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Besleaga A, Apetrei A, Sirghi L. Atomic force spectroscopy with magainin 1 functionalized tips and biomimetic supported lipid membranes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:29-40. [PMID: 35031815 DOI: 10.1007/s00249-021-01580-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/11/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Antimicrobial peptides are molecules synthesized by living organisms as the first line of defense against bacteria, fungi, parasites, or viruses. Since their biological activity is based on destabilization of the microbial membranes, a study of direct interaction forces between antimicrobial peptides and biomimetic membranes is very important for understanding the molecular mechanisms of their action. Herein, we use atomic force spectroscopy to probe the interaction between atomic force microscopy (AFM) tips functionalized with magainin 1 and supported lipid bilayers (SLBs) mimicking electrically uncharged membranes of normal eukaryotic cells and negatively charged membranes of bacterial cells. The investigations performed on negatively charged SLBs showed that the magainin 1 functionalized AFM tips are quickly adsorbed into the SLBs when they approach, while they adhere strongly to the lipid membrane when retracted. On contrary, same investigations performed on neutral SLBs showed mechanical resistance of the lipid membrane to the tip breakthrough and negligible adhesion force at detachment.
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Affiliation(s)
- Alexandra Besleaga
- Iasi Plasma Advanced Research Center (IPARC), Faculty of Physics, Alexandru Ioan Cuza University of Iasi, Blvd. Carol I nr. 11, 700506, Iasi, Romania
| | - Aurelia Apetrei
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, 700506, Iasi, Romania
| | - Lucel Sirghi
- Iasi Plasma Advanced Research Center (IPARC), Faculty of Physics, Alexandru Ioan Cuza University of Iasi, Blvd. Carol I nr. 11, 700506, Iasi, Romania.
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Marcuello C, Frempong GA, Balsera M, Medina M, Lostao A. Atomic Force Microscopy to Elicit Conformational Transitions of Ferredoxin-Dependent Flavin Thioredoxin Reductases. Antioxidants (Basel) 2021; 10:antiox10091437. [PMID: 34573070 PMCID: PMC8469568 DOI: 10.3390/antiox10091437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Flavin and redox-active disulfide domains of ferredoxin-dependent flavin thioredoxin reductase (FFTR) homodimers should pivot between flavin-oxidizing (FO) and flavin-reducing (FR) conformations during catalysis, but only FR conformations have been detected by X-ray diffraction and scattering techniques. Atomic force microscopy (AFM) is a single-molecule technique that allows the observation of individual biomolecules with sub-nm resolution in near-native conditions in real-time, providing sampling of molecular properties distributions and identification of existing subpopulations. Here, we show that AFM is suitable to evaluate FR and FO conformations. In agreement with imaging under oxidizing condition, only FR conformations are observed for Gloeobacter violaceus FFTR (GvFFTR) and isoform 2 of Clostridium acetobutylicum FFTR (CaFFTR2). Nonetheless, different relative dispositions of the redox-active disulfide and FAD-binding domains are detected for FR homodimers, indicating a dynamic disposition of disulfide domains regarding the central protein core in solution. This study also shows that AFM can detect morphological changes upon the interaction of FFTRs with their protein partners. In conclusion, this study paves way for using AFM to provide complementary insight into the FFTR catalytic cycle at pseudo-physiological conditions. However, future approaches for imaging of FO conformations will require technical developments with the capability of maintaining the FAD-reduced state within the protein during AFM scanning.
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Affiliation(s)
- Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (C.M.); (G.A.F.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Gifty Animwaa Frempong
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (C.M.); (G.A.F.)
| | - Mónica Balsera
- Department of Abiotic Stress, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain;
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: (M.M.); (A.L.); Tel.: +34-97-676-2476 (M.M.); +34-87-655-5357 (A.L.)
| | - Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain; (C.M.); (G.A.F.)
- Laboratorio de Microscopías Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundación ARAID, 50018 Zaragoza, Spain
- Correspondence: (M.M.); (A.L.); Tel.: +34-97-676-2476 (M.M.); +34-87-655-5357 (A.L.)
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Abstract
As with any other microscopic technique, in atomic force microscopy (AFM), problems can arise. Some of these happen due to improper use of the microscope by the operator, and some are due to particular characteristics of the sample. Some occur depending on the type of instrument, or from probe damage. Some of them are artifacts inherent in the technique. Knowledge of these issues is important for correct data acquisition and interpretation, and in many cases, training in AFM is inadequate. In this chapter we show examples of common artifacts in AFM and describe, where possible, how to overcome them. Other practical issues important for best practice in AFM operation, such as noise reduction and data processing, are also discussed.
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Affiliation(s)
- Peter Eaton
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,UCIBIO/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
| | - Krystallenia Batziou
- UCIBIO/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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Evans CT, Payton O, Picco L, Allen MJ. Algal Viruses: The (Atomic) Shape of Things to Come. Viruses 2018; 10:E490. [PMID: 30213102 PMCID: PMC6165301 DOI: 10.3390/v10090490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 01/15/2023] Open
Abstract
Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.
