1
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Chitty C, Kuliga K, Xue WF. Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies. Biochem Soc Trans 2024; 52:761-771. [PMID: 38600027 DOI: 10.1042/bst20230857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point reconstruction AFM (CPR-AFM) methodology and its application in 3D reconstruction of individual helical amyloid filaments in the context of the challenges presented by the structural analysis of highly polymorphous and heterogeneous amyloid protein structures. How individual particle-level structural analysis can contribute to resolving the amyloid polymorph structure-function relationships, the environmental triggers leading to protein misfolding and aggregation into amyloid species, the influences by the conditions or minor fluctuations in the initial monomeric protein structure on the speed of amyloid fibril formation, and the extent of the different types of amyloid species that can be formed, are discussed. Future perspectives in the capabilities of AFM-based 3D structural reconstruction methodology exploiting synergies with other recent AFM technology advances are also discussed to highlight the potential of AFM as an emergent general, accessible and multimodal structural biology tool for the analysis of individual biomolecules.
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Affiliation(s)
- Claudia Chitty
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Kinga Kuliga
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Wei-Feng Xue
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
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2
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Smith JW, Carnevale LN, Das A, Chen Q. Electron videography of a lipid-protein tango. SCIENCE ADVANCES 2024; 10:eadk0217. [PMID: 38630809 PMCID: PMC11023515 DOI: 10.1126/sciadv.adk0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Lauren N. Carnevale
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Aditi Das
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Materials Research Laboratory, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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3
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Beck M, Covino R, Hänelt I, Müller-McNicoll M. Understanding the cell: Future views of structural biology. Cell 2024; 187:545-562. [PMID: 38306981 DOI: 10.1016/j.cell.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 02/04/2024]
Abstract
Determining the structure and mechanisms of all individual functional modules of cells at high molecular detail has often been seen as equal to understanding how cells work. Recent technical advances have led to a flush of high-resolution structures of various macromolecular machines, but despite this wealth of detailed information, our understanding of cellular function remains incomplete. Here, we discuss present-day limitations of structural biology and highlight novel technologies that may enable us to analyze molecular functions directly inside cells. We predict that the progression toward structural cell biology will involve a shift toward conceptualizing a 4D virtual reality of cells using digital twins. These will capture cellular segments in a highly enriched molecular detail, include dynamic changes, and facilitate simulations of molecular processes, leading to novel and experimentally testable predictions. Transferring biological questions into algorithms that learn from the existing wealth of data and explore novel solutions may ultimately unveil how cells work.
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Affiliation(s)
- Martin Beck
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany; Goethe University Frankfurt, Frankfurt, Germany.
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
| | - Inga Hänelt
- Goethe University Frankfurt, Frankfurt, Germany.
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4
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Allen FI, De Teresa JM, Onoa B. Focused Helium Ion and Electron Beam-Induced Deposition of Organometallic Tips for Dynamic Atomic Force Microscopy of Biomolecules in Liquid. ACS APPLIED MATERIALS & INTERFACES 2024; 16:4439-4448. [PMID: 38244049 DOI: 10.1021/acsami.3c16407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
We demonstrate the fabrication of sharp nanopillars of high aspect ratio onto specialized atomic force microscopy (AFM) microcantilevers and their use for high-speed AFM of DNA and nucleoproteins in liquid. The fabrication technique uses localized charged-particle-induced deposition with either a focused beam of helium ions or electrons in a helium ion microscope (HIM) or scanning electron microscope (SEM). This approach enables customized growth onto delicate substrates with nanometer-scale placement precision and in situ imaging of the final tip structures using the HIM or SEM. Tip radii of <10 nm are obtained and the underlying microcantilever remains intact. Instead of the more commonly used organic precursors employed for bio-AFM applications, we use an organometallic precursor (tungsten hexacarbonyl) resulting in tungsten-containing tips. Transmission electron microscopy reveals a thin layer of carbon on the tips. The interaction of the new tips with biological specimens is therefore likely very similar to that of standard carbonaceous tips, with the added benefit of robustness. A further advantage of the organometallic tips is that compared to carbonaceous tips they better withstand UV-ozone cleaning treatments to remove residual organic contaminants between experiments, which are inevitable during the scanning of soft biomolecules in liquid. Our tips can also be grown onto the blunted tips of previously used cantilevers, thus providing a means to recycle specialized cantilevers and restore their performance to the original manufacturer specifications. Finally, a focused helium ion beam milling technique to reduce the tip radii and thus further improve lateral spatial resolution in the AFM scans is demonstrated.
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Affiliation(s)
- Frances I Allen
- Department of Materials Science and Engineering, University of California, Berkeley, California 97420, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 97420, United States
| | - José María De Teresa
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Bibiana Onoa
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
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5
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Chien YC, Wang YS, Sridharan D, Kuo CW, Chien CT, Uchihashi T, Kato K, Angata T, Meng TC, Hsu STD, Khoo KH. High Density of N- and O-Glycosylation Shields and Defines the Structural Dynamics of the Intrinsically Disordered Ectodomain of Receptor-type Protein Tyrosine Phosphatase Alpha. JACS AU 2023; 3:1864-1875. [PMID: 37502146 PMCID: PMC10369406 DOI: 10.1021/jacsau.3c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/29/2023]
Abstract
The intracellular phosphatase domain of the receptor-type protein tyrosine phosphatase alpha (PTPRA) is known to regulate various signaling pathways related to cell adhesion through c-Src kinase activation. In contrast, the functional significance of its relatively short, intrinsically disordered, and heavily glycosylated ectodomain remains unclear. Through detailed mass spectrometry analyses of a combination of protease and glycosidase digests, we now provide the first experimental evidence for its site-specific glycosylation pattern. This includes the occurrence of O-glycan at the N-glycosylation sequon among the more than 30 O-glycosylation sites confidently identified beside the 7 N-glycosylation sites. The closely spaced N- and O-glycans appear to have mutually limited the extent of further galactosylation and sialylation. An immature smaller form of full-length PTPRA was found to be deficient in O-glycosylation, most likely due to failure to transit the Golgi. N-glycosylation, on the other hand, is dispensable for cell surface expression and contributes less than the extensive O-glycosylation to the overall solution structure of the ectodomain. The glycosylation information is combined with the overall structural features of the ectodomain derived from small-angle X-ray scattering and high-speed atomic force microscopy monitoring to establish a dynamic structural model of the densely glycosylated PTPRA ectodomain. The observed high structural flexibility, as manifested by continuous transitioning from fully to partially extended and fold-back conformations, suggests that the receptor-type phosphatase is anchored to the membrane and kept mostly at a monomeric state through an ectodomain shaped and fully shielded by glycosylation.
