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Bao P, Phillips K, Raval R. Membrane Proteins in Action Monitored by pH-Responsive Liquid Crystal Biosensors. ACS APPLIED MATERIALS & INTERFACES 2024; 16:31843-31850. [PMID: 38841859 PMCID: PMC11194810 DOI: 10.1021/acsami.4c06614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
Liquid crystal (LC) biosensors have received significant attention for their potential applications for point-of-care devices due to their sensitivity, low cost, and easy read-out. They have been employed to detect a wide range of important biological molecules. However, detecting the function of membrane proteins has been extremely challenging due to the difficulty of integrating membrane proteins, lipid membranes, and LCs into one system. In this study, we addressed this challenge by monitoring the proton-pumping function of bacteriorhodopsin (bR) using a pH-sensitive LC thin film biosensor. To achieve this, we deposited purple membranes (PMs) containing a 2D crystal form of bRs onto an LC-aqueous interface. Under light, the PM patches changed the local pH at the LC-aqueous interface, causing a color change in the LC thin film that is observable through a polarizing microscope with crossed polarizers. These findings open up new opportunities to study the biofunctions of membrane proteins and their induced local environmental changes in a solution using LC biosensors.
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Affiliation(s)
- Peng Bao
- Open Innovation
Hub for Antimicrobial
Surfaces, Surface Science Research Centre, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K.
| | - Kyle Phillips
- Open Innovation
Hub for Antimicrobial
Surfaces, Surface Science Research Centre, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K.
| | - Rasmita Raval
- Open Innovation
Hub for Antimicrobial
Surfaces, Surface Science Research Centre, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K.
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2
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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3
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Qin Y, Yang W, Chu H, Li Y, Cai S, Yu H, Liu L. Atomic Force Microscopy for Tumor Research at Cell and Molecule Levels. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-18. [PMID: 35257653 DOI: 10.1017/s1431927622000290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tumors have posed a serious threat to human life and health. Researchers can determine whether or not cells are cancerous, whether the cancer cells are invasive or metastatic, and what the effects of drugs are on cancer cells by the physical properties such as hardness, adhesion, and Young's modulus. The atomic force microscope (AFM) has emerged as a key important tool for biomechanics research on tumor cells due to its ability to image and collect force spectroscopy information of biological samples with nano-level spatial resolution and under near-physiological conditions. This article reviews the existing results of the study of cancer cells with AFM. The main foci are the operating principle of AFM and research advances in mechanical property measurement, ultra-microtopography, and molecular recognition of tumor cells, which allows us to outline what we do know it in a systematic way and to summarize and to discuss future directions.
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Affiliation(s)
- Yitong Qin
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai264005, China
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai264005, China
| | - Honghui Chu
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai264005, China
| | - Yan Li
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai264005, China
| | - Shuxiang Cai
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai264005, China
| | - Haibo Yu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang110016, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang110016, China
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4
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Sharafeldin M, Davis JJ. Characterising the biosensing interface. Anal Chim Acta 2022; 1216:339759. [DOI: 10.1016/j.aca.2022.339759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022]
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Riedel R, Frese N, Yang F, Wortmann M, Dalpke R, Rhinow D, Hampp N, Gölzhäuser A. Fusion of purple membranes triggered by immobilization on carbon nanomembranes. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:93-101. [PMID: 33564606 PMCID: PMC7849249 DOI: 10.3762/bjnano.12.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
A freestanding ultrathin hybrid membrane was synthesized comprising two functional layers, that is, first, a carbon nanomembrane (CNM) produced by electron irradiation-induced cross-linking of a self-assembled monolayer (SAM) of 4'-nitro-1,1'-biphenyl-4-thiol (NBPT) and second, purple membrane (PM) containing genetically modified bacteriorhodopsin (BR) carrying a C-terminal His-tag. The NBPT-CNM was further modified to carry nitrilotriacetic acid (NTA) terminal groups for the interaction with the His-tagged PMs forming a quasi-monolayer of His-tagged PM on top of the CNM-NTA. The formation of the Ni-NTA/His-tag complex leads to the unidirectional orientation of PM on the CNM substrate. Electrophoretic sedimentation was employed to optimize the surface coverage and to close gaps between the PM patches. This procedure for the immobilization of oriented dense PM facilitates the spontaneous fusion of individual PM patches, forming larger membrane areas. This is, to our knowledge, the very first procedure described to induce the oriented fusion of PM on a solid support. The resulting hybrid membrane has a potential application as a light-driven two-dimensional proton-pumping membrane, for instance, for light-driven seawater desalination as envisioned soon after the discovery of PM.
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Affiliation(s)
- René Riedel
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Natalie Frese
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Fang Yang
- Nano Biomaterials Group, Ningbo Institute of Industrial Technology, Chinese Academy of Science, China
| | - Martin Wortmann
- Faculty of Engineering and Mathematics, Bielefeld University of Applied Sciences, Interaktion 1, D-33619 Bielefeld, Germany
| | - Raphael Dalpke
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Daniel Rhinow
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany
| | - Norbert Hampp
- Faculty of Chemistry and Materials Sciences Center, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Armin Gölzhäuser
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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Direct and Label-Free Determination of Human Glycated Hemoglobin Levels Using Bacteriorhodopsin as the Biosensor Transducer. SENSORS 2020; 20:s20247274. [PMID: 33353006 PMCID: PMC7765918 DOI: 10.3390/s20247274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/08/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023]
Abstract
Glycated hemoglobin (HbA1c) levels are an important index for the diagnosis and long-term control of diabetes. This study is the first to use a direct and label-free photoelectric biosensor to determine HbA1c using bacteriorhodopsin-embedded purple membranes (PM) as a transducer. A biotinylated PM (b-PM) coated electrode that is layered with protein A-oriented antibodies against hemoglobin (Hb) readily captures non-glycated Hb (HbA0) and generates less photocurrent. The spectra of bacteriorhodopsin and Hb overlap so the photocurrent is reduced because of the partial absorption of the incident light by the captured Hb molecules. Two HbA0 and HbA1c aptasensors that are prepared by conjugating specific aptamers on b-PM coated electrodes single-step detect HbA0 and HbA1c in 15 min, without cross reactivity, with detection limits of ≤0.1 μg/mL and a dynamic range of 0.1–100 μg/mL. Both aptasensors exhibit high selectivity and long-term stability. For the clinical samples, HbA0 concentrations and HbA1c levels that are measured with aptasensors correlate well with total Hb concentrations and the HbA1c levels that are determined using standard methods (correlation gradient = 0.915 ± 0.004 and 0.981 ± 0.001, respectively). The use of these aptasensors for diabetes care is demonstrated.