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Affiliation(s)
- Christopher T Evans
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Oliver Payton
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
| | - Loren Picco
- Interface Analysis Centre, Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, UK.
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Michael J Allen
- Plymouth Marine Laboratory, Plymouth PL1 3DH, UK.
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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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: 38] [Impact Index Per Article: 6.3] [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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Vielmuth F, Spindler V, Waschke J. Atomic Force Microscopy Provides New Mechanistic Insights into the Pathogenesis of Pemphigus. Front Immunol 2018; 9:485. [PMID: 29643851 PMCID: PMC5883869 DOI: 10.3389/fimmu.2018.00485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/23/2018] [Indexed: 12/19/2022] Open
Abstract
Autoantibodies binding to the extracellular domains of desmoglein (Dsg) 3 and 1 are critical in the pathogenesis of pemphigus by mechanisms leading to impaired function of desmosomes and blister formation in the epidermis and mucous membranes. Desmosomes are highly organized protein complexes which provide strong intercellular adhesion. Desmosomal cadherins such as Dsgs, proteins of the cadherin superfamily which interact via their extracellular domains in Ca2+-dependent manner, are the transmembrane adhesion molecules clustered within desmosomes. Investigations on pemphigus cover a wide range of experimental approaches including biophysical methods. Especially atomic force microscopy (AFM) has recently been applied increasingly because it allows the analysis of native materials such as cultured cells and tissues under near-physiological conditions. AFM provides information about the mechanical properties of the sample together with detailed interaction analyses of adhesion molecules. With AFM, it was recently demonstrated that autoantibodies directly inhibit Dsg interactions on the surface of living keratinocytes, a phenomenon which has long been considered the main mechanism causing loss of cell cohesion in pemphigus. In addition, AFM allows to study how signaling pathways altered in pemphigus control binding properties of Dsgs. More general, AFM and other biophysical studies recently revealed the importance of keratin filaments for regulation of Dsg binding and keratinocyte mechanical properties. In this mini-review, we reevaluate AFM studies in pemphigus and keratinocyte research, recapitulate what is known about the interaction mechanisms of desmosomal cadherins and discuss the advantages and limitations of AFM in these regards.
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Affiliation(s)
| | | | - Jens Waschke
- Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
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Ramakrishnan S, Subramaniam S, Stewart AF, Grundmeier G, Keller A. Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks. ACS APPLIED MATERIALS & INTERFACES 2016; 8:31239-31247. [PMID: 27779405 DOI: 10.1021/acsami.6b10535] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.
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Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Sivaraman Subramaniam
- Department of Genomics, Biotechnology Center, Technische Universität Dresden , Tatzberg 47-51, 01307 Dresden, Germany
| | - A Francis Stewart
- Department of Genomics, Biotechnology Center, Technische Universität Dresden , Tatzberg 47-51, 01307 Dresden, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University , Warburger Strasse 100, 33098 Paderborn, Germany
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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Das P, Reches M. Review insights into the interactions of amino acids and peptides with inorganic materials using single molecule force spectroscopy. Biopolymers 2015; 104:480-94. [DOI: 10.1002/bip.22655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Accepted: 03/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem; 91904 Jerusalem Israel
- The Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; 91904 Jerusalem Israel
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Ares P, Jaafar M, Gil A, Gómez-Herrero J, Asenjo A. Magnetic Force Microscopy in Liquids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4731-6. [PMID: 26150330 DOI: 10.1002/smll.201500874] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/14/2015] [Indexed: 05/03/2023]
Abstract
In this work, the use of magnetic force microscopy (MFM) to acquire images of magnetic nanostructures in liquid environments is presented. Optimization of the MFM signal acquisition in liquid media is performed and it is applied to characterize the magnetic signal of magnetite nanoparticles. The ability for detecting magnetic nanostructures along with the well-known capabilities of atomic force microscopy in liquids suggests potential applications in fields such as nanomedicine, nanobiotechnology, or nanocatalysis.
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Affiliation(s)
- Pablo Ares
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Miriam Jaafar
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, E-28049, Madrid, Spain
| | - Adriana Gil
- Nanotec Electrónica S.L, E-28760, Tres Cantos, Madrid, Spain
| | - Julio Gómez-Herrero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
- INC and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Agustina Asenjo
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas, E-28049, Madrid, Spain
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Gimeno A, Ares P, Horcas I, Gil A, Gómez-Rodríguez JM, Colchero J, Gómez-Herrero J. ‘Flatten plus’: a recent implementation in WSxM for biological research: Fig. 1. Bioinformatics 2015; 31:2918-20. [DOI: 10.1093/bioinformatics/btv278] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/24/2015] [Indexed: 11/12/2022] Open
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Action of the Hsp70 chaperone system observed with single proteins. Nat Commun 2015; 6:6307. [PMID: 25686738 DOI: 10.1038/ncomms7307] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 01/16/2015] [Indexed: 11/08/2022] Open
Abstract
In Escherichia coli, the binding of non-native protein substrates to the Hsp70 chaperone DnaK is mediated by the co-chaperone DnaJ. DnaJ accelerates ATP hydrolysis on DnaK, by closing the peptide-binding cleft of DnaK. GrpE catalysed nucleotide exchange and ATP re-binding then lead to substrate release from DnaK, allowing folding. Here we refold immunoglobulin 27 (I27) to better understand how DnaJ-DnaK-GrpE chaperones cooperate. When DnaJ is present, I27 is less likely to misfold and more likely to fold, whereas the unfolded state remains unaffected. Thus, the 'holdase' DnaJ shows foldase behaviour. Misfolding of I27 is fully abrogated when DnaJ cooperates with DnaK, which stabilizes the unfolded state and increases the probability of folding. Addition of GrpE shifts the unfolded fraction of I27 to pre-chaperone levels. These insights reveal synergistic mechanisms within the evolutionary highly conserved Hsp70 system that prevent substrates from misfolding and promote their productive transition to the native state.
