungs in the Hbp structure which are clamped by stacked aromatic residues. Our results suggest a secretion mechanism that is initiated by a stable C-terminal structure and driven forward by several folding intermediates that build up the β-helical backbone.
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Affiliation(s)
- Marian Baclayon
- Physics of Living Systems & LaserLaB Amsterdam, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Peter van Ulsen
- Molecular Microbiology & Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Halima Mouhib
- Computer Science & Bioinformatics, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, 52056 Aachen, Germany
| | - Maryam Hashemi Shabestari
- Physics of Living Systems & LaserLaB Amsterdam, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Timo Verzijden
- Computer Science & Bioinformatics, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Sanne Abeln
- Computer Science & Bioinformatics, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
| | - Wouter H Roos
- Physics of Living Systems & LaserLaB Amsterdam, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen , 9712 CP Groningen, The Netherlands
| | - Gijs J L Wuite
- Physics of Living Systems & LaserLaB Amsterdam, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands
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20
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Maver U, Velnar T, Gaberšček M, Planinšek O, Finšgar M. Recent progressive use of atomic force microscopy in biomedical applications. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.03.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Leitner M, Stock LG, Traxler L, Leclercq L, Bonazza K, Friedbacher G, Cottet H, Stutz H, Ebner A. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging. Anal Chim Acta 2016; 930:39-48. [PMID: 27265903 DOI: 10.1016/j.aca.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated.
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Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Lorenz G Stock
- Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Lukas Traxler
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Laurent Leclercq
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier, France
| | - Klaus Bonazza
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Gernot Friedbacher
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna, Austria
| | - Hervé Cottet
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier, France
| | - Hanno Stutz
- Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria; Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria.
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22
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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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23
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Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy. Acta Pharmacol Sin 2015; 36:769-82. [PMID: 26027658 DOI: 10.1038/aps.2015.28] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/13/2015] [Indexed: 02/06/2023] Open
Abstract
Knowledge of the nanoscale changes that take place in individual cells in response to a drug is useful for understanding the drug action. However, due to the lack of adequate techniques, such knowledge was scarce until the advent of atomic force microscopy (AFM), which is a multifunctional tool for investigating cellular behavior with nanometer resolution under near-physiological conditions. In the past decade, researchers have applied AFM to monitor the morphological and mechanical dynamics of individual cells following drug stimulation, yielding considerable novel insight into how the drug molecules affect an individual cell at the nanoscale. In this article we summarize the representative applications of AFM in characterization of drug actions on cell membrane, including topographic imaging, elasticity measurements, molecular interaction quantification, native membrane protein imaging and manipulation, etc. The challenges that are hampering the further development of AFM for studies of cellular activities are aslo discussed.
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24
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Stetter FWS, Kienle S, Krysiak S, Hugel T. Investigating single molecule adhesion by atomic force spectroscopy. J Vis Exp 2015:e52456. [PMID: 25867282 DOI: 10.3791/52456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.
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Affiliation(s)
- Frank W S Stetter
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Sandra Kienle
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Stefanie Krysiak
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München
| | - Thorsten Hugel
- Physik-Department E22a, Technische Universität München; IMETUM, Technische Universität München;
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25
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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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26
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Pi J, Jin H, Yang F, Chen ZW, Cai J. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine. NANOSCALE 2014; 6:12229-12249. [PMID: 25227707 DOI: 10.1039/c4nr04195j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In this review, we attempt to summarize the characteristics of these advanced techniques for use in the in situ single molecule imaging of cell membranes. We believe that this work will help to promote the technological and methodological developments of super-resolution techniques for the single molecule imaging of cell membranes and help researchers better understand which technique is most suitable for their future exploring of membrane biomolecules; ultimately promoting further developments in cell biology, immunology and medicine.
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Affiliation(s)
- Jiang Pi
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technique, Macau, China.