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Hammond K, Ryadnov MG, Hoogenboom BW. Atomic force microscopy to elucidate how peptides disrupt membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183447. [PMID: 32835656 DOI: 10.1016/j.bbamem.2020.183447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.
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Affiliation(s)
- Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; Department of Physics, King's College London, Strand Lane, London WC2R 2LS, UK.
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
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Stauffer M, Hirschi S, Ucurum Z, Harder D, Schlesinger R, Fotiadis D. Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies. Methods Protoc 2020; 3:mps3030051. [PMID: 32707904 PMCID: PMC7563565 DOI: 10.3390/mps3030051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 11/16/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (BR) from the extreme halophilic archaeon Halobacterium salinarum is a retinal-binding protein, which forms highly ordered and thermally stable 2D crystals in native membranes (termed purple membranes). BR and purple membranes (PMs) have been and are still being intensively studied by numerous researchers from different scientific disciplines. Furthermore, PMs are being successfully used in new, emerging technologies such as bioelectronics and bionanotechnology. Most published studies used the wild-type form of BR, because of the intrinsic difficulty to produce genetically modified versions in purple membranes homologously. However, modification and engineering is crucial for studies in basic research and, in particular, to tailor BR for specific applications in applied sciences. We present an extensive and detailed protocol ranging from the genetic modification and cultivation of H. salinarum to the isolation, and biochemical, biophysical and functional characterization of BR and purple membranes. Pitfalls and problems of the homologous expression of BR versions in H. salinarum are discussed and possible solutions presented. The protocol is intended to facilitate the access to genetically modified BR versions for researchers of different scientific disciplines, thus increasing the application of this versatile biomaterial.
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Affiliation(s)
- Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: (R.S.); (D.F.)
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
- Correspondence: (R.S.); (D.F.)
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11
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Hemeda AA, Pal S, Mishra A, Torabi M, Ahmadlouydarab M, Li Z, Palko J, Ma Y. Effect of Wetting and Dewetting Dynamics on Atomic Force Microscopy Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13301-13310. [PMID: 31536702 DOI: 10.1021/acs.langmuir.9b02575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Water bridge dynamics between an atomic force microscopy (AFM) tip and a flat substrate is studied by using a multibody dissipative particle dynamics (MDPD) model. First, the numerical model is validated by comparing the present results of droplet contact angles and liquid bridges with those reported in the literature. Then, the ability of MDPD to capture the meniscus shape and behavior for different operating conditions and geometric parameters is examined for both static and dynamic cases. Hence, several parametric studies and analyses of the AFM tip configuration and its operating conditions are reported. It is found that a critical capillary number of about 0.001 is calculated based on 5% change on the force measurements between the static and dynamic results. It is also demonstrated that the hysteresis behavior in the capillary force exerted on the AFM tip can be successfully predicted by using the MDPD model when the tip approaches or retracts from the substrate. Moreover, there is an excellent agreement in the results of breakup distance for different water bridge volumes between the predictions of the MDPD model and the theory. Also, the hysteresis of capillary force exerted on an AFM tip composed of multibody design is studied. The prediction on the transition of the capillary force vs distance between the AFM tip and the substrate is in good agreement with the experimental results. Therefore, we demonstrate a validated MDPD model which can successfully capture liquid bridge dynamics. This model can be used as a powerful design tool for meniscus manipulation technology, such as dip-pen nanolithography, as well as for studying dynamic, e.g., tapping mode AFM tip, interactions with a liquid bridge.
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Affiliation(s)
- A A Hemeda
- School of Engineering , University of California, Merced , Merced , California 95343 , United States
- Aerospace Engineering Department , Cairo University , Giza 12613 , Egypt
| | - S Pal
- Department of Mechanical Engineering , McMaster University , Hamilton , ON L8S 4L7 , Canada
| | - A Mishra
- School of Engineering , University of California, Merced , Merced , California 95343 , United States
| | - M Torabi
- School of Engineering , University of California, Merced , Merced , California 95343 , United States
| | - M Ahmadlouydarab
- Faculty of Chemical and Petroleum Engineering , University of Tabriz , Tabriz , Iran
| | - Z Li
- Department of Mechanical Engineering , Clemson University , Clemson , South Carolina 29634 , United States
| | - J Palko
- School of Engineering , University of California, Merced , Merced , California 95343 , United States
| | - Y Ma
- School of Engineering , University of California, Merced , Merced , California 95343 , United States
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Ungai-Salánki R, Peter B, Gerecsei T, Orgovan N, Horvath R, Szabó B. A practical review on the measurement tools for cellular adhesion force. Adv Colloid Interface Sci 2019; 269:309-333. [PMID: 31128462 DOI: 10.1016/j.cis.2019.05.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 01/03/2023]
Abstract
Cell-cell and cell-matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response, pathogen-host interactions, and tumor development. The success of tissue engineering and stem cell implantations strongly depends on the fine control of live cell adhesion on the surface of natural or biomimetic scaffolds. Therefore, the quantitative and precise measurement of the adhesion strength of living cells is critical, not only in basic research but in modern technologies, too. Several techniques have been developed or are under development to quantify cell adhesion. All of them have their pros and cons, which has to be carefully considered before the experiments and interpretation of the recorded data. Current review provides a guide to choose the appropriate technique to answer a specific biological question or to complete a biomedical test by measuring cell adhesion.