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Wang C, Jin Y, Desai UR, Yadavalli VK. Investigation of the heparin-thrombin interaction by dynamic force spectroscopy. Biochim Biophys Acta Gen Subj 2015; 1850:1099-106. [PMID: 25647100 DOI: 10.1016/j.bbagen.2015.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/08/2015] [Accepted: 01/25/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. METHODS In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. RESULTS Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. CONCLUSIONS An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. GENERAL SIGNIFICANCE These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions.
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Affiliation(s)
- Congzhou Wang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond VA 23284, United States
| | - Yingzi Jin
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Vamsi K Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond VA 23284, United States.
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Novel methods for liposome preparation. Chem Phys Lipids 2014; 177:8-18. [DOI: 10.1016/j.chemphyslip.2013.10.011] [Citation(s) in RCA: 373] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 12/18/2022]
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Safenkova IV, Zherdev AV, Dzantievf BB. Application of atomic force microscopy for characteristics of single intermolecular interactions. BIOCHEMISTRY (MOSCOW) 2013; 77:1536-52. [PMID: 23379527 DOI: 10.1134/s000629791213010x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.
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Affiliation(s)
- I V Safenkova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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Mammadov R, Tekinay AB, Dana A, Guler MO. Microscopic characterization of peptide nanostructures. Micron 2012; 43:69-84. [DOI: 10.1016/j.micron.2011.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 10/18/2022]
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Measurement of interaction forces between fibrinogen coated probes and mica surface with the atomic force microscope: The pH and ionic strength effect. Biointerphases 2010; 3:1-8. [PMID: 20408656 DOI: 10.1116/1.2840052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The study of protein-surface interactions is of great significance in the design of biomaterials and the evaluation of molecular processes in tissue engineering. The authors have used atomic force microscopy (AFM) to directly measure the force of attraction/adhesion of fibrinogen coated tips to mica surfaces and reveal the effect of the surrounding solution pH and ionic strength on this interaction. Silica colloid spheres were attached to the AFM cantilevers and, after plasma deposition of poly(acrylic acid), fibrinogen molecules were covalently bound on them with the help of the cross-linker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) in the presence of N-hydroxysulfosuccinimide (sulfo-NHS). The measurements suggest that fibrinogen adsorption is controlled by the screening of electrostatic repulsion as the salt concentration increases from 15 to 150 mM, whereas at higher ionic strength (500 mM) the hydration forces and the compact molecular conformation become crucial, restricting adsorption. The protein attraction to the surface increases at the isoelectric point of fibrinogen (pH 5.8), compared with the physiological pH. At pH 3.5, apart from fibrinogen attraction to the surface, evidence of fibrinogen conformational changes is observed, as the pH and the ionic strength are set back and forth, and these changes may account for fibrinogen aggregation in the protein solution at this pH.
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Bizzarri AR, Cannistraro S. The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process. Chem Soc Rev 2010; 39:734-49. [DOI: 10.1039/b811426a] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Hamon L, Curmi PA, Pastré D. High-resolution imaging of microtubules and cytoskeleton structures by atomic force microscopy. Methods Cell Biol 2010; 95:157-74. [PMID: 20466134 DOI: 10.1016/s0091-679x(10)95009-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Atomic force microscopy (AFM), which combines a nanometer-scale resolution and a unique capacity to image biomolecular interactions in liquid environment, is a promising tool for the investigation of biological samples. In contrast with nucleic acids and nucleoprotein complexes, for which AFM is now of common use and participates in the recent advances in the knowledge of DNA-related biomolecular processes, AFM investigations of cytoskeleton structures and especially microtubules remain rare. The most critical step to observe biomolecules using AFM is the spreading of the biological material on a flat surface. This issue is now better documented concerning DNA but a lot remains to be done concerning microtubules. This is a prerequisite to further document this issue for a proper and large use of AFM to study cytoskeleton structures. We present here an overview of the various procedures previously used to spread microtubules on a flat surface and advance an easy-to-use and efficient experimental protocol for microtubule imaging by AFM in air. We show application of this protocol to observe intermediate structures of microtubule assembly without using any stabilizing agent and the observation of more complex systems like proteins or messenger ribonucleoprotein particles in interaction with microtubules.