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27
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Saha B, Evers TH, Prins MWJ. How Antibody Surface Coverage on Nanoparticles Determines the Activity and Kinetics of Antigen Capturing for Biosensing. Anal Chem 2014; 86:8158-66. [DOI: 10.1021/ac501536z] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bedabrata Saha
- Philips Research, High Tech Campus, 5656 AE Eindhoven, The Netherlands
| | - Toon H. Evers
- Philips Research, High Tech Campus, 5656 AE Eindhoven, The Netherlands
| | - Menno W. J. Prins
- Philips Research, High Tech Campus, 5656 AE Eindhoven, The Netherlands
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28
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Jiao F, Fan H, Yang G, Zhang F, He P. Directly investigating the interaction between aptamers and thrombin by atomic force microscopy. J Mol Recognit 2014; 26:672-8. [PMID: 24277612 DOI: 10.1002/jmr.2312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 07/21/2013] [Accepted: 08/21/2013] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded nucleic acid molecules that can be used for protein recognition, detection, and inhibition. Over the past decades, two thrombin-binding aptamers (15apt and 27apt) were reported by systemic evolution of ligands by exponential enrichment technique. Though many studies have been reported about the interactions between the aptamers and thrombin by atomic force microscopy, the thrombins in those studies were all immobilized by chemical agents. Recently, we developed a new method using atomic force microscopy to directly investigate the specific interactions between thrombin and its two aptamers without immobilizing the thrombin. Furthermore, the unbinding dynamics and dissociation energy landscapes of aptamer/thrombin were discussed. The results indicate that the underlying interaction mechanisms of thrombin with its two aptamers will be similar despite that the structures of 15apt and 27apt are different in buffer solution.
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Affiliation(s)
- Fang Jiao
- Department of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
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29
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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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30
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Rangl M, Leitner M, Riihimäki T, Lehtonen S, Hytönen VP, Gruber HJ, Kulomaa M, Hinterdorfer P, Ebner A. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy. J Mol Recognit 2014; 27:92-7. [DOI: 10.1002/jmr.2337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Martina Rangl
- Institute of Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Michael Leitner
- Institute of Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Tiina Riihimäki
- Institute of Biomedical Technology; University of Tampere and Tampere University Hospital; Biokatu 6 33520 Tampere Finland
| | - Soili Lehtonen
- Institute of Biomedical Technology; University of Tampere and Tampere University Hospital; Biokatu 6 33520 Tampere Finland
| | - Vesa P. Hytönen
- Institute of Biomedical Technology; University of Tampere and Tampere University Hospital; Biokatu 6 33520 Tampere Finland
- Fimlab Laboratories; Biokatu 4 33520 Tampere Finland
| | - Hermann J. Gruber
- Institute of Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
| | - Markku Kulomaa
- Institute of Biomedical Technology; University of Tampere and Tampere University Hospital; Biokatu 6 33520 Tampere Finland
| | - Peter Hinterdorfer
- Institute of Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
- Center for Advanced Bioanalysis; Gruberstrasse 40 4020 Linz Austria
| | - Andreas Ebner
- Institute of Biophysics; Johannes Kepler University Linz; Gruberstrasse 40 4020 Linz Austria
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31
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Balzer BN, Micciulla S, Dodoo S, Zerball M, Gallei M, Rehahn M, V Klitzing R, Hugel T. Adhesion property profiles of supported thin polymer films. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6300-6306. [PMID: 23738613 DOI: 10.1021/am4013424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Polymer coatings are frequently utilized to control and modify substrate properties. The performance of the coatings is often determined by the first polymer layers between the substrate and the bulk polymer material, which are termed interphase. Standard methods have failed to completely characterize this interphase, because its properties change significantly over a few nanometers. Here we determine the spatially resolved adhesion properties of the interphase in polyelectrolyte multilayers (PEMs) by desorbing a single polymer covalently bound to an atomic force microscope cantilever tip from PEMs with varying thickness. We show that the adhesion properties of the first few layers (up to three double layers) is dominated by the surface potential of the substrate, while thicker PEMs are controlled by cohesion in between the PEM polymers. For cohesion, the local film conformation is the crucial parameter. This finding is generalized by utilizing oligoelectrolyte multilayer (OEM) as coatings and both hydrophilic and hydrophobic polymers as polymeric force sensors.