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15
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Thoma J, Sapra KT, Müller DJ. Single-Molecule Force Spectroscopy of Transmembrane β-Barrel Proteins. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:375-395. [PMID: 29894225 DOI: 10.1146/annurev-anchem-061417-010055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule force spectroscopy (SMFS) has been widely applied to study the mechanical unfolding and folding of transmembrane proteins. Here, we review the recent progress in characterizing bacterial and human transmembrane β-barrel proteins by SMFS. First, we describe the mechanical unfolding of transmembrane β-barrels, which follows a general mechanism dictated by the sequential unfolding and extraction of individual β-strands and β-hairpins from membranes. Upon force relaxation, the unfolded polypeptide can insert stepwise into the membrane as single β-strands or β-hairpins to fold as the native β-barrel. The refolding can be followed at a high spatial and temporal resolution, showing that small β-barrels are able to fold without assistance, whereas large and complex β-barrels require chaperone cofactors. Applied in the dynamic mode, SMFS can quantify the kinetic and mechanical properties of single β-hairpins and reveal complementary insight into the membrane protein structure and function relationship. We further outline the challenges that SMFS experiments must overcome for a comprehensive understanding of the folding and function of transmembrane β-barrel proteins.
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Affiliation(s)
- Johannes Thoma
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
| | | | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
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16
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Pleshakova TO, Bukharina NS, Archakov AI, Ivanov YD. Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization. Int J Mol Sci 2018; 19:E1142. [PMID: 29642632 PMCID: PMC5979402 DOI: 10.3390/ijms19041142] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.
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Affiliation(s)
| | - Natalia S Bukharina
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
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17
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Moores AN, Cadby AJ. Simultaneous AFM and fluorescence imaging: A method for aligning an AFM-tip with an excitation beam using a 2D galvanometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:023708. [PMID: 29495824 DOI: 10.1063/1.5006724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
Correlative fluorescence and atomic force microscopy (AFM) imaging is a highly attractive technique for use in biological imaging, enabling force and mechanical measurements of particular structures whose locations are known due to the specificity of fluorescence imaging. The ability to perform these two measurements simultaneously (rather than consecutively with post-processing correlation) is highly valuable because it would allow the mechanical properties of a structure to be tracked over time as changes in the sample occur. We present an instrument which allows simultaneous AFM and fluorescence imaging by aligning an incident fluorescence excitation beam with an AFM-tip. Alignment was performed by calibrating a 2D galvanometer present in the excitation beam path and using it to reposition the incident beam. Two programs were developed (one manual and one automated) which correlate sample features between the AFM and fluorescence images, calculating the distance required to translate the incident beam towards the AFM-tip. Using this method, we were able to obtain beam-tip alignment (and therefore field-of-view alignment) from an offset of >15 μm to within one micron in two iterations of the program. With the program running alongside data acquisition for real-time feedback between AFM and optical images, this offset was maintained over a time period of several hours. Not only does this eliminate the need to image large areas with both techniques to ensure that fields-of-view overlap, but it also raises the possibility of using this instrument for tip-enhanced fluorescence applications, a technique in which super-resolution images have previously been achieved.
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Affiliation(s)
- A N Moores
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - A J Cadby
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
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18
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Franz J, Grünebaum J, Schäfer M, Mulac D, Rehfeldt F, Langer K, Kramer A, Riethmüller C. Rhombic organization of microvilli domains found in a cell model of the human intestine. PLoS One 2018; 13:e0189970. [PMID: 29320535 PMCID: PMC5761853 DOI: 10.1371/journal.pone.0189970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Symmetry is rarely found on cellular surfaces. An exception is the brush border of microvilli, which are essential for the proper function of transport epithelia. In a healthy intestine, they appear densely packed as a 2D-hexagonal lattice. For in vitro testing of intestinal transport the cell line Caco-2 has been established. As reported by electron microscopy, their microvilli arrange primarily in clusters developing secondly into a 2D-hexagonal lattice. Here, atomic force microscopy (AFM) was employed under aqueous buffer conditions on Caco-2 cells, which were cultivated on permeable filter membranes for optimum differentiation. For analysis, the exact position of each microvillus was detected by computer vision; subsequent Fourier transformation yielded the type of 2D-lattice. It was confirmed, that Caco-2 cells can build a hexagonal lattice of microvilli and form clusters. Moreover, a second type of arrangement was discovered, namely a rhombic lattice, which appeared at sub-maximal densities of microvilli with (29 ± 4) microvilli / μm2. Altogether, the findings indicate the existence of a yet undescribed pattern in cellular organization.
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Affiliation(s)
- Jonas Franz
- Faculty of Physics, Georg-August-Universität, Göttingen, Germany
- Max Planck Institute for Dynamics and Self-Organization, Theoretical Neurophysics, Göttingen, Germany
| | - Jonas Grünebaum
- Institute for Pharmaceutical Technology and Biopharmacy, University of Münster, Münster, Germany
| | - Marcus Schäfer
- nanoAnalytics GmbH, Centre for Nanotechnology, Münster, Germany
| | - Dennis Mulac
- Institute for Pharmaceutical Technology and Biopharmacy, University of Münster, Münster, Germany
| | - Florian Rehfeldt
- Third Institute of Physics—Biophysics, Georg-August-Universität, Göttingen, Germany
| | - Klaus Langer
- Institute for Pharmaceutical Technology and Biopharmacy, University of Münster, Münster, Germany
| | - Armin Kramer
- Serend-ip GmbH, Centre for Nanotechnology, Münster, Germany
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Delguste M, Koehler M, Alsteens D. Probing Single Virus Binding Sites on Living Mammalian Cells Using AFM. Methods Mol Biol 2018; 1814:483-514. [PMID: 29956251 DOI: 10.1007/978-1-4939-8591-3_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the last years, atomic force microscopy (AFM)-based approaches have evolved into a powerful multiparametric tool that allows biological samples ranging from single receptors to membranes and tissues to be probed. Force-distance curve-based AFM (FD-based AFM) nowadays enables to image living cells at high resolution and simultaneously localize and characterize specific ligand-receptor binding events. In this chapter, we present how FD-based AFM permits to investigate virus binding to living mammalian cells and quantify the kinetic and thermodynamic parameters that describe the free-energy landscape of the single virus-receptor-mediated binding. Using a model virus, we probed the specific interaction with cells expressing its cognate receptor and measured the affinity of the interaction. Furthermore, we observed that the virus rapidly established specific multivalent interactions and found that each bond formed in sequence strengthens the attachment of the virus to the cell.
