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Application of Atomic Force Microscopy in Molecular and Cell Biology

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: 30 July 2024 | Viewed by 3201

Special Issue Editor


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Guest Editor
Prof. Richard Wong’s Lab, Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
Interests: nuclear pore complex; AFM; nanomedicine; cancer biology; virology; tumor immunology

Special Issue Information

Dear Colleagues,

Atomic force microscopy has been robustly used in life science for various purposes, such as nanoimaging of biological samples, measurement of molecular binding affinities, and dynamic biomolecular events. Although conventional atomic force microscopy provides high-resolution images, it is not fast enough to capture conformational dynamics of biomolecules effectively. The advent of high-speed atomic force microscopy (HS-AFM) has provided a significant solution for scientists to visualize the dynamic behaviors of biomolecules and organelles in a real-time manner with high spatiotemporal resolution. HS-AFM is label-free, and it does not require sample pre-treatment, e.g., fixation. In addition, HS-AFM scanning can be performed under physiological buffer conditions.

HS-AFM, particularly the version developed by Prof. Toshio Ando, has been widely applied in various life science studies. For example, the classic walking myosin V along actin filaments, dynamic FG-filaments in the nuclear pore complex of human colorectal cancer cells, the fusogenic transition of influenza A hemagglutinin, nano-topographical features of exosomes, DNA-wrapping on single histone H2A protein, amongst others. Recently, the development of an ultra-wide scanner with megapixel resolution has enabled HS-AFM to perform live-cell time-lapse imaging. The application of HS-AFM is versatile; not only can it help to answer basic scientific questions, but it is also applicable to studying potential therapeutics that could inhibit target protein activities in certain diseases—amyloid aggregates in Alzheimer’s disease, for example.

In this Special Issue, we invite you to contribute original research articles and reviews on all aspects related to the theme of the “Application of Atomic Force Microscopy in Molecular and Cell Biology”. We especially hope to highlight novel findings in the biophysical properties of biomolecules/organelles and interaction between biomolecules and biomolecule–organelles.

Dr. Kee Siang Lim
Guest Editor

Manuscript Submission Information

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Keywords

  • atomic force microscopy
  • biophysics
  • biomolecule interactions
  • organelles
  • biomolecule self-assembly
  • live cell imaging
  • nanoimaging

Published Papers (3 papers)