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Affiliation(s)
- Yu-Chun Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Deepa Sridharan
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chu-Wei Kuo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Takayuki Uchihashi
- Department
of Physics, Nagoya University, Nagoya 464-8602, Japan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Koichi Kato
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki 444-8787, Japan
- Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya 467-8603, Japan
| | - Takashi Angata
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tzu-Ching Meng
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- International
Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima 739-8527, Japan
| | - Kay-Hooi Khoo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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6
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Ohtomo H, Yamane T, Oda T, Kodera N, Kurita JI, Tsunaka Y, Amyot R, Ikeguchi M, Nishimura Y. Dynamic solution structures of whole human NAP1 dimer bound to one and two histone H2A-H2B heterodimers obtained by integrative methods. J Mol Biol 2023:168189. [PMID: 37380014 DOI: 10.1016/j.jmb.2023.168189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.
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Affiliation(s)
- Hideaki Ohtomo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Romain Amyot
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8258, Japan.
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7
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Wang H, Lee D, Wei L. Toward the Next Frontiers of Vibrational Bioimaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:3-17. [PMID: 37122829 PMCID: PMC10131268 DOI: 10.1021/cbmi.3c00004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 05/02/2023]
Abstract
Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.
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Affiliation(s)
- Haomin Wang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Dongkwan Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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8
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Flechsig H, Ando T. Protein dynamics by the combination of high-speed AFM and computational modeling. Curr Opin Struct Biol 2023; 80:102591. [PMID: 37075535 DOI: 10.1016/j.sbi.2023.102591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/21/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) allows direct observation of biological molecules in dynamic action. However, HS-AFM has no atomic resolution. This article reviews recent progress of computational methods to infer high-resolution information, including the construction of 3D atomistic structures, from experimentally acquired resolution-limited HS-AFM images.
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Affiliation(s)
- Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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9
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Kozai T, Fernandez-Martinez J, van Eeuwen T, Gallardo P, Kapinos LE, Mazur A, Zhang W, Tempkin J, Panatala R, Delgado-Izquierdo M, Raveh B, Sali A, Chait BT, Veenhoff LM, Rout MP, Lim RYH. Dynamic molecular mechanism of the nuclear pore complex permeability barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535055. [PMID: 37066338 PMCID: PMC10103940 DOI: 10.1101/2023.03.31.535055] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic transport of specific macromolecules while impeding the exchange of unsolicited material. However, key aspects of this gating mechanism remain controversial. To address this issue, we determined the nanoscopic behavior of the permeability barrier directly within yeast S. cerevisiae NPCs at transport-relevant timescales. We show that the large intrinsically disordered domains of phenylalanine-glycine repeat nucleoporins (FG Nups) exhibit highly dynamic fluctuations to create transient voids in the permeability barrier that continuously shape-shift and reseal, resembling a radial polymer brush. Together with cargo-carrying transport factors the FG domains form a feature called the central plug, which is also highly dynamic. Remarkably, NPC mutants with longer FG domains show interweaving meshwork-like behavior that attenuates nucleocytoplasmic transport in vivo. Importantly, the bona fide nanoscale NPC behaviors and morphologies are not recapitulated by in vitro FG domain hydrogels. NPCs also exclude self-assembling FG domain condensates in vivo, thereby indicating that the permeability barrier is not generated by a self-assembling phase condensate, but rather is largely a polymer brush, organized by the NPC scaffold, whose dynamic gating selectivity is strongly enhanced by the presence of transport factors.
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Affiliation(s)
- Toshiya Kozai
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | | | - Adam Mazur
- Biozentrum, University of Basel, Switzerland
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Jeremy Tempkin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, U.S.A. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, U.S.A
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Netherlands
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, U.S.A
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
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10
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Kolbeck P, Dass M, Martynenko IV, van Dijk-Moes RJA, Brouwer KJH, van Blaaderen A, Vanderlinden W, Liedl T, Lipfert J. DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging. NANO LETTERS 2023; 23:1236-1243. [PMID: 36745573 PMCID: PMC9951250 DOI: 10.1021/acs.nanolett.2c04299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/25/2022] [Indexed: 06/01/2023]
Abstract
Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.
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Affiliation(s)
- Pauline
J. Kolbeck
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Mihir Dass
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Irina V. Martynenko
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Relinde J. A. van Dijk-Moes
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Kelly J. H. Brouwer
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Alfons van Blaaderen
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Willem Vanderlinden
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Tim Liedl
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Jan Lipfert
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
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11
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Venugopal A, Ruiz-Perez L, Swamynathan K, Kulkarni C, Calò A, Kumar M. Caught in Action: Visualizing Dynamic Nanostructures Within Supramolecular Systems Chemistry. Angew Chem Int Ed Engl 2023; 62:e202208681. [PMID: 36469792 DOI: 10.1002/anie.202208681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Supramolecular systems chemistry has been an area of active research to develop nanomaterials with life-like functions. Progress in systems chemistry relies on our ability to probe the nanostructure formation in solution. Often visualizing the dynamics of nanostructures which transform over time is a formidable challenge. This necessitates a paradigm shift from dry sample imaging towards solution-based techniques. We review the application of state-of-the-art techniques for real-time, in situ visualization of dynamic self-assembly processes. We present how solution-based techniques namely optical super-resolution microscopy, solution-state atomic force microscopy, liquid-phase transmission electron microscopy, molecular dynamics simulations and other emerging techniques are revolutionizing our understanding of active and adaptive nanomaterials with life-like functions. This Review provides the visualization toolbox and futuristic vision to tap the potential of dynamic nanomaterials.