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Affiliation(s)
- Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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20
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QIN GG, LI WH, XU JC, KOU XL, ZHAO R, LUO F, FANG XH. Development of Integrated Atomic Force Microscopy and Fluorescence Microscopy for Single-Molecule Analysis in Living Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61056-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Laskowski PR, Pfreundschuh M, Stauffer M, Ucurum Z, Fotiadis D, Müller DJ. High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox. ACS NANO 2017; 11:8292-8301. [PMID: 28745869 DOI: 10.1021/acsnano.7b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.
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Affiliation(s)
- Pawel R Laskowski
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
| | - Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich , 4058 Basel, Switzerland
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22
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Liu H, Wang N, Zhang Z, Wang H, Du J, Tang J. Effects of Tumor Necrosis Factor- α on Morphology and Mechanical Properties of HCT116 Human Colon Cancer Cells Investigated by Atomic Force Microscopy. SCANNING 2017; 2017:2027079. [PMID: 29109804 PMCID: PMC5661774 DOI: 10.1155/2017/2027079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/03/2016] [Indexed: 05/27/2023]
Abstract
Chronic inflammation orchestrates the tumor microenvironment and is strongly associated with cancer. Tumor necrosis factor-α (TNFα) is involved in tumor invasion and metastasis by inducing epithelial to mesenchymal transition (EMT). This process is defined by the loss of epithelial characteristics and gain of mesenchymal traits. The mechanisms of TNFα-induced EMT in cancer cells have been well studied. However, mechanical properties have not yet been probed. In this work, atomic force microscopy (AFM) was applied to investigate the morphology and mechanical properties of EMT in HCT116 human colon cancer cells. A remarkable morphological change from cobblestone shape to spindle-like morphology was observed. In parallel, AFM images showed that the cellular cytoskeleton was rearranged from a cortical to a stress-fiber pattern. Moreover, cell stiffness measurements indicated that Young's modulus of cells gradually reduced from 1 to 3 days with TNFα-treatment, but it has an apparent increase after 4 days of treatment compared with that for 3 days. Additionally, Young's modulus of the cells treated with TNFα for 4 days is slightly larger than that for 1 or 2 days, but still less than that of the untreated cells. Our work contributes to a better understanding of colorectal cancer metastasis induced by inflammation.
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Affiliation(s)
- Huiqing Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Nan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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23
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Pfreundschuh M, Harder D, Ucurum Z, Fotiadis D, Müller DJ. Detecting Ligand-Binding Events and Free Energy Landscape while Imaging Membrane Receptors at Subnanometer Resolution. NANO LETTERS 2017; 17:3261-3269. [PMID: 28361535 DOI: 10.1021/acs.nanolett.7b00941] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force-distance curve-based atomic force microscopy has emerged into a sophisticated technique for imaging cellular membranes and for detecting specific ligand-binding events of native membrane receptors. However, so far the resolution achieved has been insufficient to structurally map ligand-binding sites onto membrane proteins. Here, we introduce experimental and theoretical approaches for overcoming this limitation. To establish a structurally and functionally well-defined reference sample, we engineer a ligand-binding site to the light-driven proton pump bacteriorhodopsin of purple membrane. Functionalizing the AFM stylus with an appropriate linker-system tethering the ligand and optimizing the AFM conditions allows for imaging the engineered bacteriorhodopsin at subnanometer resolution while structurally mapping the specific ligand-receptor binding events. Improved data analysis allows reconstructing the ligand-binding free energy landscape from the experimental data, thus providing thermodynamic and kinetic insight into the ligand-binding process. The nanoscopic method introduced is generally applicable for imaging receptors in native membranes at subnanometer resolution and for systematically mapping and quantifying the free energy landscape of ligand binding.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern , 3012 Bern, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich , 4058 Basel, Switzerland
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24
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Dufrêne YF, Ando T, Garcia R, Alsteens D, Martinez-Martin D, Engel A, Gerber C, Müller DJ. Imaging modes of atomic force microscopy for application in molecular and cell biology. NATURE NANOTECHNOLOGY 2017; 12:295-307. [PMID: 28383040 DOI: 10.1038/nnano.2017.45] [Citation(s) in RCA: 482] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.
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Affiliation(s)
- Yves F Dufrêne
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - Toshio Ando
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - David Alsteens
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - David Martinez-Martin
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andreas Engel
- Department of BioNanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christoph Gerber
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 80, 4057 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
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25
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Bronder AM, Bieker A, Elter S, Etzkorn M, Häussinger D, Oesterhelt F. Oriented Membrane Protein Reconstitution into Tethered Lipid Membranes for AFM Force Spectroscopy. Biophys J 2016; 111:1925-1934. [PMID: 27806274 PMCID: PMC5103026 DOI: 10.1016/j.bpj.2016.08.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
Membrane proteins act as a central interface between the extracellular environment and the intracellular response and as such represent one of the most important classes of drug targets. The characterization of the molecular properties of integral membrane proteins, such as topology and interdomain interaction, is key to a fundamental understanding of their function. Atomic force microscopy (AFM) and force spectroscopy have the intrinsic capabilities of investigating these properties in a near-native setting. However, atomic force spectroscopy of membrane proteins is traditionally carried out in a crystalline setup. Alternatively, model membrane systems, such as tethered bilayer membranes, have been developed for surface-dependent techniques. While these setups can provide a more native environment, data analysis may be complicated by the normally found statistical orientation of the reconstituted protein in the model membrane. We have developed a model membrane system that enables the study of membrane proteins in a defined orientation by single-molecule force spectroscopy. Our approach is demonstrated using cell-free expressed bacteriorhodopsin coupled to a quartz glass surface in a defined orientation through a protein anchor and reconstituted inside an artificial membrane system. This approach offers an effective way to study membrane proteins in a planar lipid bilayer. It can be easily transferred to all membrane proteins that possess a suitable tag and can be reconstituted into a lipid bilayer. In this respect, we anticipate that this technique may contribute important information on structure, topology, and intra- and intermolecular interactions of other seven-transmembrane helical receptors.