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Affiliation(s)
- Bizan N Balzer
- IMETUM and Physik-Department, Technische Universität München, Garching, Germany
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32
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Last JA, Thomasy SM, Croasdale CR, Russell P, Murphy CJ. Compliance profile of the human cornea as measured by atomic force microscopy. Micron 2012; 43:1293-8. [PMID: 22421334 PMCID: PMC3622051 DOI: 10.1016/j.micron.2012.02.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/17/2012] [Accepted: 02/17/2012] [Indexed: 11/30/2022]
Abstract
The ability to accurately determine the elastic modulus of each layer of the human cornea is a crucial step in the design of better corneal prosthetics. In addition, knowledge of the elastic modulus will allow design of substrates with relevant mechanical properties for in vitro investigations of cellular behavior. Previously, we have reported elastic modulus values for the anterior basement membrane and Descemet's membrane of the human cornea, the surfaces in contact with the epithelial and endothelial cells, respectively. We have completed the compliance profile of the stromal elements of the human cornea by obtaining elastic modulus values for Bowman's layer and the anterior stroma. Atomic force microscopy (AFM) was used to determine the elastic modulus, which is a measure of the tissue stiffness and is inversely proportional to the compliance. The elastic response of the tissue allows analysis with the Hertz equation, a model that provides a relationship between the indentation force and depth and is a function of the tip radius and the modulus of the substrate. The elastic modulus values for each layer of the cornea are: 7.5±4.2 kPa (anterior basement membrane), 109.8±13.2 kPa (Bowman's layer), 33.1±6.1 kPa (anterior stroma), and 50±17.8 kPa (Descemet's membrane). These results indicate that the biophysical properties, including elastic modulus, of each layer of the human cornea are unique and may play a role in the maintenance of homeostasis as well as in the response to therapeutic agents and disease states. The data will also inform the design and fabrication of improved corneal prosthetics.
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Affiliation(s)
- Julie A. Last
- Laboratory for Optical and Computational Instrumentation and the Materials Science Center, University of Wisconsin-Madison
| | - Sara M. Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis
| | | | - Paul Russell
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis
| | - Christopher J. Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis
- Department of Ophthalmology and Vision Science, School of Medicine, University of California, Davis
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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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Liu J, Butte MJ. Single molecule labeling of an atomic force microscope cantilever tip. APPLIED PHYSICS LETTERS 2012; 101:163705. [PMID: 23152642 PMCID: PMC3487922 DOI: 10.1063/1.4760283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/03/2012] [Indexed: 06/01/2023]
Abstract
In this paper, we present a method to functionalize the very apex of an atomic force microscope cantilever with a single or a few molecules. In force spectroscopy or interaction mapping, the cantilever must be functionalized with only a few molecules to avoid noise or spurious measurements. Here, we covalently attached single molecules to the cantilever by touching it to a paper wetted with a solution of quantum dots. The paper competes with wicking up the hydrophilic surface of the tip. This method has broad applications in scanning probe microscopy where small numbers of molecules are needed on the tip.
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Affiliation(s)
- Jianwei Liu
- Department of Pediatrics, Division of Immunology and Allergy, Stanford University, Stanford, California 94305, USA
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35
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Quilès F, Polyakov P, Humbert F, Francius G. Production of extracellular glycogen by Pseudomonas fluorescens: spectroscopic evidence and conformational analysis by biomolecular recognition. Biomacromolecules 2012; 13:2118-27. [PMID: 22686500 DOI: 10.1021/bm300497c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycogen is mainly found as the principal storage form of glucose in cells. Many bacteria are able to synthesize large amounts of glycogen under unfavorable life conditions. By combining infrared spectroscopy, single molecule force spectroscopy (SMFS) and immuno-staining technique, we evidenced that planktonic P. fluorescens (Pf) cells are also able to produce glycogen as an extracellular polymeric substance. For this purpose, Pf suspensions were examined at 3 and 21 h of growth in nutritive medium (LB, 0.5 g/L). The conformation of the extracellular glycogen, revealed through its infrared spectral signature, has been investigated by SMFS measurements using Freely Jointed Chain model. The analysis of force versus distance curves showed over growth time that the increase of glycogen production was accompanied by an increase in glycogen contour lengths and ramifications. These results demonstrated that the production of extracellular bacterial glycogen can occur even if the cells are not subjected to unfavorable life conditions.