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Affiliation(s)
- Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM - UEVE UMR U829, Evry 91025, France
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Goldsbury CS, Scheuring S, Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2009; Chapter 17:17.7.1-17.7.19. [DOI: 10.1002/0471140864.ps1707s58] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Laurent Kreplak
- Dalhousie University, Department of Physics & Atmospheric Science Halifax Canada
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23
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Tsapikouni TS, Missirlis YF. Measuring the force of single protein molecule detachment from surfaces with AFM. Colloids Surf B Biointerfaces 2009; 75:252-9. [PMID: 19783413 DOI: 10.1016/j.colsurfb.2009.08.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 08/04/2009] [Accepted: 08/27/2009] [Indexed: 10/20/2022]
Abstract
Atomic force microscopy (AFM) was used to measure the non-specific detachment force of single fibrinogen molecules from glass surfaces. The identification of single unbinding events was based on the characteristics of the parabolic curves, recorded during the stretching of protein molecules. Fibrinogen molecules were covalently bound to Si(3)N(4) AFM tips, previously modified with 3-aminopropyl-dimethyl-ethoxysilane, through a homobifunctional poly(ethylene glycol) linker bearing two hydroxysulfosuccinimide esters. The most probable detachment force was found to be 210 pN, when the tip was retracting with a velocity of 1400 nm/s, while the distribution of the detachment distances indicated that the fibrinogen chain can be elongated beyond the length of the physical conformation before detachment. The dependence of the most probable detachment force on the loading rate was examined and the dynamics of fibrinogen binding to the surface were found amenable to the simple expression of the Bell-Evans theory. The theory's expansion, however, by incorporating the concept of the rupture of parallel residue-surface bonds could only describe the detachment of fibrinogen for a small number of such bonds. Finally, the mathematical expression of the Worm-Like Chain model was used to fit the stretching curves before rupture and two interpretations are suggested for the description of the AFM curves with multiple detachment events.
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Affiliation(s)
- Theodora S Tsapikouni
- Laboratory of Biomechanics and Biomedical Engineering, Mechanical Engineering and Aeronautics Department, University of Patras, Patras 26504, Greece.
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24
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Strategies to prepare and characterize native membrane proteins and protein membranes by AFM. Curr Opin Colloid Interface Sci 2008. [DOI: 10.1016/j.cocis.2007.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Struckmeier J, Wahl R, Leuschner M, Nunes J, Janovjak H, Geisler U, Hofmann G, Jähnke T, Müller DJ. Fully automated single-molecule force spectroscopy for screening applications. NANOTECHNOLOGY 2008; 19:384020. [PMID: 21832579 DOI: 10.1088/0957-4484/19/38/384020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
With the introduction of single-molecule force spectroscopy (SMFS) it has become possible to directly access the interactions of various molecular systems. A bottleneck in conventional SMFS is collecting the large amount of data required for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based SMFS requires the user to tediously 'fish' for single molecules. In addition, most experimental and environmental conditions must be manually adjusted. Here, we developed a fully automated single-molecule force spectroscope. The instrument is able to perform SMFS while monitoring and regulating experimental conditions such as buffer composition and temperature. Cantilever alignment and calibration can also be automatically performed during experiments. This, combined with in-line data analysis, enables the instrument, once set up, to perform complete SMFS experiments autonomously.
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Affiliation(s)
- Jens Struckmeier
- Cellular Machines, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, D-01307 Dresden, Germany. nAmbition GmbH, Tatzberg 47, D-01307 Dresden, Germany
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26
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Goldsbury C, Scheuring S. Introduction to atomic force microscopy (AFM) in biology. ACTA ACUST UNITED AC 2008; Chapter 17:17.7.1-17.7.17. [PMID: 18429225 DOI: 10.1002/0471140864.ps1707s29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The atomic force microscope has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated. Importantly, the measurements are made in buffer solutions, allowing biological samples to stay alive within a physiological-like environment while temporal changes in structure are measured. This overview provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins. The physical principles of the technique and methodological aspects of its practical use and applications are also described.