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Affiliation(s)
- Anna M Bronder
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany.
| | - Adeline Bieker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Shantha Elter
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectiology, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Filipp Oesterhelt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany; Department for Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
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26
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Chen HM, Jheng KR, Yu AD, Hsu CC, Lin JH. Intercalating purple membranes into 2D β-alanine crystals to enhance photoelectric and nonlinear optical properties. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Perrino AP, Garcia R. How soft is a single protein? The stress-strain curve of antibody pentamers with 5 pN and 50 pm resolutions. NANOSCALE 2016; 8:9151-8. [PMID: 26732032 DOI: 10.1039/c5nr07957h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Understanding the mechanical functionalities of complex biological systems requires the measurement of the mechanical compliance of their smallest components. Here, we develop a force microscopy method to quantify the softness of a single antibody pentamer by measuring the stress-strain curve with force and deformation resolutions, respectively, of 5 pN and 50 pm. The curve shows three distinctive regions. For ultrasmall compressive forces (5-75 pN), the protein's central region shows that the strain and stress are proportional (elastic regime). This region has an average Young's modulus of 2.5 MPa. For forces between 80 and 220 pN, the stress is roughly proportional to the strain with a Young's modulus of 9 MPa. Higher forces lead to irreversible deformations (plastic regime). Full elastic recovery could reach deformations amounting to 40% of the protein height. The existence of two different elastic regions is explained in terms of the structure of the antibody central region. The stress-strain curve explains the capability of the antibody to sustain multiple collisions without any loss of biological functionality.
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Affiliation(s)
- Alma P Perrino
- Instituto de Ciencia de Materiales de Madrid (CSIC), c/ Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid (CSIC), c/ Sor Juana Ines de la Cruz 3, 28049 Madrid, Spain.
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28
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Senapati S, Lindsay S. Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy. Acc Chem Res 2016; 49:503-10. [PMID: 26934674 DOI: 10.1021/acs.accounts.5b00533] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Atomic force microscopy (AFM) is an extremely powerful tool in the field of bionanotechnology because of its ability to image single molecules and make measurements of molecular interaction forces with piconewton sensitivity. It works in aqueous media, enabling studies of molecular phenomenon taking place under physiological conditions. Samples can be imaged in their near-native state without any further modifications such as staining or tagging. The combination of AFM imaging with the force measurement added a new feature to the AFM technique, that is, molecular recognition imaging. Molecular recognition imaging enables mapping of specific interactions between two molecules (one attached to the AFM tip and the other to the imaging substrate) by generating simultaneous topography and recognition images (TREC). Since its discovery, the recognition imaging technique has been successfully applied to different systems such as antibody-protein, aptamer-protein, peptide-protein, chromatin, antigen-antibody, cells, and so forth. Because the technique is based on specific binding between the ligand and receptor, it has the ability to detect a particular protein in a mixture of proteins or monitor a biological phenomenon in the native physiological state. One key step for recognition imaging technique is the functionalization of the AFM tips (generally, silicon, silicon nitrides, gold, etc.). Several different functionalization methods have been reported in the literature depending on the molecules of interest and the material of the tip. Polyethylene glycol is routinely used to provide flexibility needed for proper binding as a part of the linker that carries the affinity molecule. Recently, a heterofunctional triarm linker has been synthesized and successfully attached with two different affinity molecules. This novel linker, when attached to AFM tip, helped to detect two different proteins simultaneously from a mixture of proteins using a so-called "two-color" recognition image. Biological phenomena in nature often involve multimolecular interactions, and this new linker could be ideal for studying them using AFM recognition imaging. It also has the potential to be used extensively in the diagnostics technique. This Account includes fundamentals behind AFM recognition imaging, a brief discussion on tip functionalization, recent advancements, and future directions and possibilities.
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Affiliation(s)
- Subhadip Senapati
- Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of
Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Stuart Lindsay
- Biodesign Institute, ‡Department of Chemistry and Biochemistry, and §Department of
Physics, Arizona State University, Tempe, Arizona 85287, United States
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29
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Priest M, Bezanilla F. Functional Site-Directed Fluorometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 869:55-76. [PMID: 26381940 DOI: 10.1007/978-1-4939-2845-3_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Initially developed in the mid-1990s to examine the conformational changes of the canonical Shaker voltage-gated potassium channel, functional site-directed fluorometry has since been expanded to numerous other voltage-gated and ligand-gated ion channels as well as transporters, pumps, and other integral membrane proteins. The power of functional site-directed fluorometry, also known as voltage-clamp fluorometry, lies in its ability to provide information on the conformational changes in a protein in response to changes in its environment with high temporal resolution while simultaneously monitoring the function of that protein. Over time, applications of site-directed fluorometry have expanded to examine the interactions of ion channels with modulators ranging from membrane potential to ligands to accessory protein subunits to lipids. In the future, the range of questions answerable by functional site-directed fluorometry and its interpretive power should continue to improve, making it an even more powerful technique for dissecting the conformational dynamics of ion channels and other membrane proteins.
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Affiliation(s)
- Michael Priest
- Department of Biochemistry and Molecular Biology and Committee on Neurobiology, University of Chicago, Gordon Center for Integrative Science W229M, 929 East 57th Street, 60637, Chicago, IL, USA.
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology and Committee on Neurobiology, University of Chicago, Gordon Center for Integrative Science W229M, 929 East 57th Street, 60637, Chicago, IL, USA.