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Affiliation(s)
- Fabienne Quilès
- Université de Lorraine, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, LCPME, UMR 7564, Villers-lès-Nancy, France.
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36
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Liu Z, Galli F, Waterreus WJ, Meulenbroek E, Koning RI, Lamers GEM, Olsthoorn RCL, Pannu N, Oosterkamp TH, Koster AJ, Dame RT, Abrahams JP. Single-Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA-Protein Interactions. Chemphyschem 2012; 13:1569-75. [DOI: 10.1002/cphc.201100896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/31/2012] [Indexed: 11/07/2022]
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Neundlinger I, Poturnayova A, Karpisova I, Rankl C, Hinterdorfer P, Snejdarkova M, Hianik T, Ebner A. Characterization of enhanced monovalent and bivalent thrombin DNA aptamer binding using single molecule force spectroscopy. Biophys J 2012; 101:1781-7. [PMID: 21961605 DOI: 10.1016/j.bpj.2011.07.054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/27/2011] [Accepted: 07/28/2011] [Indexed: 11/15/2022] Open
Abstract
Thrombin aptamer binding strength and stability is dependent on sterical parameters when used for atomic force microscopy sensing applications. Sterical improvements on the linker chemistry were developed for high-affinity binding. For this we applied single molecule force spectroscopy using two enhanced biotinylated thrombin aptamers, BFF and BFA immobilized on the atomic force microscopy tip via streptavidin. BFF is a dimer composed of two single-stranded aptamers (aptabody) connected to each other by a complementary sequence close to the biotinylated end. In contrast, BFA consists of a single DNA strand and a complementary strand in the supporting biotinylated part. By varying the pulling velocity in force-distance cycles the formed thrombin-aptamer complexes were ruptured at different force loadings allowing determination of the energy landscape. As a result, BFA aptamer showed a higher binding force at the investigated loading rates and a significantly lower dissociation rate constant, k(off), compared to BFF. Moreover, the potential of the aptabody BFF to form a bivalent complex could clearly be demonstrated.
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38
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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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40
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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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41
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Creasey R, Sharma S, Gibson CT, Craig JE, Ebner A, Becker T, Hinterdorfer P, Voelcker NH. Atomic force microscopy-based antibody recognition imaging of proteins in the pathological deposits in pseudoexfoliation syndrome. Ultramicroscopy 2011; 111:1055-61. [PMID: 21740868 DOI: 10.1016/j.ultramic.2011.03.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/22/2011] [Accepted: 03/11/2011] [Indexed: 10/18/2022]
Abstract
The phenomenon of protein aggregation is of considerable interest to various disciplines, including the field of medicine. A range of disease pathologies are associated with this phenomenon. One of the ocular diseases hallmarked by protein aggregation is the Pseudoexfoliation (PEX) Syndrome. This condition is characterized by the deposition of insoluble proteinaceous material on the anterior human lens capsule. Genomic and proteomic analyses have revealed an association of specific genetic markers and various proteins, respectively, with PEX syndrome. However, the ultrastructure of the protein aggregates is poorly characterized. This study seeks to build capacity to determine the molecular nature of PEX aggregates on human lens capsules in their native state by AFM-based antibody recognition imaging. Lysyl oxidase-Like 1 (LOXL1), a protein identified as a component of PEX aggregates, is detected by an antibody-modified AFM probe. Topographical AFM images and antibody recognition images are obtained using three AFM-based techniques: TREC, phase and force-volume imaging. LOXL1 is found to be present on the lens capsule surface, and is localized around fibrous protein aggregates. Our evaluation shows that TREC imaging is best suited for human tissue imaging and holds significant potential for imaging of human disease tissues in their native state.