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Affiliation(s)
- Akhil Venugopal
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Lorena Ruiz-Perez
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - K Swamynathan
- Soft Condensed Matter, Raman Research Institute, C. V. Raman Avenue, Sadashivanagar, Bangalore-560080, India.,Department of Chemistry, NITTE Meenakshi Institute of Technology, Yelahanka, Bengaluru 560064, India
| | - Chidambar Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Annalisa Calò
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Department of Electronic and Biomedical Engineering, University of Barcelona, Calle Marti i Fraquès 1-11, 08028, Barcelona, Spain
| | - Mohit Kumar
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Calle Marti i Fraquès 1-11, 08028, Barcelona, Spain
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12
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Radhakrishnan RM, Kizhakkeduth ST, Nair VM, Ayyappan S, Lakshmi RB, Babu N, Prasannajith A, Umeda K, Vijayan V, Kodera N, Manna TK. Kinetochore-microtubule attachment in human cells is regulated by the interaction of a conserved motif of Ska1 with EB1. J Biol Chem 2023; 299:102853. [PMID: 36592928 PMCID: PMC9926122 DOI: 10.1016/j.jbc.2022.102853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 01/02/2023] Open
Abstract
The kinetochore establishes the linkage between chromosomes and the spindle microtubule plus ends during mitosis. In vertebrates, the spindle-kinetochore-associated (Ska1,2,3) complex stabilizes kinetochore attachment with the microtubule plus ends, but how Ska is recruited to and stabilized at the kinetochore-microtubule interface is not understood. Here, our results show that interaction of Ska1 with the general microtubule plus end-associated protein EB1 through a conserved motif regulates Ska recruitment to kinetochores in human cells. Ska1 forms a stable complex with EB1 via interaction with the motif in its N-terminal disordered loop region. Disruption of this interaction either by deleting or mutating the motif disrupts Ska complex recruitment to kinetochores and induces chromosome alignment defects, but it does not affect Ska complex assembly. Atomic-force microscopy imaging revealed that Ska1 is anchored to the C-terminal region of the EB1 dimer through its loop and thereby promotes formation of extended structures. Furthermore, our NMR data showed that the Ska1 motif binds to the residues in EB1 that are the binding sites of other plus end targeting proteins that are recruited to microtubules by EB1 through a similar conserved motif. Collectively, our results demonstrate that EB1-mediated Ska1 recruitment onto the microtubule serves as a general mechanism for the formation of vertebrate kinetochore-microtubule attachments and metaphase chromosome alignment.
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Affiliation(s)
- Renjith M Radhakrishnan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Safwa T Kizhakkeduth
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Vishnu M Nair
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Shine Ayyappan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - R Bhagya Lakshmi
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Neethu Babu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Anjaly Prasannajith
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Vinesh Vijayan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Tapas K Manna
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India.
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13
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Melo MCR, Gomes DEB, Bernardi RC. Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. J Am Chem Soc 2023; 145:70-77. [PMID: 36455202 DOI: 10.1021/jacs.2c07674] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The unbinding pathway of a protein complex can vary significantly depending on biochemical and mechanical factors. Under mechanical stress, a complex may dissociate through a mechanism different from that used in simple thermal dissociation, leading to different dissociation rates under shear force and thermal dissociation. This is a well-known phenomenon studied in biomechanics whose molecular and atomic details are still elusive. A particularly interesting case is the complex formed by bacterial adhesins with their human peptide target. These protein interactions have a force resilience equivalent to those of covalent bonds, an order of magnitude stronger than the widely used streptavidin:biotin complex, while having an ordinary affinity, much lower than that of streptavidin:biotin. Here, in an in silico single-molecule force spectroscopy approach, we use molecular dynamics simulations to investigate the dissociation mechanism of adhesin/peptide complexes. We show how the Staphylococcus epidermidis adhesin SdrG uses a catch-bond mechanism to increase complex stability with increasing mechanical stress. While allowing for thermal dissociation in a low-force regime, an entirely different mechanical dissociation path emerges in a high-force regime, revealing an intricate mechanism that does not depend on the peptide's amino acid sequence. Using a dynamic network analysis approach, we identified key amino acid contacts that describe the mechanics of this complex, revealing differences in dynamics that hinder thermal dissociation and establish the mechanical dissociation path. We then validate the information content of the selected amino acid contacts using their dynamics to successfully predict the rupture forces for this complex through a machine learning model.
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Affiliation(s)
- Marcelo C R Melo
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Diego E B Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Rafael C Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
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14
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Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
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15
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Kahle ER, Patel N, Sreenivasappa HB, Marcolongo MS, Han L. Targeting cell-matrix interface mechanobiology by integrating AFM with fluorescence microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 176:67-81. [PMID: 36055517 PMCID: PMC9691605 DOI: 10.1016/j.pbiomolbio.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Mechanosensing at the interface of a cell and its surrounding microenvironment is an essential driving force of physiological processes. Understanding molecular activities at the cell-matrix interface has the potential to provide novel targets for improving tissue regeneration and early disease intervention. In the past few decades, the advancement of atomic force microscopy (AFM) has offered a unique platform for probing mechanobiology at this crucial microdomain. In this review, we describe key advances under this topic through the use of an integrated system of AFM (as a biomechanical testing tool) with complementary immunofluorescence (IF) imaging (as an in situ navigation system). We first describe the body of work investigating the micromechanics of the pericellular matrix (PCM), the immediate cell micro-niche, in healthy, diseased, and genetically modified tissues, with a focus on articular cartilage. We then summarize the key findings in understanding cellular biomechanics and mechanotransduction, in which, molecular mechanisms governing transmembrane ion channel-mediated mechanosensing, cytoskeleton remodeling, and nucleus remodeling have been studied in various cell and tissue types. Lastly, we provide an overview of major technical advances that have enabled more in-depth studies of mechanobiology, including the integration of AFM with a side-view microscope, multiple optomicroscopy, a fluorescence recovery after photobleaching (FRAP) module, and a tensile stretching device. The innovations described here have contributed greatly to advancing the fundamental knowledge of extracellular matrix biomechanics and cell mechanobiology for improved understanding, detection, and intervention of various diseases.
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Affiliation(s)
- Elizabeth R Kahle
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Neil Patel
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Harini B Sreenivasappa
- Cell Imaging Center, Office of Research and Innovation, Drexel University, PA 19104, United States
| | - Michele S Marcolongo
- Department of Mechanical Engineering, Villanova University, Villanova, PA 19085, United States
| | - Lin Han
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, United States.
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16
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Loose M, Auer A, Brognara G, Budiman HR, Kowalski L, Matijević I. In vitro
reconstitution of small
GTPase
regulation. FEBS Lett 2022; 597:762-777. [PMID: 36448231 DOI: 10.1002/1873-3468.14540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
Abstract
Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.