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30
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Assemblies of pore-forming toxins visualized by atomic force microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:500-11. [PMID: 26577274 DOI: 10.1016/j.bbamem.2015.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 10/23/2015] [Accepted: 11/09/2015] [Indexed: 02/05/2023]
Abstract
A number of pore-forming toxins (PFTs) can assemble on lipid membranes through their specific interactions with lipids. The oligomeric assemblies of some PFTs have been successfully revealed either by electron microscopy (EM) and/or atomic force microscopy (AFM). Unlike EM, AFM imaging can be performed under physiological conditions, enabling the real-time visualization of PFT assembly and the transition from the prepore state, in which the toxin does not span the membrane, to the pore state. In addition to characterizing PFT oligomers, AFM has also been used to examine toxin-induced alterations in membrane organization. In this review, we summarize the contributions of AFM to the understanding of both PFT assembly and PFT-induced membrane reorganization. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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31
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Odermatt PD, Shivanandan A, Deschout H, Jankele R, Nievergelt AP, Feletti L, Davidson MW, Radenovic A, Fantner GE. High-Resolution Correlative Microscopy: Bridging the Gap between Single Molecule Localization Microscopy and Atomic Force Microscopy. NANO LETTERS 2015; 15:4896-904. [PMID: 26121585 DOI: 10.1021/acs.nanolett.5b00572] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanoscale characterization of living samples has become essential for modern biology. Atomic force microscopy (AFM) creates topological images of fragile biological structures from biomolecules to living cells in aqueous environments. However, correlating nanoscale structure to biological function of specific proteins can be challenging. To this end we have built and characterized a correlated single molecule localization microscope (SMLM)/AFM that allows localizing specific, labeled proteins within high-resolution AFM images in a biologically relevant context. Using direct stochastic optical reconstruction microscopy (dSTORM)/AFM, we directly correlate and quantify the density of localizations with the 3D topography using both imaging modalities along (F-)actin cytoskeletal filaments. In addition, using photo activated light microscopy (PALM)/AFM, we provide correlative images of bacterial cells in aqueous conditions. Moreover, we report the first correlated AFM/PALM imaging of live mammalian cells. The complementary information provided by the two techniques opens a new dimension for structural and functional nanoscale biology.
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Affiliation(s)
| | | | | | | | | | | | - Michael W Davidson
- §National High Magnetic Field Laboratory and Department of Biological Science, Florida State University, Tallahassee, Florida 32306 United States
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Tanaka A, Tanaka R, Kasai N, Tsukada S, Okajima T, Sumitomo K. Time-lapse imaging of morphological changes in a single neuron during the early stages of apoptosis using scanning ion conductance microscopy. J Struct Biol 2015; 191:32-8. [DOI: 10.1016/j.jsb.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/30/2022]
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33
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Petrosyan R, Bippes CA, Walheim S, Harder D, Fotiadis D, Schimmel T, Alsteens D, Müller DJ. Single-molecule force spectroscopy of membrane proteins from membranes freely spanning across nanoscopic pores. NANO LETTERS 2015; 15:3624-3633. [PMID: 25879249 DOI: 10.1021/acs.nanolett.5b01223] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy (SMFS) provides detailed insight into the mechanical (un)folding pathways and structural stability of membrane proteins. So far, SMFS could only be applied to membrane proteins embedded in native or synthetic membranes adsorbed to solid supports. This adsorption causes experimental limitations and raises the question to what extent the support influences the results obtained by SMFS. Therefore, we introduce here SMFS from native purple membrane freely spanning across nanopores. We show that correct analysis of the SMFS data requires extending the worm-like chain model, which describes the mechanical stretching of a polypeptide, by the cubic extension model, which describes the bending of a purple membrane exposed to mechanical stress. This new experimental and theoretical approach allows to characterize the stepwise (un)folding of the membrane protein bacteriorhodopsin and to assign the stability of single and grouped secondary structures. The (un)folding and stability of bacteriorhodopsin shows no significant difference between freely spanning and directly supported purple membranes. Importantly, the novel experimental SMFS setup opens an avenue to characterize any protein from freely spanning cellular or synthetic membranes.
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Affiliation(s)
- Rafayel Petrosyan
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Christian A Bippes
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Stefan Walheim
- †Institute of Applied Physics and Center for Functional Nanostructures (CFN) and Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Daniel Harder
- §Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- §Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Thomas Schimmel
- †Institute of Applied Physics and Center for Functional Nanostructures (CFN) and Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - David Alsteens
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
| | - Daniel J Müller
- ‡Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058 Basel, Switzerland
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Akrami SMR, Nakayachi H, Watanabe-Nakayama T, Asakawa H, Fukuma T. Significant improvements in stability and reproducibility of atomic-scale atomic force microscopy in liquid. NANOTECHNOLOGY 2014; 25:455701. [PMID: 25327221 DOI: 10.1088/0957-4484/25/45/455701] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent advancement of dynamic-mode atomic force microscopy (AFM) for liquid-environment applications enabled atomic-scale studies on various interfacial phenomena. However, instabilities and poor reproducibility of the measurements often prevent systematic studies. To solve this problem, we have investigated the effect of various tip treatment methods for atomic-scale imaging and force measurements in liquid. The tested methods include Si coating, Ar plasma, Ar sputtering and UV/O₃ cleaning. We found that all the methods provide significant improvements in both the imaging and force measurements in spite of the tip transfer through the air. Among the methods, we found that the Si coating provides the best stability and reproducibility in the measurements. To understand the origin of the fouling resistance of the cleaned tip surface and the difference between the cleaning methods, we have investigated the tip surface properties by x-ray photoelectron spectroscopy and contact angle measurements. The results show that the contaminations adsorbed on the tip during the tip transfer through the air should desorb from the surface when it is immersed in aqueous solution due to the enhanced hydrophilicity by the tip treatments. The tip surface prepared by the Si coating is oxidized when it is immersed in aqueous solution. This creates local spots where stable hydration structures are formed. For the other methods, there is no active mechanism to create such local hydration sites. Thus, the hydration structure formed under the tip apex is not necessarily stable. These results reveal the desirable tip properties for atomic-scale AFM measurements in liquid, which should serve as a guideline for further improvements of the tip treatment methods.