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Research

10 pages, 1423 KiB  
Communication
A New Strategy to Investigate RNA:DNA Triplex Using Atomic Force Microscopy
by Giovanni Merici, Davide Amidani, Giorgio Dieci and Claudio Rivetti
Int. J. Mol. Sci. 2024, 25(5), 3035; https://doi.org/10.3390/ijms25053035 - 6 Mar 2024
Viewed by 682
Abstract
Over the past decade, long non-coding RNAs (lncRNAs) have been recognized as key players in gene regulation, influencing genome organization and expression. The locus-specific binding of these non-coding RNAs (ncRNAs) to DNA involves either a non-covalent interaction with DNA-bound proteins or a direct [...] Read more.
Over the past decade, long non-coding RNAs (lncRNAs) have been recognized as key players in gene regulation, influencing genome organization and expression. The locus-specific binding of these non-coding RNAs (ncRNAs) to DNA involves either a non-covalent interaction with DNA-bound proteins or a direct sequence-specific interaction through the formation of RNA:DNA triplexes. In an effort to develop a novel strategy for characterizing a triple-helix formation, we employed atomic force microscopy (AFM) to visualize and study a regulatory RNA:DNA triplex formed between the Khps1 lncRNA and the enhancer of the proto-oncogene SPHK1. The analysis demonstrates the successful formation of RNA:DNA triplexes under various conditions of pH and temperature, indicating the effectiveness of the AFM strategy. Despite challenges in discriminating between the triple-helix and R-loop configurations, this approach opens new perspectives for investigating the role of lncRNAs in gene regulation at the single-molecule level. Full article
(This article belongs to the Special Issue Application of Atomic Force Microscopy in Molecular and Cell Biology)
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20 pages, 5035 KiB  
Article
Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions
by Heng Sun, Fenghui Liao, Yichen Tian, Yongrong Lei, Yuna Fu and Jianhua Wang
Int. J. Mol. Sci. 2024, 25(5), 2474; https://doi.org/10.3390/ijms25052474 - 20 Feb 2024
Viewed by 711
Abstract
Apoptosis signaling controls the cell cycle through the protein–protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the [...] Read more.
Apoptosis signaling controls the cell cycle through the protein–protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the kinetics of BAX and Bcl-2 activities. The utilization of natural polyphenols to regulate the binding process of PPIs is feasible. However, the mechanism of this modulation has not been studied in detail. Here, we utilized atomic force microscopy (AFM) to evaluate the effects of polyphenols (kaempferol, quercetin, dihydromyricetin, baicalin, curcumin, rutin, epigallocatechin gallate, and gossypol) on the BAX/Bcl-2 binding mechanism. We demonstrated at the molecular scale that polyphenols quantitatively affect the interaction forces, kinetics, thermodynamics, and structural properties of BAX/Bcl-2 complex formation. We observed that rutin, epigallocatechin gallate, and baicalin reduced the binding affinity of BAX/Bcl-2 by an order of magnitude. Combined with surface free energy and molecular docking, the results revealed that polyphenols are driven by multiple forces that affect the orientation freedom of PPIs, with hydrogen bonding, hydrophobic interactions, and van der Waals forces being the major contributors. Overall, our work provides valuable insights into how molecules tune PPIs to modulate their function. Full article
(This article belongs to the Special Issue Application of Atomic Force Microscopy in Molecular and Cell Biology)
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17 pages, 7455 KiB  
Article
Observing Dynamic Conformational Changes within the Coiled-Coil Domain of Different Laminin Isoforms Using High-Speed Atomic Force Microscopy
by Lucky Akter, Holger Flechsig, Arin Marchesi and Clemens M. Franz
Int. J. Mol. Sci. 2024, 25(4), 1951; https://doi.org/10.3390/ijms25041951 - 6 Feb 2024
Viewed by 1308
Abstract
Laminins are trimeric glycoproteins with important roles in cell-matrix adhesion and tissue organization. The laminin α, ß, and γ-chains have short N-terminal arms, while their C-termini are connected via a triple coiled-coil domain, giving the laminin molecule a well-characterized cross-shaped morphology as a [...] Read more.
Laminins are trimeric glycoproteins with important roles in cell-matrix adhesion and tissue organization. The laminin α, ß, and γ-chains have short N-terminal arms, while their C-termini are connected via a triple coiled-coil domain, giving the laminin molecule a well-characterized cross-shaped morphology as a result. The C-terminus of laminin alpha chains contains additional globular laminin G-like (LG) domains with important roles in mediating cell adhesion. Dynamic conformational changes of different laminin domains have been implicated in regulating laminin function, but so far have not been analyzed at the single-molecule level. High-speed atomic force microscopy (HS-AFM) is a unique tool for visualizing such dynamic conformational changes under physiological conditions at sub-second temporal resolution. After optimizing surface immobilization and imaging conditions, we characterized the ultrastructure of laminin-111 and laminin-332 using HS-AFM timelapse imaging. While laminin-111 features a stable S-shaped coiled-coil domain displaying little conformational rearrangement, laminin-332 coiled-coil domains undergo rapid switching between straight and bent conformations around a defined central molecular hinge. Complementing the experimental AFM data with AlphaFold-based coiled-coil structure prediction enabled us to pinpoint the position of the hinge region, as well as to identify potential molecular rearrangement processes permitting hinge flexibility. Coarse-grained molecular dynamics simulations provide further support for a spatially defined kinking mechanism in the laminin-332 coiled-coil domain. Finally, we observed the dynamic rearrangement of the C-terminal LG domains of laminin-111 and laminin-332, switching them between compact and open conformations. Thus, HS-AFM can directly visualize molecular rearrangement processes within different laminin isoforms and provide dynamic structural insight not available from other microscopy techniques. Full article
(This article belongs to the Special Issue Application of Atomic Force Microscopy in Molecular and Cell Biology)
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