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Affiliation(s)
- Martin Loose
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Albert Auer
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Gabriel Brognara
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | | | - Lukasz Kowalski
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
| | - Ivana Matijević
- Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria
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17
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Hayakawa Y, Takaine M, Ngo KX, Imai T, Yamada MD, Behjat AB, Umeda K, Hirose K, Yurtsever A, Kodera N, Tokuraku K, Numata O, Fukuma T, Ando T, Nakano K, Uyeda TQP. Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II. Life Sci Alliance 2022; 6:6/1/e202201469. [PMID: 36288901 PMCID: PMC9610768 DOI: 10.26508/lsa.202201469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
We report a case in which sub-stoichiometric binding of an actin-binding protein has profound structural and functional consequences, providing an insight into the fundamental properties of actin regulation. Rng2 is an IQGAP contained in contractile rings in the fission yeast Schizosaccharomyces pombe Here, we used high-speed atomic force microscopy and electron microscopy and found that sub-stoichiometric binding of the calponin-homology actin-binding domain of Rng2 (Rng2CHD) induces global structural changes in skeletal muscle actin filaments, including shortening of the filament helical pitch. Sub-stoichiometric binding of Rng2CHD also reduced the affinity between actin filaments and muscle myosin II carrying ADP and strongly inhibited the motility of actin filaments on myosin II in vitro. On skeletal muscle myosin II-coated surfaces, Rng2CHD stopped the actin movements at a binding ratio of 11%. Rng2CHD also inhibited actin movements on myosin II of the amoeba Dictyostelium, but in this case, by detaching actin filaments from myosin II-coated surfaces. Thus, sparsely bound Rng2CHD induces apparently cooperative structural changes in actin filaments and inhibits force generation by actomyosin II.
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Affiliation(s)
- Yuuki Hayakawa
- Department of Physics, Faculty of Science and Engineering, Graduate School of Waseda University, Shinjuku, Japan
| | - Masak Takaine
- Department of Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Kien Xuan Ngo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Taiga Imai
- Department of Applied Sciences, Muroran Institute of Technology, Muroran, Japan
| | - Masafumi D Yamada
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Arash Badami Behjat
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Keiko Hirose
- Department of Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ayhan Yurtsever
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Kiyotaka Tokuraku
- Department of Applied Sciences, Muroran Institute of Technology, Muroran, Japan
| | - Osamu Numata
- Department of Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Kentaro Nakano
- Department of Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Taro QP Uyeda
- Department of Physics, Faculty of Science and Engineering, Graduate School of Waseda University, Shinjuku, Japan,Department of Biology, Degree Programs in Life and Earth Sciences, Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan,Correspondence: ;
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18
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Liao HS, Akhtar I, Werner C, Slipets R, Pereda J, Wang JH, Raun E, Nørgaard LO, Dons FE, Hwu EET. Open-source controller for low-cost and high-speed atomic force microscopy imaging of skin corneocyte nanotextures. HARDWAREX 2022; 12:e00341. [PMID: 35936941 PMCID: PMC9352456 DOI: 10.1016/j.ohx.2022.e00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/02/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
High-speed atomic force microscopes (HS-AFMs) with high temporal resolution enable dynamic phenomena to be visualized at nanoscale resolution. However, HS-AFMs are more complex and costlier than conventional AFMs, and particulars of an open-source HS-AFM controller have not been published before. These high entry barriers hinder the popularization of HS-AFMs in both academic and industrial applications. In addition, HS-AFMs generally have a small imaging area that limits the fields of implementation. This study presents an open-source controller that enables a low-cost simplified AFM to achieve a maximum tip-sample velocity of 5,093 µm/s (9.3 s/frame, 512 × 512 pixels), which is nearly 100 times higher than that of the original controller. Moreover, the proposed controller doubles the imaging area to 46.3 × 46.3 µm2 compared to that of the original system. The low-cost HS-AFM can successfully assess the severity of atopic dermatitis (AD) by measuring the nanotexture of human skin corneocytes in constant height DC mode. The open-source controller-based HS-AFM system costs less than $4,000, which provides resource-limited research institutes with affordable access to high-throughput nanoscale imaging to further expand the HS-AFM research community.
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Affiliation(s)
- Hsien-Shun Liao
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
| | - Imtisal Akhtar
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Werner
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, 38116 Braunschweig, Germany
| | - Roman Slipets
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jorge Pereda
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jen-Hung Wang
- Department of Mechatronics and Robotics, Technical University of Munich, Germany
| | - Ellen Raun
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Laura Olga Nørgaard
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Frederikke Elisabet Dons
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Edwin En Te Hwu
- The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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19
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Three-Way DNA Junction as an End Label for DNA in Atomic Force Microscopy Studies. Int J Mol Sci 2022; 23:ijms231911404. [PMID: 36232705 PMCID: PMC9569629 DOI: 10.3390/ijms231911404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes.
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20
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Glia A, Deliorman M, Qasaimeh MA. 3D Generation of Multipurpose Atomic Force Microscopy Tips. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201489. [PMID: 35853246 PMCID: PMC9507387 DOI: 10.1002/advs.202201489] [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: 03/15/2022] [Revised: 05/24/2022] [Indexed: 05/02/2023]
Abstract
In this work, 3D polymeric atomic force microscopy (AFM) tips, referred to as 3DTIPs, are manufactured with great flexibility in design and function using two-photon polymerization. With the technology holding a great potential in developing next-generation AFM tips, 3DTIPs prove effective in obtaining high-resolution and high-speed AFM images in air and liquid environments, using common AFM modes. In particular, it is shown that the 3DTIPs provide high-resolution imaging due to their extremely low Hamaker constant, high speed scanning rates due to their low quality factor, and high durability due to their soft nature and minimal isotropic tip wear; the three important features for advancing AFM studies. It is also shown that refining the tip end of the 3DTIPs by focused ion beam etching and by carbon nanotube inclusion substantially extends their functionality in high-resolution AFM imaging, reaching angstrom scales. Altogether, the multifunctional capabilities of 3DTIPs can bring next-generation AFM tips to routine and advanced AFM applications, and expand the fields of high speed AFM imaging and biological force measurements.
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Affiliation(s)
- Ayoub Glia
- Division of EngineeringNew York University Abu Dhabi (NYUAD)Abu DhabiUAE
| | | | - Mohammad A. Qasaimeh
- Division of EngineeringNew York University Abu Dhabi (NYUAD)Abu DhabiUAE
- Department of Mechanical and Aerospace EngineeringNew York UniversityBrooklynNY11201USA
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21
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Ngo KX, Nguyen PDN, Furusho H, Miyata M, Shimonaka T, Chau NNB, Vinh NP, Nghia NA, Mohammed TO, Ichikawa T, Kodera N, Konno H, Fukuma T, Quoc NB. Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity. PHYTOPATHOLOGY 2022; 112:1524-1536. [PMID: 35238604 DOI: 10.1094/phyto-09-21-0397-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.