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Affiliation(s)
- S M R Akrami
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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35
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Yokoyama Y, Yamada K, Higashi Y, Ozaki S, Wang H, Koito N, Watanabe N, Sonoyama M, Mitaku S. Dependence of Purple Membrane Bump Curvature on pH and Ionic Strength Analyzed Using Atomic Force Microscopy Combined with Solvent Exchange. J Phys Chem B 2014; 118:9322-8. [DOI: 10.1021/jp5036234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasunori Yokoyama
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Kosuke Yamada
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Yosuke Higashi
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Satoshi Ozaki
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Haorang Wang
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Naoki Koito
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | | | - Masashi Sonoyama
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Shigeki Mitaku
- Department
of Applied Physics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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36
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Sharma S, Grintsevich E, Woo J, Gurel PS, Higgs HN, Reisler E, Gimzewski JK. Nanostructured self-assembly of inverted formin 2 (INF2) and F-actin-INF2 complexes revealed by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7533-7539. [PMID: 24915113 PMCID: PMC4082382 DOI: 10.1021/la501748x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/08/2014] [Indexed: 06/03/2023]
Abstract
Self-organization of cytoskeletal proteins such as actin and tubulin into filaments and microtubules is frequently assisted by the proteins binding to them. Formins are regulatory proteins that nucleate the formation of new filaments and are essential for a wide range of cellular functions. The vertebrate inverted formin 2 (INF2) has both actin filament nucleating and severing/depolymerizing activities connected to its ability to encircle actin filaments. Using atomic force microscopy, we report that a formin homology 2 (FH2) domain-containing construct of INF2 (INF2-FH1-FH2-C or INF2-FFC) self-assembles into nanoscale ringlike oligomeric structures in the absence of actin filaments, demonstrating an inherent ability to reorganize from a dimeric to an oligomeric state. A construct lacking the C-terminal region (INF2-FH1-FH2 or INF2-FF) also oligomerizes, confirming the dominant role of FH2-mediated interactions. Moreover, INF2-FFC domains were observed to organize into ringlike structures around single actin filaments. This is the first demonstration that formin FH2 domains can self-assemble into oligomers in the absence of filaments and has important implications for observing unaveraged decoration and/or remodeling of filaments by actin binding proteins.
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Affiliation(s)
- Shivani Sharma
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elena
E. Grintsevich
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - JungReem Woo
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Pinar S. Gurel
- Department
of Biochemistry, Geisel School of Medicine
at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Henry N. Higgs
- Department
of Biochemistry, Geisel School of Medicine
at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Emil Reisler
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- Molecular
Biology Institute, University of California, Los Angeles, California 90095, United States
| | - James K. Gimzewski
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, University
of California, Los Angeles, California 90095, United States
- International
Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
- Centre for
Nanoscience and Quantum Information, University
of Bristol, Bristol BS8 1TH, U.K.
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37
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Eghiaian F, Rico F, Colom A, Casuso I, Scheuring S. High-speed atomic force microscopy: Imaging and force spectroscopy. FEBS Lett 2014; 588:3631-8. [DOI: 10.1016/j.febslet.2014.06.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 10/25/2022]
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38
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Bull MS, Sullan RMA, Li H, Perkins TT. Improved single molecule force spectroscopy using micromachined cantilevers. ACS NANO 2014; 8:4984-95. [PMID: 24670198 DOI: 10.1021/nn5010588] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Enhancing the short-term force precision of atomic force microscopy (AFM) while maintaining excellent long-term force stability would result in improved performance across multiple AFM modalities, including single molecule force spectroscopy (SMFS). SMFS is a powerful method to probe the nanometer-scale dynamics and energetics of biomolecules (DNA, RNA, and proteins). The folding and unfolding rates of such macromolecules are sensitive to sub-pN changes in force. Recently, we demonstrated sub-pN stability over a broad bandwidth (Δf = 0.01-16 Hz) by removing the gold coating from a 100 μm long cantilever. However, this stability came at the cost of increased short-term force noise, decreased temporal response, and poor sensitivity. Here, we avoided these compromises while retaining excellent force stability by modifying a short (L = 40 μm) cantilever with a focused ion beam. Our process led to a ∼10-fold reduction in both a cantilever's stiffness and its hydrodynamic drag near a surface. We also preserved the benefits of a highly reflective cantilever while mitigating gold-coating induced long-term drift. As a result, we extended AFM's sub-pN bandwidth by a factor of ∼50 to span five decades of bandwidth (Δf ≈ 0.01-1000 Hz). Measurements of mechanically stretching individual proteins showed improved force precision coupled with state-of-the-art force stability and no significant loss in temporal resolution compared to the stiffer, unmodified cantilever. Finally, these cantilevers were robust and were reused for SFMS over multiple days. Hence, we expect these responsive, yet stable, cantilevers to broadly benefit diverse AFM-based studies.
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Affiliation(s)
- Matthew S Bull
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder, Colorado 80309, United States
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39
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Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc 2014; 9:1113-30. [DOI: 10.1038/nprot.2014.070] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Chen HM, Lin CJ, Jheng KR, Kosasih A, Chang JY. Effect of graphene oxide on affinity-immobilization of purple membranes on solid supports. Colloids Surf B Biointerfaces 2014; 116:482-8. [DOI: 10.1016/j.colsurfb.2014.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/14/2014] [Accepted: 01/25/2014] [Indexed: 11/29/2022]
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41
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Timmel T, Schuelke M, Spuler S. Identifying dynamic membrane structures with atomic-force microscopy and confocal imaging. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:514-520. [PMID: 24524258 DOI: 10.1017/s1431927613014098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Combining the biological specificity of fluorescence microscopy with topographical features revealed by atomic force microscopy (AFM) provides new insights into cell biology. However, the lack of systematic alignment capabilities especially in scanning-tip AFM has limited the combined application approach as AFM drift leads to increasing image mismatch over time. We present an alignment correction method using the cantilever tip as a reference landmark. Since the precise tip position is known in both the fluorescence and AFM images, exact re-alignment becomes possible. We used beads to demonstrate the validity of the method in a complex artificial sample. We then extended this method to biological samples to depict membrane structures in fixed and living human fibroblasts. We were able to map nanoscale membrane structures, such as clathrin-coated pits, to their respective fluorescent spots. Reliable alignment between fluorescence signals and topographic structures opens possibilities to assess key biological processes at the cell surface such as endocytosis and exocytosis.