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Affiliation(s)
- Claire Goldsbury
- Cytoskeleton Group, Max Planck Unit for Structural Molecular Biology, Hamburg, Germany
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27
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Denisov NN, Shcheglova LA, Sekatskii SK, Dietler G, Nadtochenko VA. Single-molecule force spectroscopy of a protein globule covalently bound to a calcite surface. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2008. [DOI: 10.1134/s1990793108030032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Denisov N, Chtcheglova L, Sekatskii S, Dietler G. Covalent attachment of proteins to calcite surface for the single molecule experiments. Colloids Surf B Biointerfaces 2008; 63:282-6. [DOI: 10.1016/j.colsurfb.2007.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 10/05/2007] [Accepted: 12/17/2007] [Indexed: 11/27/2022]
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29
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Minařik A, Humenik M, Li S, Huang Y, Krausch G, Sprinzl M. Ligand-Directed Immobilization of Proteins through an Esterase 2 Fusion Tag Studied by Atomic Force Microscopy. Chembiochem 2008; 9:124-30. [DOI: 10.1002/cbic.200700409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Wang P, Li H, Yang HJ, Wang HB, Lü JH, Zhang Y, Hu J. Glycerol facilitates the disaggregation of recombinant adeno-associated virus serotype 2 on mica surface. Colloids Surf B Biointerfaces 2007; 60:264-7. [PMID: 17692508 DOI: 10.1016/j.colsurfb.2007.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2007] [Revised: 06/21/2007] [Accepted: 06/23/2007] [Indexed: 10/23/2022]
Abstract
Preparation of distributed virus on a solid substrate is a prerequisite for investigation of the properties and individualism of virus, while many previous studies showed that virus has a tendency to aggregate on solid substrates. In this communication, we report a novel approach by which well-separated recombinant adeno-associated virus serotype 2 (rAAV2) could be prepared on bare mica surface. The key technique in this approach is the addition of less than 3% (v/v) glycerol into the virus solution and subsequently deposition onto mica surface for the sample preparation. The possible mechanisms are also briefly discussed.
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Affiliation(s)
- Peng Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, PR China
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31
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Nehilla BJ, Vu TQ, Desai TA. Stoichiometry-dependent formation of quantum dot-antibody bioconjugates: a complementary atomic force microscopy and agarose gel electrophoresis study. J Phys Chem B 2007; 109:20724-30. [PMID: 16853686 DOI: 10.1021/jp052613+] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The unique advantages of quantum dot (QD) bioconjugates have motivated their application in biological assays. However, physical characterization of bioconjugated QDs after surface modification has often been overlooked. Here, biotinylated antibodies (biotin-IgG) were attached to commercial streptavidin-conjugated quantum dots (strep-QDs) at different stoichiometric ratios, and these QD bioconjugates were characterized with atomic force microscopy and discontinuous sodium dodecyl sulfate agarose gel electrophoresis (SDS-AGE). The results from these complementary analytical techniques showed that the molar ratio determined the relative sizes, molecular weights and morphologies of the QD bioconjugates. Additionally, the novel discontinuous SDS-AGE analysis confirmed specific binding between biotin-IgG and strep-QDs. Researchers who design QD bioconjugates for cell-based assays should consider stoichiometry-dependent differences in the physical properties of their QD bioconjugates.
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Affiliation(s)
- Barrett J Nehilla
- Department of Biomedical Engineering, Whitaker Labs Room 701, Boston University, 44 Cummington Street, Boston, MA 02215, USA
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32
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The morphology of adsorbed extracellular matrix assemblies is critically dependent on solution calcium concentration. Matrix Biol 2007; 26:156-66. [DOI: 10.1016/j.matbio.2006.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 10/30/2006] [Accepted: 10/31/2006] [Indexed: 12/31/2022]
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33
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Erker W, Scheumann V, Möller M, Knoll W, Rühe J, Decker H. Immobilization and AFM of single 4×6-mer tarantula hemocyanin molecules. Micron 2006; 37:735-41. [PMID: 16632369 DOI: 10.1016/j.micron.2006.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2005] [Revised: 03/06/2006] [Accepted: 03/06/2006] [Indexed: 10/24/2022]
Abstract
The high molecular mass respiratory protein of the tarantula Eurypelma californicum, a 4 x 6-mer hemocyanin, was investigated by atomic force microscopy (AFM). Various substrates and methods were evaluated for immobilization of individual hemocyanin molecules on a solid surface. Samples were imaged after physisorption on mica and self-assembled monolayers, and after chemisorption on Au(111) and N-hydroxy-succinimide (NHS) functionalized surfaces. AFM measurements were carried out preferable in solution and contact mode, but also in Tapping mode and on air-dried samples. Adsorption of the protein on mica followed by drying and carrying out the measurements in Tapping mode gave the best results. In the AFM images the four hexamers of the native 4 x 6-mer hemocyanin have been defined. The results were compared with independent available structural data and represent a validation case for this technique applied for the first time on such giant and complex molecules. As observable in images taken by transmission electron microscopy and also proposed from SAXS data, 4 x 6-mers could be found where the half-molecules are tilted against each other. This study is a step in resolving conformational heterogeneities, involved in oxygen binding of hemocyanins, at the single-molecule level by AFM.
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Affiliation(s)
- Wolfgang Erker
- Institute for Physical Chemistry, University Mainz, Germany.