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Affiliation(s)
- Kien Xuan Ngo
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Phuong Doan N Nguyen
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
- Research Institute for Biotechnology and Environment, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Hirotoshi Furusho
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Tomomi Shimonaka
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Nguyen Ngoc Bao Chau
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City, Vietnam
| | | | | | - Tareg Omer Mohammed
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Takehiko Ichikawa
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Hiroki Konno
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Takeshi Fukuma
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Nguyen Bao Quoc
- Research Institute for Biotechnology and Environment, Nong Lam University, Ho Chi Minh City, Vietnam
- Faculty of Biological Sciences, Nong Lam University, Ho Chi Minh City, Vietnam
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22
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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23
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Leiva-Sabadini C, Schuh CM, Barrera NP, Aguayo S. Ultrastructural characterisation of young and aged dental enamel by atomic force microscopy. J Microsc 2022; 288:185-192. [PMID: 35621144 DOI: 10.1111/jmi.13126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022]
Abstract
Recent advances in atomic force microscopy (AFM) have allowed the characterisation of dental-associated biomaterials and biological surfaces with high-resolution. In this context, the topography of dental enamel - the hardest mineralised tissue in the body - has been explored with AFM-based approaches at the micro-scale. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure because of ageing have not yet been explored with nanoscale resolution. Therefore, the aim of this exploratory work was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, a total of six teeth were collected from human donors from which enamel specimens were prepared. By employing intermittent contact (AC mode) imaging, HA crystals were characterised in both transversal and longitudinal orientation (respect to surface plane) with high-resolution in environmental conditions. The external enamel surface displayed the presence of a pellicle-like coating on its surface, that was not observable on cleaned specimens. Acid-etching exposed crystals that were imaged and morphologically characterised in high-resolution at the nanoscale in both the external and internal regions of enamel in older and younger specimens. Our results demonstrated important individual variations in HA crystal width and roughness parameters across the analysed specimens; however, an increase in surface roughness and decrease in HA width was observed for the pooled older external enamel group compared to younger specimens. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure. Future work should focus on exploring the ageing of dental enamel with increased sample sizes to compensate for individual differences as well as other potential confounding factors such as behavioural habits and mechanical forces. Lay abstract: Currently, advanced microscopy techniques such as atomic force microscopy (AFM) can be used to characterise surfaces relevant to dentistry with great detail. Among these surfaces of interest, dental enamel - the hardest mineralised tissue in the body- is important as it protects the deeper areas of the tooth from harmful stimuli such as sudden temperature changes, bacterial penetration, and chemical attack. Also, dental enamel is an important surface for the adhesion of some types of dental restorations; thus, its structure and organisation is highly relevant for both dental scientists and clinicians. With age, teeth are known to suffer changes that can impact their structural stability and function; however, changes in enamel structure as a result of ageing have not yet been explored with nanoscale resolution. It is necessary to develop and optimise AFM-based techniques in order to process specimens from dental samples across different age groups for ageing-associated nanoscale studies in the future. Therefore, the aim of this investigation was to optimise an approach to characterise the ultrastructure of dental enamel and determine potential differences in enamel topography, hydroxyapatite (HA) crystal size, and surface roughness at the nanoscale associated to ageing. For this, human enamel specimens obtained from a total of six teeth were collected and analysed with AFM, and HA crystals were characterised in both transversal and longitudinal orientation with high-resolution in environmental conditions. Upon AFM observation, sound superficial enamel displayed the presence of a pellicle-like coating on its surface, that was not observable after specimens were cleaned. Furthermore, acid-etching exposed HA crystals that were imaged and morphologically characterised in high-resolution at the nanoscale across different regions of enamel in older and younger specimens. We observed important individual variations in HA crystal width and roughness parameters across the analysed specimens and groups, suggesting individual as well as age-associated differences. Overall, high-resolution AFM was an effective approach for the qualitative and quantitative characterisation of human dental enamel ultrastructure at the nanometer range with minimal sample preparation. This proof-of-concept work can pave the way for future studies employing increased sample sizes to compensate for individual differences and population level factors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Camila Leiva-Sabadini
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christina Map Schuh
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastian Aguayo
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Review on the applications of atomic force microscopy imaging in proteins. Micron 2022; 159:103293. [DOI: 10.1016/j.micron.2022.103293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022]
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25
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Fuchigami S, Takada S. Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations. Front Mol Biosci 2022; 9:882989. [PMID: 35573735 PMCID: PMC9100425 DOI: 10.3389/fmolb.2022.882989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022] Open
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful technique to image the structural dynamics of biomolecules. We can obtain atomic-resolution structural information from the measured AFM image by superimposing a structural model on the image. We previously developed a flexible fitting molecular dynamics (MD) simulation method that allows for modest conformational changes when superimposed on an AFM image. In this study, for a molecular motor, myosin V (which changes its chemical state), we examined whether the conformationally distinct state in each HS-AFM image could be inferred via flexible fitting MD simulation. We first built models of myosin V bound to the actin filament in two conformational states, the “down-up” and “down-down” states. Then, for the previously obtained HS-AFM image of myosin bound to the actin filament, we performed flexible-fitting MD simulations using the two states. By comparing the fitting results, we inferred the conformational and chemical states from the AFM image.