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Affiliation(s)
- Rhiannon Creasey
- School of Chemical and Physical Sciences, Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Australia
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42
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Last JA, Russell P, Nealey PF, Murphy CJ. The applications of atomic force microscopy to vision science. Invest Ophthalmol Vis Sci 2011; 51:6083-94. [PMID: 21123767 DOI: 10.1167/iovs.10-5470] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The atomic force microscope (AFM) is widely used in materials science and has found many applications in biological sciences but has been limited in use in vision science. The AFM can be used to image the topography of soft biological materials in their native environments. It can also be used to probe the mechanical properties of cells and extracellular matrices, including their intrinsic elastic modulus and receptor-ligand interactions. In this review, the operation of the AFM is described along with a review of how it has been thus far used in vision science. It is hoped that this review will serve to stimulate vision scientists to consider incorporating AFM as part of their research toolkit.
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Affiliation(s)
- Julie A Last
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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43
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Ebner A, Schillers H, Hinterdorfer P. Normal and pathological erythrocytes studied by atomic force microscopy. Methods Mol Biol 2011; 736:223-241. [PMID: 21660731 DOI: 10.1007/978-1-61779-105-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Erythrocytes (red blood cells, RBCs) are the most common type of blood cells in vertebrates. Many diseases and dysfunctions directly affect their structure and function. Employing the atomic force microscope (AFM) physical, chemical, and biological/physiological properties of RBCs can be studied even under near-physiological conditions. In this chapter, we present the application of different AFM techniques to investigate and compare normal and pathological RBCs. We give a detailed description for nondestructive immobilization of whole intact RBCs and explain preparation techniques for isolated native RBC membranes. High-resolution imaging of morphological details and pathological differences are demonstrated with healthy and systemic lupus erythematosus (SLE) erythrocytes revealing substructural changes due to SLE. We also present the technique of simultaneous topography and recognition imaging, which was used to map the distribution of cystic fibrosis transmembrane conductance regulator sites on erythrocyte membranes in healthy and cystic fibrosis-positive RBCs.
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Affiliation(s)
- Andreas Ebner
- Institute for Biophysics, University of Linz, Linz, Austria
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44
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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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45
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Creasey R, Sharma S, Craig JE, Gibson CT, Ebner A, Hinterdorfer P, Voelcker NH. Detecting protein aggregates on untreated human tissue samples by atomic force microscopy recognition imaging. Biophys J 2010; 99:1660-7. [PMID: 20816080 DOI: 10.1016/j.bpj.2010.06.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 06/15/2010] [Accepted: 06/18/2010] [Indexed: 10/19/2022] Open
Abstract
We apply topography and recognition (TREC) imaging to the analysis of whole, untreated human tissue for what we believe to be the first time. Pseudoexfoliation syndrome (PEX), a well-known cause of irreversible blindness worldwide, is characterized by abnormal protein aggregation on the anterior lens capsule of the eye. However, the development of effective therapies has been hampered by a lack of detailed knowledge of the protein constituents in these pathological deposits and their distribution. Using both TREC and immunofluorescence, one of the proteins implicated in the PEX pathology--the apolipoprotein clusterin--was detected, and differences in its distribution pattern on the surface of untreated human lens capsule tissue in both PEX and normal control samples were investigated. Our study shows the potential of TREC imaging for the analysis of whole, untreated human tissue samples.