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Affiliation(s)
- Tobias Timmel
- 1 Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine Berlin, Lindenberger Weg 80, D-13125 Berlin, Germany
| | - Markus Schuelke
- 2 Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité Universitätsmedizin, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Simone Spuler
- 1 Muscle Research Unit, Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine Berlin, Lindenberger Weg 80, D-13125 Berlin, Germany
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42
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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43
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Vukosavljevic D, Hutter JL, Helmerhorst EJ, Xiao Y, Custodio W, Zaidan FC, Oppenheim FG, Siqueira WL. Nanoscale adhesion forces between enamel pellicle proteins and hydroxyapatite. J Dent Res 2014; 93:514-9. [PMID: 24591293 DOI: 10.1177/0022034514526599] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The acquired enamel pellicle (AEP) is important for minimizing the abrasion caused by parafunctional conditions as they occur, for instance, during bruxism. It is a remarkable feature of the AEP that a protein/peptide film can provide enough protection in normofunction to prevent teeth from abrasion and wear. Despite its obvious critical role in the protection of tooth surfaces, the essential adhesion features of AEP proteins on the enamel surface are poorly characterized. The objective of this study was to measure the adhesion force between histatin 5, a primary AEP component, and hydroxyapatite (HA) surfaces. Both biotinylated histatin 5 and biotinylated human serum albumin were allowed to adsorb to streptavidin-coated silica microspheres attached to atomic force microscope (AFM) cantilevers. A multimode AFM with a Nanoscope IIIa controller was used to measure the adhesion force between protein-functionalized silica microspheres attached to cantilever tips and the HA surface. The imaging was performed in tapping mode with a Si3N4 AFM cantilever, while the adhesion forces were measured in AFM contact mode. A collection of force-distance curves (~3,000/replicate) was obtained to generate histograms from which the adhesion forces between histatin 5 or albumin and the HA surface were measured. We found that histatin 5 exhibited stronger adhesion forces (90% >1.830 nN) to the HA surface than did albumin (90% > 0.282 nN). This study presents an objective approach to adhesion force measurements between histatin 5 and HA, and provides the experimental basis for measuring the same parameters for other AEP constituents. Such knowledge will help in the design of synthetic proteins and peptides with preventive and therapeutic benefits for tooth enamel.
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Affiliation(s)
- D Vukosavljevic
- Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON N5A 6C1, Canada
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44
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de Pablo PJ, Carrión-Vázquez M. Imaging biological samples with atomic force microscopy. Cold Spring Harb Protoc 2014; 2014:167-77. [PMID: 24492779 DOI: 10.1101/pdb.top080473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Atomic force microscopy (AFM) is an invaluable tool both for obtaining high-resolution topographical images and for determining the values of mechanical and structural properties of specimens adsorbed onto a surface. AFM is useful in an array of fields and applications, from materials science to biology. It is an extremely versatile technique that can be applied to almost any surface-mounted sample and can be operated in ambient air, ultrahigh vacuum, and, most importantly for biology, liquids. AFM can be used to explore samples ranging in size from atoms to molecules, molecular aggregates, and cells. Individual biomolecules can be viewed and manipulated at the nanoscale, providing fundamental biological information. In particular, the study of the mechanical properties of biomolecular aggregates at the nanoscale constitutes an important source of data to elaborate mechanochemical structure/function models of single-particle biomachines, expanding and complementing the information obtained from bulk experiments.
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45
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Berweger S, Nguyen DM, Muller EA, Bechtel HA, Perkins TT, Raschke MB. Nano-chemical infrared imaging of membrane proteins in lipid bilayers. J Am Chem Soc 2013; 135:18292-5. [PMID: 24251914 DOI: 10.1021/ja409815g] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The spectroscopic characterization of biomolecular structures requires nanometer spatial resolution and chemical specificity. We perform full spatio-spectral imaging of dried purple membrane patches purified from Halobacterium salinarum with infrared vibrational scattering-type scanning near-field optical microscopy (s-SNOM). Using near-field spectral phase contrast based on the Amide I resonance of the protein backbone, we identify the protein distribution with 20 nm spatial resolution and few-protein sensitivity. This demonstrates the general applicability of s-SNOM vibrational nanospectroscopy, with potential extension to a wide range of biomolecular systems.
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Affiliation(s)
- Samuel Berweger
- Department of Physics and Department of Chemistry, ‡Department of Chemical and Biological Engineering, and §Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado, 80309, United States
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46
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Rajendran A, Endo M, Sugiyama H. State-of-the-Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins. Chem Rev 2013; 114:1493-520. [DOI: 10.1021/cr300253x] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Arivazhagan Rajendran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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47
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Pfreundschuh M, Hensen U, Müller DJ. Quantitative imaging of the electrostatic field and potential generated by a transmembrane protein pore at subnanometer resolution. NANO LETTERS 2013; 13:5585-5593. [PMID: 24079830 DOI: 10.1021/nl403232z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Elucidating the mechanisms by which proteins translocate small molecules and ions through transmembrane pores and channels is of great interest in biology, medicine, and nanotechnology. However, the characterization of pore forming proteins in their native state lacks suitable methods that are capable of high-resolution imaging (~1 nm) while simultaneously mapping physical and chemical properties. Here we report how force-distance (FD) curve-based atomic force microscopy (AFM) imaging can be applied to image the native pore forming outer membrane protein F (OmpF) at subnanometer resolution and to quantify the electrostatic field and potential generated by the transmembrane pore. We further observe the electrostatic field and potential of the OmpF pore switching "on" and "off" in dependence of the electrolyte concentration. Because electrostatic field and potential select for charged molecules and ions and guide them to the transmembrane pore the insights are of fundamental importance to understand the pore function. These experimental results establish FD-based AFM as a unique tool to image biological systems to subnanometer resolution and to quantify their electrostatic properties.
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Affiliation(s)
- Moritz Pfreundschuh
- Department of Biosystems Science and Engineering, ETH Zurich , CH-4058 Basel, Switzerland
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48
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Sharma S, Zhu H, Grintsevich EE, Reisler E, Gimzewski JK. Correlative nanoscale imaging of actin filaments and their complexes. NANOSCALE 2013; 5:5692-702. [PMID: 23727693 PMCID: PMC4030708 DOI: 10.1039/c3nr01039b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.
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Affiliation(s)
- Shivani Sharma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Huanqi Zhu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Elena E. Grintsevich
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - James K. Gimzewski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
- International Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
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49
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Li M, Liu L, Xi N, Wang Y, Dong Z, Xiao X, Zhang W. Progress of AFM single-cell and single-molecule morphology imaging. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5906-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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50
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Surface Characterization Using Atomic Force Microscopy (AFM) in Liquid Environments. SURFACE SCIENCE TECHNIQUES 2013. [DOI: 10.1007/978-3-642-34243-1_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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