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34
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Alessandrini A, Corni S, Facci P. Unravelling single metalloprotein electron transfer by scanning probe techniques. Phys Chem Chem Phys 2006; 8:4383-97. [PMID: 17001404 DOI: 10.1039/b607021c] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review is intended to account for the experimental and theoretical achievements obtained in a period of about 15 years on the investigation of the electron transport through single redox metalloproteins by scanning probe techniques. A highly focussed research effort has been deployed by the scientists active in this particular field towards measuring and interpreting electronic current signals flowing via blue copper, redox metalloproteins (e.g. azurin). The field has taken a remarkable advantage of the use of electrochemically assisted scanning tunnelling microscope (EC-STM) which has allowed to probe single molecule signals under full control of all the potential values involved in the experiments. This experimental activity has both triggered more comprehensive theoretical interpretations and has been, in its turn, stimulated by theoreticians to test always new predictions. The authors hope to have succeeded in providing the reader with a valuable appraisal of this fascinating field.
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Affiliation(s)
- Andrea Alessandrini
- National Research Center, nanoStructures and bioSystems at Surfaces-S3 of CNR-INFM, Via G. Campi, 213/A, I-41100, Modena, Italy
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35
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Hinterdorfer P, Dufrêne YF. Detection and localization of single molecular recognition events using atomic force microscopy. Nat Methods 2006; 3:347-55. [PMID: 16628204 DOI: 10.1038/nmeth871] [Citation(s) in RCA: 695] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Because of its piconewton force sensitivity and nanometer positional accuracy, the atomic force microscope (AFM) has emerged as a powerful tool for exploring the forces and the dynamics of the interaction between individual ligands and receptors, either on isolated molecules or on cellular surfaces. These studies require attaching specific biomolecules or cells on AFM tips and on solid supports and measuring the unbinding forces between the modified surfaces using AFM force spectroscopy. In this review, we describe the current methodology for molecular recognition studies using the AFM, with an emphasis on strategies available for preparing AFM tips and samples, and on procedures for detecting and localizing single molecular recognition events.
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Affiliation(s)
- Peter Hinterdorfer
- Institute for Biophysics, Johannes Kepler University of Linz, Altenbergerstr. 69, A-4040 Linz, Austria.
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36
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Janovjak H, Kedrov A, Cisneros DA, Sapra KT, Struckmeier J, Muller DJ. Imaging and detecting molecular interactions of single transmembrane proteins. Neurobiol Aging 2005; 27:546-61. [PMID: 16253393 DOI: 10.1016/j.neurobiolaging.2005.03.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2004] [Revised: 03/15/2005] [Accepted: 03/19/2005] [Indexed: 10/25/2022]
Abstract
Single-molecule atomic force microscopy (AFM) provides novel ways to characterize structure-function relationships of native membrane proteins. High-resolution AFM-topographs allow observing substructures of single membrane proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. Complementary to AFM imaging, single-molecule force spectroscopy experiments allow detecting molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to detect the interactions that stabilize secondary structures such as transmembrane alpha-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the position of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes. We review current and future potential of these approaches to reveal insights into membrane protein structure, function, and unfolding as we recognize that they could help answering key questions in the molecular basis of certain neuro-pathological dysfunctions.
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Affiliation(s)
- Harald Janovjak
- Center of Biotechnology, University of Technology and Max-Planck-Institute of Molecular Cell Biology and Genetics, Tatzberg 49, D-01307 Dresden, Germany
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37
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El Kirat K, Burton I, Dupres V, Dufrene YF. Sample preparation procedures for biological atomic force microscopy. J Microsc 2005; 218:199-207. [PMID: 15958012 DOI: 10.1111/j.1365-2818.2005.01480.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since the late 1980s, atomic force microscopy (AFM) has been increasingly used in biological sciences and it is now established as a versatile tool to address the structure, properties and functions of biological specimens. AFM is unique in that it provides three-dimensional images of biological structures, including biomolecules, lipid films, 2D protein crystals and cells, under physiological conditions and with unprecedented resolution. A crucial prerequisite for successful, reliable biological AFM is that the samples need to be well attached to a solid substrate using appropriate, nondestructive methods. In this review, we discuss common techniques for immobilizing biological specimens for AFM studies.
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Affiliation(s)
- K El Kirat
- Unité de chimie des interfaces, Université catholique de Louvain, Belgium
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38
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Bhushan B, Tokachichu DR, Keener MT, Lee SC. Morphology and adhesion of biomolecules on silicon based surfaces. Acta Biomater 2005; 1:327-41. [PMID: 16701811 DOI: 10.1016/j.actbio.2005.01.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 01/25/2005] [Accepted: 01/26/2005] [Indexed: 11/28/2022]
Abstract
Biomolecules such as proteins, on silicon based surfaces are of extreme importance in various applications including microfabricated silicon implants, in the fabrication of microdevices with protein compounds (e.g., biosensors), and therapeutics. Morphology of silicon based surfaces with and without biomolecules and their adhesion with the substrate govern performance and reliability of the biological application. In this research, step by step morphological changes of silicon as well as adhesion during its surface modification have been studied using atomic force microscopy. To improve adhesion between biomolecules and the silicon based surfaces, chemical conjugation as well as surface patterning have been used. Changes in adhesion as a result of surface modification have been analyzed with the help of contact angle measurements. Phase imaging technique was used to confirm the presence of biomolecules on the surface. To understand the relationship between morphology and local values of adhesion, adhesion mapping and local stiffness mapping were carried out.