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Affiliation(s)
| | - Shoji Takada
- *Correspondence: Sotaro Fuchigami, ; Shoji Takada,
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26
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Murphy JG, Raybin JG, Sibener SJ. Correlating polymer structure, dynamics, and function with atomic force microscopy. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20210321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julia G. Murphy
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
| | - Jonathan G. Raybin
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
| | - Steven J. Sibener
- The James Franck Institute and Department of Chemistry The University of Chicago Chicago Illinois USA
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27
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Yamaguchi H, Kawahara H, Kodera N, Kumaki A, Tada Y, Tang Z, Sakai K, Ono K, Yamada M, Hanayama R. Extracellular Vesicles Contribute to the Metabolism of Transthyretin Amyloid in Hereditary Transthyretin Amyloidosis. Front Mol Biosci 2022; 9:839917. [PMID: 35402512 PMCID: PMC8983912 DOI: 10.3389/fmolb.2022.839917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Hereditary (variant) transthyretin amyloidosis (ATTRv amyloidosis), which is caused by variants in the transthyretin (TTR) gene, leads to TTR amyloid deposits in multiple organs and various symptoms such as limb ataxia, muscle weakness, and cardiac failure. Interaction between amyloid proteins and extracellular vesicles (EVs), which are secreted by various cells, is known to promote the clearance of the proteins, but it is unclear whether EVs are involved in the formation and deposition of TTR amyloid in ATTRv amyloidosis. To clarify the relationship between ATTRv amyloidosis and EVs, serum-derived EVs were analyzed. In this study, we showed that cell-derived EVs are involved in the formation of TTR amyloid deposits on the membrane of small EVs, as well as the deposition of TTR amyloid in cells. Human serum-derived small EVs also altered the degree of aggregation and deposition of TTR. Furthermore, the amount of TTR aggregates in serum-derived small EVs in patients with ATTRv amyloidosis was lower than that in healthy controls. These results indicate that EVs contribute to the metabolism of TTR amyloid, and suggest that TTR in serum-derived small EVs is a potential target for future ATTRv amyloidosis diagnosis and therapy.
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Affiliation(s)
- Hiroki Yamaguchi
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Neurology and Neurobiology of Aging, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hironori Kawahara
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kanazawa, Japan
- *Correspondence: Hironori Kawahara, ; Rikinari Hanayama,
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Ayanori Kumaki
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yasutake Tada
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Neurology and Neurobiology of Aging, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Zixin Tang
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kenji Sakai
- Department of Neurology and Neurobiology of Aging, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kenjiro Ono
- Department of Neurology and Neurobiology of Aging, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Internal Medicine, Division of Neurology, Kudanzaka Hospital, Tokyo, Japan
| | - Rikinari Hanayama
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kanazawa, Japan
- *Correspondence: Hironori Kawahara, ; Rikinari Hanayama,
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28
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Amyot R, Marchesi A, Franz CM, Casuso I, Flechsig H. Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Comput Biol 2022; 18:e1009970. [PMID: 35294442 PMCID: PMC8959186 DOI: 10.1371/journal.pcbi.1009970] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/28/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.
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Affiliation(s)
- Romain Amyot
- Aix Marseille University, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Arin Marchesi
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
| | - Clemens M. Franz
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
| | - Ignacio Casuso
- Aix Marseille University, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
- * E-mail:
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29
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Sharafeldin M, Davis JJ. Characterising the biosensing interface. Anal Chim Acta 2022; 1216:339759. [DOI: 10.1016/j.aca.2022.339759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022]
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30
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Wang H, Xie Q, Xu XG. Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope. Adv Drug Deliv Rev 2022; 180:114080. [PMID: 34906646 DOI: 10.1016/j.addr.2021.114080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 11/19/2022]
Abstract
Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.
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Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Xie
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA.
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31
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Willaert RG, Kasas S. High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions Using DNA Origami Frames. Methods Mol Biol 2022; 2516:157-167. [PMID: 35922627 DOI: 10.1007/978-1-0716-2413-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Direct, live imaging of protein-DNA interactions under physiological conditions is invaluable for understanding the mechanism and kinetics of binding and understanding the topological changes of the DNA strand. The DNA origami technology allows for precise placement of target molecules in a designed nanostructure. Here, we describe a protocol for the self-assembly of DNA origami frames with 2 stretched DNA sequences containing the binding site of a transcription factor, i.e., the Protein FadR, which is a TetR-family tanscription factor regulator for fatty acid metabolism in the archaeal organism Sulfolobus acidocaldarius. These frames can be used to study the dynamics of transcription factor binding using high-speed AFM and obtain mechanistic insights into the mechanism of action of transcription factors.
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Affiliation(s)
- Ronnie G Willaert
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), Brussels, Belgium.
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Brussels, Belgium.
| | - Sandor Kasas
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Brussels, Belgium
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Centre Universitaire Romand de Médecine Légale, UFAM, Université de Lausanne, Lausanne, Switzerland
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32
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Shimizu M, Okamoto C, Umeda K, Watanabe S, Ando T, Kodera N. An ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz for high-speed atomic force microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:013701. [PMID: 35104993 DOI: 10.1063/5.0072722] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The Z-scanner is the major component limiting the speed performance of all current high-speed atomic force microscopy systems. Here, we present an ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz, achieving a record response time of ∼0.14 µs, approximately twice as fast as conventional piezoelectric-based Z-scanners. In the mechanical design, a small piezo-stack is supported at its bottom four vertices on a cone-like hollow, allowing the resonance frequency of the Z-scanner to remain as high as that of the piezo in free vibration. Its maximum displacement, ∼190 nm at 50 V, is large enough for imaging bio-molecules. For imaging bio-molecules in a buffer solution, the upper half of the Z-scanner is wrapped in a thin film resistant to water and chemicals, providing an excellent waterproof and mechanical durability without lowering the resonance frequency. We demonstrate that this Z-scanner can observe actin filaments, fragile biological polymers, for more than five times longer than the conventional Z-scanner at a tip velocity of 800 µm/s.
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Affiliation(s)
- Masahiro Shimizu
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Chihiro Okamoto
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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33
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Cha W, Campbell MF, Hasz K, Nicaise SM, Lilley DE, Sato T, Carpick RW, Bargatin I. Hollow Atomic Force Microscopy Cantilevers with Nanoscale Wall Thicknesses. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102979. [PMID: 34713587 DOI: 10.1002/smll.202102979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/02/2021] [Indexed: 06/13/2023]
Abstract
In atomic force microscopy, the cantilever probe is a critical component whose properties determine the resolution and speed at which images with nanoscale resolution can be obtained. Traditional cantilevers, which have moderate resonant frequencies and high quality factors, have relatively long response times and low bandwidths. In addition, cantilevers can be easily damaged by excessive deformation, and tips can be damaged by wear, requiring them to be replaced frequently. To address these issues, new cantilever probes that have hollow cross-sections and walls of nanoscale thicknesses made of alumina deposited by atomic layer deposition are introduced. It is demonstrated that the probes exhibit spring constants up to ≈100 times lower and bandwidths up to ≈50 times higher in air than their typical solid counterparts, allowing them to react to topography changes more quickly. Moreover, it is shown that the enhanced robustness of the hollow cantilevers enables them to withstand large bending displacements more readily and to be more resistant to tip wear.
