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Special Issue "Atomic Force Microscopy for Biological Applications"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (28 September 2018).

Special Issue Editors

Assoc. Prof. Dr. Georg E. Fantner
E-Mail Website
Guest Editor
Ecole Polytechnique Federale de Lausanne, School of Engineering, Lausanne, Switzerland
Interests: atomic force microscopy (AFM); instrumentation; high speed AFM; time lapse AFM; nanoscale biology; biomaterials; microbiology; microfabrication; nanopositioning; correlative microscopy
Dr. Haig Alexander Eskandarian
E-Mail Website
Guest Editor
Ecole Polytechnique Federale de Lausanne, School of Engineering, Lausanne, Switzerland
Interests: long-term time-lapse AFM; microbiology; single-cell biology; quantitative biology; bacterial cell cycle; growth dynamics; dynamic force mapping; physical forces in biology

Special Issue Information

Dear Colleagues,

The development and use of Atomic Force Microscopy in biology has been undergoing a transformation in recent years. New AFM imaging techniques are emerging from the development of techniques to image, not only faster, but also in a more stable and quantitative manner.  Altogether, AFM is allowing biologists and biophysicists to go beyond simply making a picture of the biological specimen.  Studies are emerging that reveal new principles of molecular interactions, membrane trafficking, cell physiology, cell dynamics, how cells grow and divide, as well as how physical properties of cells manifest.

This Special Issue will offer a platform for bringing together an interdisciplinary mix of AFM development for imaging and quantifying biological samples, as well as novel studies spanning from imaging single cells down to single molecules.  This Special Issue will offer an opportunity to highlight the variety of ways in which AFM is being used to study living systems, with minimal disruption, and to characterize novel biological phenotypes by AFM.  We are seeking research and review articles that will highlight: 1) novel AFM development towards imaging biological systems, and 2) characterizing novel biological phenotypes revealed uniquely by AFM at the organismal, sub-cellular and molecular levels.

Assoc. Prof. Dr. Georg E. Fantner
Dr. Haig Alexander Eskandarian
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cell adhesion
  • cell motility
  • antibiotic resistance/persistence
  • cell physiology
  • cell morphogenesis
  • cell growth
  • cell division
  • protein folding dynamics
  • molecular self-assembly
  • lipid membranes
  • membrane trafficking
  • membrane protein dynamics
  • nuclear pore complex
  • sub-cellular imaging
  • cell surface force mapping
  • high speed AFM
  • time lapse AFM
  • correlative microscopy
  • mechanical properties measurements

Published Papers (13 papers)