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Affiliation(s)
- Bharat Bhushan
- Nanotribology Laboratory for Information storage and MEMS/NEMS, The Ohio State University, 650 Ackerman Road, Suite 255, Columbus, OH 43202, USA.
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Davies E, Teng KS, Conlan RS, Wilks SP. Ultra-high resolution imaging of DNA and nucleosomes using non-contact atomic force microscopy. FEBS Lett 2005; 579:1702-6. [PMID: 15757664 DOI: 10.1016/j.febslet.2005.02.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 02/02/2005] [Accepted: 02/02/2005] [Indexed: 10/25/2022]
Abstract
Visualisation of nano-scale biomolecules aids understanding and development in molecular biology and nanotechnology. Detailed structure of nucleosomes adsorbed to mica has been captured in the absence of chemical-anchoring techniques, demonstrating the usefulness of non-contact atomic force microscopy (NC-AFM) for ultra-high resolution biomolecular imaging. NC-AFM offers significant advantages in terms of resolution, speed and ease of sample preparation when compared to techniques such as cryo-electron microscopy and X-ray crystallography. In the absence of chemical modification, detailed structure of DNA deposited on a gold substrate was observed for the first time using NC-AFM, opening up possibilities for investigating the electrical properties of unmodified DNA.
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Affiliation(s)
- Emma Davies
- Multidisciplinary Nanotechnology Centre, School of Engineering, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK.
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40
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Pastré D, Piétrement O, Zozime A, Le Cam E. Study of the DNA/ethidium bromide interactions on mica surface by atomic force microscope: influence of the surface friction. Biopolymers 2005; 77:53-62. [PMID: 15578645 DOI: 10.1002/bip.20185] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The influence of mica surface on DNA/ethidium bromide interactions is investigated by atomic force microscopy (AFM). We describe the diffusion mechanism of a DNA molecule on a mica surface by using a simple analytical model. It appears that the DNA diffusion on a mica surface is limited by the surface friction due to the counterion correlations between the divalent counterions condensed on both mica and DNA surfaces. We also study the structural changes of linear DNA adsorbed on mica upon ethidium bromide binding by AFM. It turns out that linear DNA molecules adsorbed on a mica surface are unable to relieve the topological constraint upon ethidium bromide binding. In particular, strongly adsorbed molecules tend to be highly entangled, while loosely bound DNA molecules appear more extended with very few crossovers. Adsorbed DNA molecules cannot move freely on the surface because of the surface friction. Therefore, the topological constraint increases due to the ethidium bromide binding. Moreover, we show that ethidium bromide has a lower affinity for strongly bound molecules due to the topological constraint induced by the surface friction.
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Affiliation(s)
- David Pastré
- Laboratoire d'étude des Milieux Nanométriques, Université d'Evry-Val-d'essonne Rue du Père Jarlan, 91025 Evry Cedex, France.
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41
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Dufrêne YF, Müller DJ. Microbial Surfaces Investigated Using Atomic Force Microscopy. METHODS IN MICROBIOLOGY 2004. [DOI: 10.1016/s0580-9517(04)34006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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42
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Abstract
Densely pegylated particles that can serve as a model system for artificial cells were prepared by covalently grafting amino polyethylene glycol (PEG, molecular weight 3400 or 5000) onto carboxyl polystyrene particles (PS-COOH) using carbodiimide chemistry. PEG-modified particles (PS-PEG) were characterized by determination of the PEG surface concentration, zeta-potential, size, and morphology. Under optimized grafting conditions, a dense "brush-like" PEG layer was formed. A PEG surface concentration of approximately 60 pmol/cm2, corresponding with an average distance between grafted PEG chains of approximately 17 A can be realized. It was shown that grafting of PEG onto PS-COOH reduced the adsorption of proteins from human plasma (85 vol %) in phosphate-buffered saline up to 90%.
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Affiliation(s)
- Fenghua Meng
- Polymer Chemistry and Biomaterials Group, Department of Chemical Technology, Institute for Biomedical Technology (BMTI), University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Abstract
With the advent of the atomic force microscope (AFM), the study of biological samples has become more realistic because, in most cases, samples are not covered or fixed, which makes it possible to observe them while the cells are alive. This advantage of the AFM allowed the advent of a new invention: nanobiosensors using the cantilever (probe) of the AFM and, in this case, it is possible to observe the entering or exiting of specific molecules (including medications) from living cells. This is the smallest biosensor in the world, measuring about 100 microm long (about the width of a hair). Beyond sensing the area of interest with this biosensor, it is also possible to see the area and exactly what is occurring on it, in real time. This new tool will be very useful for several areas: molecular pharmacology, enzymology, physiology, molecular biology, biotechnology, biophysics, physical chemistry, analytical chemistry, and organic chemistry. This article discusses, mainly, the applications of this new technique to the field of pharmacology.