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Affiliation(s)
- Rhiannon Creasey
- School of Chemical and Physical Sciences, Flinders University, Bedford Park, Australia
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46
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Madwar C, Kwan WC, Deng L, Ramström O, Schmidt R, Zou S, Cuccia LA. Perfluorophenyl azide immobilization chemistry for single molecule force spectroscopy of the concanavalin A/mannose interaction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:16677-16680. [PMID: 20964389 DOI: 10.1021/la1036579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The versatility of perfluorophenyl azide (PFPA) derivatives makes them useful for attaching a wide variety of biomolecules and polymers to surfaces. Herein, a single molecule force spectroscopy (SMFS) study of the concanavalin A/mannose interaction was carried out using PFPA immobilization chemistry. SMFS of the concanavalin A/mannose interaction yielded an average unbinding force of 70-80 pN for loading rates between 8000 and 40,000 pN/s for mannose surfaces on aminated glass, and an unbinding force of 57 ± 20 pN at 6960 pN/s for mannose surfaces on gold-coated glass. Dynamic force spectroscopy was used to determine the dissociation rate constant, k(off), for this interaction to be 0.16 s(-1).
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Affiliation(s)
- Carolin Madwar
- Department of Chemistry & Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
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47
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Sekatskii SK, Favre M, Dietler G, Mikhailov AG, Klinov DV, Lukash SV, Deyev SM. Force spectroscopy of barnase-barstar single molecule interaction. J Mol Recognit 2010; 23:583-8. [DOI: 10.1002/jmr.1030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Baclayon M, Roos WH, Wuite GJL. Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 2010; 9:1678-88. [PMID: 20562411 PMCID: PMC2938060 DOI: 10.1074/mcp.r110.001461] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 12/17/2022] Open
Abstract
To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.
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Affiliation(s)
- Marian Baclayon
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Gijs J. L. Wuite
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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49
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Enzymatic glycosylation, inhibitor design, and synthesis and formation of glyco-self assembled monolayers for simulation of recognition. Eur J Cell Biol 2010; 89:39-52. [DOI: 10.1016/j.ejcb.2009.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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50
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Rangl M, Nevo R, Liashkovich I, Shahin V, Reich Z, Ebner A, Hinterdorfer P. Stable, non-destructive immobilization of native nuclear membranes to micro-structured PDMS for single-molecule force spectroscopy. Chemphyschem 2009; 10:1553-8. [PMID: 19507204 PMCID: PMC3013320 DOI: 10.1002/cphc.200900219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Indexed: 11/08/2022]
Abstract
In eukaryotic cells the nucleus is separated from the cytoplasm by a double-membraned nuclear envelope (NE). Exchange of molecules between the two compartments is mediated by nuclear pore complexes (NPCs) that are embedded in the NE membranes. The translocation of molecules such as proteins and RNAs through the nuclear membrane is executed by transport shuttling factors (karyopherines). They thereby dock to particular binding sites located all over the NPC, the so-called phenylalanine-glycin nucleoporines (FG Nups). Molecular recognition force spectroscopy (MRFS) allows investigations of the binding at the single-molecule level. Therefore the AFM tip carries a ligand for example, a particular karyopherin whereas the nuclear membrane with its receptors is mounted on a surface. Hence, one of the first requirements to study the nucleocytoplasmatic transport mechanism using MRFS is the development of an optimized membrane preparation that preserves structure and function of the NPCs. In this study we present a stable non-destructive preparation method of Xenopus laevis nuclear envelopes. We use micro-structured polydimethylsiloxane (PDMS) that provides an ideal platform for immobilization and biological integrity due to its elastic, chemical and mechanical properties. It is a solid basis for studying molecular recognition, transport interactions, and translocation processes through the NPC. As a first recognition system we investigate the interaction between an important transport shuttling factor, importin beta, and its binding sites on the NPC, the FG-domains.
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Affiliation(s)
- Martina Rangl
- Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, 4040 Linz (Austria)
| | - Reinat Nevo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100 (Israel)
| | - Ivan Liashkovich
- Department of Physiology, University of Münster, Robert-Koch-str. 27b, 48149 Münster (Germany)
| | - Victor Shahin
- Department of Physiology, University of Münster, Robert-Koch-str. 27b, 48149 Münster (Germany)
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100 (Israel)
| | - Andreas Ebner
- Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, 4040 Linz (Austria)
| | - Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, 4040 Linz (Austria)
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