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Research

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Open AccessArticle
Transforming Growth Factor-β Promotes Morphomechanical Effects Involved in Epithelial to Mesenchymal Transition in Living Hepatocellular Carcinoma
Int. J. Mol. Sci. 2019, 20(1), 108; https://doi.org/10.3390/ijms20010108 - 28 Dec 2018
Cited by 2
Abstract
The epithelial mesenchymal transition (EMT) is a physiological multistep process involving epithelial cells acquiring a mesenchymal-like phenotype. It is widely demonstrated that EMT is linked to tumor progression and metastasis. The transforming growth factor (TGF)-β pathways have been widely investigated, but its role [...] Read more.
The epithelial mesenchymal transition (EMT) is a physiological multistep process involving epithelial cells acquiring a mesenchymal-like phenotype. It is widely demonstrated that EMT is linked to tumor progression and metastasis. The transforming growth factor (TGF)-β pathways have been widely investigated, but its role in the hepatocarcinoma EMT is still unclear. While the biochemical pathways have been extensively studied, the alteration of biomechanical behavior correlated to cellular phenotype and motility is not yet fully understood. To better define the involvement of TGF-β1 in the metastatic progression process in different hepatocarcinoma cell lines (HepG2, PLC/PRF/5, HLE), we applied a systematic morphomechanical approach in order to investigate the physical and the structural characteristics. In addition, we evaluated the antitumor effect of LY2157299, a TGF-βR1 kinase inhibitor, from a biomechanical point of view, using Atomic Force and Confocal Microscopy. Our approach allows for validation of biological data, therefore it may be used in the future as a diagnostic tool to be combined with conventional biomolecular techniques. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Cholesterol Increases Lipid Binding Rate and Changes Binding Behavior of Bacillus thuringiensis Cytolytic Protein
Int. J. Mol. Sci. 2018, 19(12), 3819; https://doi.org/10.3390/ijms19123819 - 30 Nov 2018
Cited by 1
Abstract
Cytolytic protein (Cyt) is a member of insecticidal proteins produced by Bacillus thuringiensis. Cyt protein has activity against insect cells and mammalian cells, which differ in lipid and cholesterol composition. This study presents the lipid binding behavior of Cyt2Aa2 protein on model [...] Read more.
Cytolytic protein (Cyt) is a member of insecticidal proteins produced by Bacillus thuringiensis. Cyt protein has activity against insect cells and mammalian cells, which differ in lipid and cholesterol composition. This study presents the lipid binding behavior of Cyt2Aa2 protein on model membranes containing different levels of cholesterol content by combining Quartz Crystal Microbalance with Dissipation (QCM-D) and Atomic Force Microscopy (AFM). QCM-D results revealed that cholesterol enhances the binding rate of Cyt2Aa2 protein onto lipid bilayers. In addition, the thicker lipid bilayer was observed for the highest cholesterol content. These results were confirmed by AFM. The analysis of protein surface coverage as a function of time showed a slower process for 5:0 and 5:0.2 (POPC:Chol) ratios than for 5:1 and 5:2 (POPC:Chol) ratios. Significantly, the Cyt2Aa2-lipid binding behavior and the protein–lipid layer were different for the 5:3 (POPC:Chol) ratio. Furthermore, AFM images revealed a transformation of Cyt2Aa2/lipid layer structure from strip pattern to ring shape structures (which showed a strong repulsion with AFM tip). In summary, cholesterol increases the binding rate and alters the lipid binding behavior of Cyt2Aa2 protein, although it is not required for Cyt2Aa2 protein binding onto lipid bilayers. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Photothermal Off-Resonance Tapping for Rapid and Gentle Atomic Force Imaging of Live Cells
Int. J. Mol. Sci. 2018, 19(10), 2984; https://doi.org/10.3390/ijms19102984 - 30 Sep 2018
Cited by 2
Abstract
Imaging living cells by atomic force microscopy (AFM) promises not only high-resolution topographical data, but additionally, mechanical contrast, both of which are not obtainable with other microscopy techniques. Such imaging is however challenging, as cells need to be measured with low interaction forces [...] Read more.
Imaging living cells by atomic force microscopy (AFM) promises not only high-resolution topographical data, but additionally, mechanical contrast, both of which are not obtainable with other microscopy techniques. Such imaging is however challenging, as cells need to be measured with low interaction forces to prevent either deformation or detachment from the surface. Off-resonance modes which periodically probe the surface have been shown to be advantageous, as they provide excellent force control combined with large amplitudes, which help reduce lateral force interactions. However, the low actuation frequency in traditional off-resonance techniques limits the imaging speed significantly. Using photothermal actuation, we probe the surface by directly actuating the cantilever. Due to the much smaller mass that needs to be actuated, the achievable measurement frequency is increased by two orders of magnitude. Additionally, photothermal off-resonance tapping (PORT) retains the precise force control of conventional off-resonance modes and is therefore well suited to gentle imaging. Here, we show how photothermal off-resonance tapping can be used to study live cells by AFM. As an example of imaging mammalian cells, the initial attachment, as well as long-term detachment, of human thrombocytes is presented. The membrane disrupting effect of the antimicrobial peptide CM-15 is shown on the cell wall of Escherichia coli. Finally, the dissolution of the cell wall of Bacillus subtilis by lysozyme is shown. Taken together, these evolutionarily disparate forms of life exemplify the usefulness of PORT for live cell imaging in a multitude of biological disciplines. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
HIC1 and RassF1A Methylation Attenuates Tubulin Expression and Cell Stiffness in Cancer
Int. J. Mol. Sci. 2018, 19(10), 2884; https://doi.org/10.3390/ijms19102884 - 22 Sep 2018
Cited by 1
Abstract
Cell stiffness is a potential biomarker for monitoring cellular transformation, metastasis, and drug resistance development. Environmental factors relayed into the cell may result in formation of inheritable markers (e.g., DNA methylation), which provide selectable advantages (e.g., tumor development-favoring changes in cell stiffness). We [...] Read more.