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Affiliation(s)
- R S Pereira
- Institute of Biomedical Sciences (ICB), Rua Jean Nassif Mokarzel, 174 Barão Geraldo, Campinas, 13084-480, São Paulo, Brazil.
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45
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Abstract
The introduction of functional imaging tools and techniques that operate at molecular-length scales has provided investigators with unique approaches to characterizing biomolecular structure and function relationships. Recent advances in the field of scanning probe techniques and, in particular, atomic force microscopy have yielded tantalizing insights into the dynamics of protein self-assembly and the mechanics of protein unfolding.
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Affiliation(s)
- C M Yip
- Department of Chemical Engineering, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Ontario, Canada.
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46
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Zlatanova J, Lindsay SM, Leuba SH. Single molecule force spectroscopy in biology using the atomic force microscope. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 74:37-61. [PMID: 11106806 DOI: 10.1016/s0079-6107(00)00014-6] [Citation(s) in RCA: 305] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The importance of forces in biology has been recognized for quite a while but only in the past decade have we acquired instrumentation and methodology to directly measure interactive forces at the level of single biological macromolecules and/or their complexes. This review focuses on force measurements performed with the atomic force microscope. A general introduction to the principle of action is followed by review of the types of interactions being studied, describing the main results and discussing the biological implications.
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Affiliation(s)
- J Zlatanova
- Biochip Technology Center, Argonne National Laboratory, 9700 South Cass Avenue, Bldg. 202-A253, Argonne, IL 60439, USA.
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47
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Qian W, Yao D, Yu F, Xu B, Zhou R, Bao X, Lu Z. Immobilization of Antibodies on Ultraflat Polystyrene Surfaces. Clin Chem 2000. [DOI: 10.1093/clinchem/46.9.1456] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Background: Functional antibody surfaces were prepared on ultraflat polystyrene surfaces by physical adsorption, and the uniform distribution of monoclonal antibodies against hepatitis B surface antigen (anti-HBs) on such surfaces and the presence of dense hepatitis B surface antigen (HBsAg) particles captured by immobilized antibodies were identified.
Methods: A model polystyrene film was spin-coated directly onto a silicon wafer surface. Atomic force microscopy was used to directly monitor the immobilization of anti-HBs antibodies and their specific molecular interaction with HBsAg. Enzyme immunoassay was also used to characterize functional antibody surfaces.
Results: A mean roughness of 2 Å for areas of 25 μm2 was produced. We found a uniform distribution of anti-HBs antibodies on ultraflat polystyrene surfaces and the presence of dense HBsAg particles bound to such anti-HBs surfaces after incubation with HBsAg.
Conclusions: This study confirmed the potential of preparing dense, homogeneous, highly specific, and highly stable antibody surfaces by immobilizing antibodies on polystyrene surfaces with controlled roughness. It is expected that such biofunctional surfaces could be of interest for the development of new solid-phase immunoassay techniques and biosensor techniques.
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Affiliation(s)
- Weiping Qian
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
| | - Danfeng Yao
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
| | - Fang Yu
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
| | - Bin Xu
- Center for Clinical Laboratory Science, Jiangsu Province, Nanjing 210009, Peoples Republic of China
| | - Rong Zhou
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
| | - Xiang Bao
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
| | - Zuhong Lu
- National Laboratory of Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096, Peoples Republic of China
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Möller C, Allen M, Elings V, Engel A, Müller DJ. Tapping-mode atomic force microscopy produces faithful high-resolution images of protein surfaces. Biophys J 1999; 77:1150-8. [PMID: 10423460 PMCID: PMC1300406 DOI: 10.1016/s0006-3495(99)76966-3] [Citation(s) in RCA: 213] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Compared to contact-mode atomic force microscopy (CMAFM), tapping-mode atomic force microscopy (TMAFM) has the advantage of allowing imaging surfaces of macromolecules, even when they are only weakly attached to the support. In this study, TMAFM is applied to two different regular protein layers whose structures are known to great detail, the purple membrane from Halobacterium salinarum and the hexagonally packed intermediate (HPI) layer from Deinococcus radiodurans, to assess the faithfulness of high-resolution TMAFM images. Topographs exhibited a lateral resolution between 1.1 and 1. 5 nm and a vertical resolution of approximately 0.1 nm. For all protein surfaces, TMAFM and CMAFM topographs were in excellent agreement. TMAFM was capable of imaging the fragile polypeptide loop connecting the transmembrane alpha-helices E and F of bacteriorhodopsin in its native extended conformation. The standard deviation (SD) of averages calculated from TMAFM topographs exhibited an enhanced minimum (between 0.1 and 0.9 nm) that can be assigned to the higher noise of the raw data. However, the SD difference, indicating the flexibility of protein subunits, exhibited an excellent agreement between the two imaging modes. This demonstrates that the recently invented imaging-mode TMAFM has the ability to faithfully record high-resolution images and has sufficient sensitivity to contour individual peptide loops without detectable deformations.
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Affiliation(s)
- C Möller
- M. E. Müller Institute for Structural Biology, Biozentrum, CH-4056 Basel, Switzerland
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