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Affiliation(s)
- Wujoon Cha
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew F Campbell
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn Hasz
- Material Science & Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel M Nicaise
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Drew E Lilley
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Takaaki Sato
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert W Carpick
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Igor Bargatin
- Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
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34
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Parreira P, Martins MCL. The biophysics of bacterial infections: Adhesion events in the light of force spectroscopy. Cell Surf 2021; 7:100048. [PMID: 33665520 PMCID: PMC7898176 DOI: 10.1016/j.tcsw.2021.100048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 08/10/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023] Open
Abstract
Bacterial infections are the most eminent public health challenge of the 21st century. The primary step leading to infection is bacterial adhesion to the surface of host cells or medical devices, which is mediated by a multitude of molecular interactions. At the interface of life sciences and physics, last years advances in atomic force microscopy (AFM)-based force spectroscopy techniques have made possible to measure the forces driving bacteria-cell and bacteria-materials interactions on a single molecule/cell basis (single molecule/cell force spectroscopy). Among the bacteria-(bio)materials surface interactions, the life-threatening infections associated to medical devices involving Staphylococcus aureus and Escherichia coli are the most eminent. On the other hand, Pseudomonas aeruginosa binding to the pulmonary and urinary tract or the Helicobacter pylori binding to the gastric mucosa, are classical examples of bacteria-host cell interactions that end in serious infections. As we approach the end of the antibiotic era, acquisition of a deeper knowledge of the fundamental forces involved in bacteria - host cells/(bio)materials surface adhesion is crucial for the identification of new ligand-binding events and its assessment as novel targets for alternative anti-infective therapies. This article aims to highlight the potential of AFM-based force spectroscopy for new targeted therapies development against bacterial infections in which adhesion plays a pivotal role and does not aim to be an extensive overview on the AFM technical capabilities and theory of single molecule force spectroscopy.
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Affiliation(s)
- Paula Parreira
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - M. Cristina L. Martins
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
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35
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Nasrin SR, Ganser C, Nishikawa S, Kabir AMR, Sada K, Yamashita T, Ikeguchi M, Uchihashi T, Hess H, Kakugo A. Deformation of microtubules regulates translocation dynamics of kinesin. SCIENCE ADVANCES 2021; 7:eabf2211. [PMID: 34644102 PMCID: PMC10763888 DOI: 10.1126/sciadv.abf2211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Microtubules, the most rigid components of the cytoskeleton, can be key transduction elements between external forces and the cellular environment. Mechanical forces induce microtubule deformation, which is presumed to be critical for the mechanoregulation of cellular events. However, concrete evidence is lacking. In this work, with high-speed atomic force microscopy, we unravel how microtubule deformation regulates the translocation of the microtubule-associated motor protein kinesin-1, responsible for intracellular transport. Our results show that the microtubule deformation by bending impedes the translocation dynamics of kinesins along them. Molecular dynamics simulation shows that the hindered translocation of kinesins can be attributed to an enhanced affinity of kinesins to the microtubule structural units in microtubules deformed by bending. This study advances our understanding of the role of cytoskeletal components in mechanotransduction.
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Affiliation(s)
| | - Christian Ganser
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Seiji Nishikawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | | | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayuki Uchihashi
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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36
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Editorial. Methods 2021; 197:1-3. [PMID: 34637927 DOI: 10.1016/j.ymeth.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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37
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Niina T, Matsunaga Y, Takada S. Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure. PLoS Comput Biol 2021; 17:e1009215. [PMID: 34283829 PMCID: PMC8323932 DOI: 10.1371/journal.pcbi.1009215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/30/2021] [Accepted: 06/26/2021] [Indexed: 12/01/2022] Open
Abstract
Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological condition, but the observed data are limited to the surface height of specimens. Since the AFM images highly depend on the probe tip shape, for successful inference of molecular structures from the measurement, the knowledge of the probe shape is required, but is often missing. Here, we developed a method of the rigid-body fitting to AFM images, which simultaneously finds the shape of the probe tip and the placement of the molecular structure via an exhaustive search. First, we examined four similarity scores via twin-experiments for four test proteins, finding that the cosine similarity score generally worked best, whereas the pixel-RMSD and the correlation coefficient were also useful. We then applied the method to two experimental high-speed-AFM images inferring the probe shape and the molecular placement. The results suggest that the appropriate similarity score can differ between target systems. For an actin filament image, the cosine similarity apparently worked best. For an image of the flagellar protein FlhAC, we found the correlation coefficient gave better results. This difference may partly be attributed to the flexibility in the target molecule, ignored in the rigid-body fitting. The inferred tip shape and placement results can be further refined by other methods, such as the flexible fitting molecular dynamics simulations. The developed software is publicly available. Observation of functional dynamics of individual biomolecules is important to understand molecular mechanisms of cellular phenomena. High-speed (HS) atomic force microscopy (AFM) is a powerful tool that enables us to visualize the real-time dynamics of working biomolecules under near-physiological conditions. However, the information available by the AFM images is limited to the two-dimensional surface shape detected via the force to the probe. While the surface information is affected by the shape of the probe tip, the probe shape itself cannot be directly measured before each AFM measurement. To overcome this problem, we have developed a computational method to simultaneously infer the probe tip shape and the molecular placement from an AFM image. We show that our method successfully estimates the effective AFM tip shape and visualizes a structure with a more accurate placement. The estimation of a molecular placement with the correct probe tip shape enables us to obtain more insights into functional dynamics of the molecule from HS-AFM images.
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Affiliation(s)
- Toru Niina
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yasuhiro Matsunaga
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail:
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38
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Sanganna Gari RR, Montalvo-Acosta JJ, Heath GR, Jiang Y, Gao X, Nimigean CM, Chipot C, Scheuring S. Correlation of membrane protein conformational and functional dynamics. Nat Commun 2021; 12:4363. [PMID: 34272395 PMCID: PMC8285522 DOI: 10.1038/s41467-021-24660-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/28/2021] [Indexed: 11/09/2022] Open
Abstract
Conformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.
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Affiliation(s)
- Raghavendar Reddy Sanganna Gari
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Joel José Montalvo-Acosta
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - George R Heath
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Astbury Centre for Structural Molecular Biology, School of Physics & Astronomy, University of Leeds, Leeds, UK
| | - Yining Jiang
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Xiaolong Gao
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Crina M Nimigean
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Université de Lorraine, Vandœuvre-lès-Nancy, France. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA. .,Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA.