Cell stiffness is a potential biomarker for monitoring cellular transformation, metastasis, and drug resistance development. Environmental factors relayed into the cell may result in formation of inheritable markers (e.g., DNA methylation), which provide selectable advantages (e.g., tumor development-favoring changes in cell stiffness). We previously demonstrated that targeted methylation of two tumor suppressor genes, hypermethylated in cancer 1 (HIC1) and Ras-association domain family member 1A (RassF1A), transformed mesenchymal stem cells (MSCs). Here, transformation-associated cytoskeleton and cell stiffness changes were evaluated. Atomic force microscopy (AFM) was used to detect cell stiffness, and immunostaining was used to measure cytoskeleton expression and distribution in cultured cells as well as in vivo. HIC1 and RassF1A methylation (me_HR)-transformed MSCs developed into tumors that clonally expanded in vivo. In me_HR-transformed MSCs, cell stiffness was lost, tubulin expression decreased, and F-actin was disorganized; DNA methylation inhibitor treatment suppressed their tumor progression, but did not fully restore their F-actin organization and stiffness. Thus, me_HR-induced cell transformation was accompanied by the loss of cellular stiffness, suggesting that somatic epigenetic changes provide inheritable selection markers during tumor propagation, but inhibition of oncogenic aberrant DNA methylation cannot restore cellular stiffness fully. Therefore, cell stiffness is a candidate biomarker for cells’ physiological status. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy
Int. J. Mol. Sci. 2018, 19(9), 2582; https://doi.org/10.3390/ijms19092582 - 30 Aug 2018
Cited by 9
Abstract
During their lifespan, Red blood cells (RBC), due to their inability to self-replicate, undergo an ageing degradation phenomenon. This pathway, both in vitro and in vivo, consists of a series of chemical and morphological modifications, which include deviation from the biconcave cellular shape, [...] Read more.
During their lifespan, Red blood cells (RBC), due to their inability to self-replicate, undergo an ageing degradation phenomenon. This pathway, both in vitro and in vivo, consists of a series of chemical and morphological modifications, which include deviation from the biconcave cellular shape, oxidative stress, membrane peroxidation, lipid content decrease and uncoupling of the membrane-skeleton from the lipid bilayer. Here, we use the capabilities of atomic force microscopy based infrared nanospectroscopy (AFM-IR) to study and correlate, with nanoscale resolution, the morphological and chemical modifications that occur during the natural degradation of RBCs at the subcellular level. By using the tip of an AFM to detect the photothermal expansion of RBCs, it is possible to obtain nearly two orders of magnitude higher spatial resolution IR spectra, and absorbance images than can be obtained on diffraction-limited commercial Fourier-transform Infrared (FT-IR) microscopes. Using this approach, we demonstrate that we can identify localized sites of oxidative stress and membrane peroxidation on individual RBC, before the occurrence of neat morphological changes in the cellular shape. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Effects of PTEN Loss and Activated KRAS Overexpression on Mechanical Properties of Breast Epithelial Cells
Int. J. Mol. Sci. 2018, 19(6), 1613; https://doi.org/10.3390/ijms19061613 - 30 May 2018
Cited by 3
Abstract
It has previously been shown that the simultaneous activation of PI3K (phosphatidylinositol 3-kinase) and Ras/MAPK (mitogen-activated protein kinases) pathways facilitate tumor growth despite only inducing cancer cell dormancy individually. Determining the impacts on cellular mechanics each pathway incites alone and in unison is [...] Read more.
It has previously been shown that the simultaneous activation of PI3K (phosphatidylinositol 3-kinase) and Ras/MAPK (mitogen-activated protein kinases) pathways facilitate tumor growth despite only inducing cancer cell dormancy individually. Determining the impacts on cellular mechanics each pathway incites alone and in unison is critical to developing non-toxic cancer therapies for triple-negative breast cancers. PTEN (phosphatase and tensin homolog) knockout and activated KRAS (Kristen rat sarcoma viral oncogene homolog) overexpression in healthy MCF-10A human breast epithelial cells activated the PI3K and Ras/MAPK pathways, respectively. Cell stiffness and fluidity were simultaneously measured using atomic force microscopy. Results suggest that PTEN knockout reduced cell stiffness and increased cell fluidity independent of PI3K activation. Effects of activated KRAS overexpression on cell stiffness depends on rigidity of cell culture substrate. Activated KRAS overexpression also counteracts the effects of PTEN knockout. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Insights into the Origin of Distinct Medin Fibril Morphologies Induced by Incubation Conditions and Seeding
Int. J. Mol. Sci. 2018, 19(5), 1357; https://doi.org/10.3390/ijms19051357 - 03 May 2018
Abstract
Incubation conditions are an important factor to consider when studying protein aggregation in vitro. Here, we employed biophysical methods and atomic force microscopy to show that agitation dramatically alters the morphology of medin, an amyloid protein deposited in the aorta. Agitation reduces the [...] Read more.
Incubation conditions are an important factor to consider when studying protein aggregation in vitro. Here, we employed biophysical methods and atomic force microscopy to show that agitation dramatically alters the morphology of medin, an amyloid protein deposited in the aorta. Agitation reduces the lag time for fibrillation by ~18-fold, suggesting that the rate of fibril formation plays a key role in directing the protein packing arrangement within fibrils. Utilising preformed sonicated fibrils as seeds, we probed the role of seeding on medin fibrillation and revealed three distinct fibril morphologies, with biophysical modelling explaining the salient features of experimental observations. We showed that nucleation pathways to distinct fibril morphologies may be switched on and off depending on the properties of the seeding fibrils and growth conditions. These findings may impact on the development of amyloid-based biomaterials and enhance understanding of seeding as a pathological mechanism. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Feature Tracking for High Speed AFM Imaging of Biopolymers
Int. J. Mol. Sci. 2018, 19(4), 1044; https://doi.org/10.3390/ijms19041044 - 31 Mar 2018
Cited by 1
Abstract
The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates [...] Read more.
The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates are needed with scan ranges larger than are currently achievable. Moreover, there is a significant installed base of slower instruments that would benefit from algorithmic approaches to increasing their frame rate without requiring significant hardware modifications. In this paper, we present an experimental demonstration of high speed scanning on an existing, non-high speed instrument, through the use of a feedback-based, feature-tracking algorithm that reduces imaging time by focusing on features of interest to reduce the total imaging area. Experiments on both circular and square gratings, as well as silicon steps and DNA strands show a reduction in imaging time by a factor of 3–12 over raster scanning, depending on the parameters chosen. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessArticle
Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface
Int. J. Mol. Sci. 2018, 19(2), 365; https://doi.org/10.3390/ijms19020365 - 25 Jan 2018
Abstract
The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on [...] Read more.
The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Review

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Open AccessReview
Atomic Force Microscopy Based Tip-Enhanced Raman Spectroscopy in Biology
Int. J. Mol. Sci. 2018, 19(4), 1193; https://doi.org/10.3390/ijms19041193 - 13 Apr 2018
Cited by 4
Abstract
Most biological phenomena occur at the nanometer scale, which is not accessible by the conventional optical techniques because of the optical diffraction limitation. Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, not only can provide the topography characterization with high resolution, [...] Read more.
Most biological phenomena occur at the nanometer scale, which is not accessible by the conventional optical techniques because of the optical diffraction limitation. Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, not only can provide the topography characterization with high resolution, but also can deliver the chemical or molecular information of a sample beyond the optical diffraction limitation. Therefore, it has been widely used in various structural analyses pertaining to materials science, tissue engineering, biological processes and so on. Based on the different feedback mechanisms, TERS can be classified into three types: atomic force microscopy based TERS system (AFM-TERS), scanning tunneling microscopy based TERS system (STM-TERS) and shear force microscopy based TERS system (SFM-TERS). Among them, AFM-TERS is the most widely adopted feedback system by live biosamples because it can work in liquid and this allows the investigation of biological molecules under native conditions. In this review, we mainly focus on the applications of AFM-TERS in three biological systems: nucleic acids, proteins and pathogens. From the TERS characterization to the data analysis, this review demonstrates that AFM-TERS has great potential applications to visually characterizing the biomolecular structure and crucially detecting more nano-chemical information of biological systems. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessReview
Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization
Int. J. Mol. Sci. 2018, 19(4), 1142; https://doi.org/10.3390/ijms19041142 - 10 Apr 2018
Cited by 3
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessReview
The Role of Single-Molecule Force Spectroscopy in Unraveling Typical and Autoimmune Heparin-induced Thrombocytopenia
Int. J. Mol. Sci. 2018, 19(4), 1054; https://doi.org/10.3390/ijms19041054 - 02 Apr 2018
Abstract
For the last two decades, heparins have been widely used as anticoagulants. Besides numerous advantages, up to 5% patients with heparin administration suffer from a major adverse drug effect known as heparin-induced thrombocytopenia (HIT). This typical HIT can result in deep vein thrombosis, [...] Read more.
For the last two decades, heparins have been widely used as anticoagulants. Besides numerous advantages, up to 5% patients with heparin administration suffer from a major adverse drug effect known as heparin-induced thrombocytopenia (HIT). This typical HIT can result in deep vein thrombosis, pulmonary embolism, occlusion of a limb artery, acute myocardial infarct, stroke, and a systemic reaction or skin necrosis. The basis of HIT may lead to clinical insights. Recent studies using single-molecule force spectroscopy (SMFS)-based atomic force microscopy revealed detailed binding mechanisms of the interactions between platelet factor 4 (PF4) and heparins of different lengths in typical HIT. Especially, SMFS results allowed identifying a new mechanism of the autoimmune HIT caused by a subset of human-derived antibodies in patients without heparin exposure. The findings proved that not only heparin but also a subset of antibodies induce thrombocytopenia. In this review, the role of SMFS in unraveling a major adverse drug effect and insights into molecular mechanisms inducing thrombocytopenia by both heparins and antibodies will be discussed. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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Open AccessReview
Compressive Force Spectroscopy: From Living Cells to Single Proteins
Int. J. Mol. Sci. 2018, 19(4), 960; https://doi.org/10.3390/ijms19040960 - 23 Mar 2018
Cited by 1
Abstract
One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities [...] Read more.
One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these “tensile” force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development. Full article
(This article belongs to the Special Issue Atomic Force Microscopy for Biological Applications)
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