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39
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Marchesi A, Umeda K, Komekawa T, Matsubara T, Flechsig H, Ando T, Watanabe S, Kodera N, Franz CM. An ultra-wide scanner for large-area high-speed atomic force microscopy with megapixel resolution. Sci Rep 2021; 11:13003. [PMID: 34155261 PMCID: PMC8217563 DOI: 10.1038/s41598-021-92365-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/09/2021] [Indexed: 11/11/2022] Open
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualizing the dynamics of individual biomolecules. However, in single-molecule HS-AFM imaging applications, x,y-scanner ranges are typically restricted to a few hundred nanometers, preventing overview observation of larger molecular assemblies, such as 2-dimensional protein crystal growth or fibrillar aggregation. Previous advances in scanner design using mechanical amplification of the piezo-driven x,y-positioning system have extended the size of HS-AFM image frames to several tens of micrometer, but these large scanners may suffer from mechanical instabilities at high scan speeds and only record images with limited pixel numbers and comparatively low lateral resolutions (> 20–100 nm/pixel), complicating single-molecule analysis. Thus, AFM systems able to image large sample areas at high speeds and with nanometer resolution have still been missing. Here, we describe a HS-AFM sample-scanner system able to record large topographic images (≤ 36 × 36 µm2) containing up to 16 megapixels, providing molecular resolution throughout the image frame. Despite its large size, the flexure-based scanner features a high resonance frequency (> 2 kHz) and delivers stable operation even at high scans speeds of up to 7.2 mm/s, minimizing the time required for recording megapixel scans. We furthermore demonstrate that operating this high-speed scanner in time-lapse mode can simultaneously identify areas of spontaneous 2-dimensional Annexin A5 crystal growth, resolve the angular orientation of large crystalline domains, and even detect rare crystal lattice defects, all without changing scan frame size or resolution. Dynamic processes first identified from overview scans can then be further imaged at increased frame rates in reduced scan areas after switching to conventional HS-AFM scanning. The added ability to collect large-area, high-resolution images of complex samples within biological-relevant time frames extends the capabilities of HS-AFM from single-molecule imaging to the study of large dynamic molecular arrays. Moreover, large-area HS-AFM scanning can generate detailed structural data sets from a single scan, aiding the quantitative analysis of structurally heterogenous samples, including cellular surfaces.
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Affiliation(s)
- Arin Marchesi
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
| | - Kenichi Umeda
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Takumi Komekawa
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Takeru Matsubara
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Holger Flechsig
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Clemens M Franz
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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40
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Bian K, Gerber C, Heinrich AJ, Müller DJ, Scheuring S, Jiang Y. Scanning probe microscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00033-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Fuchigami S, Niina T, Takada S. Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy. Front Mol Biosci 2021; 8:636940. [PMID: 33778008 PMCID: PMC7987833 DOI: 10.3389/fmolb.2021.636940] [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: 12/02/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
The atomic force microscopy (AFM) is a powerful tool for imaging structures of molecules bound on surfaces. To gain high-resolution structural information, one often superimposes structure models on the measured images. Motivated by high flexibility of biomolecules, we previously developed a flexible-fitting molecular dynamics (MD) method that allows protein structural changes upon superimposing. Since the AFM image largely depends on the AFM probe tip geometry, the fitting process requires accurate estimation of the parameters related to the tip geometry. Here, we performed a Bayesian statistical inference to estimate a tip radius of the AFM probe from a given AFM image via flexible-fitting molecular dynamics (MD) simulations. We first sampled conformations of the nucleosome that fit well the reference AFM image by the flexible-fitting with various tip radii. We then estimated an optimal tip parameter by maximizing the conditional probability density of the AFM image produced from the fitted structure.
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Affiliation(s)
- Sotaro Fuchigami
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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42
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Fukuda S, Ando T. Faster high-speed atomic force microscopy for imaging of biomolecular processes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:033705. [PMID: 33820001 DOI: 10.1063/5.0032948] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) has enabled observing protein molecules during their functional activity at rates of 1-12.5 frames per second (fps), depending on the imaging conditions, sample height, and fragility. To meet the increasing demand for the great expansion of observable dynamic molecular processes, faster HS-AFM with less disturbance is imperatively needed. However, even a 50% improvement in the speed performance imposes tremendous challenges, as the optimization of major rate-limiting components for their fast response is nearly matured. This paper proposes an alternative method that can lower the feedback control error and thereby enhance the imaging rate. This method can be implemented in any HS-AFM system by minor modifications of the software and hardware. The resulting faster and less-disturbing imaging capabilities are demonstrated by the imaging of relatively fragile actin filaments and microtubules near the video rate, and of actin polymerization that occurs through weak intermolecular interactions, at ∼8 fps.
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Affiliation(s)
- Shingo Fukuda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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43
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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44
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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45
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Manickavasagam AK, Gutschmidt S, Sellier M. Hydrodynamic loading profiles of viscously-interacting blocks subject to different stimulus locations. J R Soc N Z 2021. [DOI: 10.1080/03036758.2020.1857802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Arun K. Manickavasagam
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
| | - Stefanie Gutschmidt
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
| | - Mathieu Sellier
- Department of Mechanical Engineering, University of Canterbury, Christchurch, New Zealand
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46
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Massively parallel cantilever-free atomic force microscopy. Nat Commun 2021; 12:393. [PMID: 33452253 PMCID: PMC7810748 DOI: 10.1038/s41467-020-20612-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/09/2020] [Indexed: 11/08/2022] Open
Abstract
Resolution and field-of-view often represent a fundamental tradeoff in microscopy. Atomic force microscopy (AFM), in which a cantilevered probe deflects under the influence of local forces as it scans across a substrate, is a key example of this tradeoff with high resolution imaging being largely limited to small areas. Despite the tremendous impact of AFM in fields including materials science, biology, and surface science, the limitation in imaging area has remained a key barrier to studying samples with intricate hierarchical structure. Here, we show that massively parallel AFM with >1000 probes is possible through the combination of a cantilever-free probe architecture and a scalable optical method for detecting probe-sample contact. Specifically, optically reflective conical probes on a comparatively compliant film are found to comprise a distributed optical lever that translates probe motion into an optical signal that provides sub-10 nm vertical precision. The scalability of this approach makes it well suited for imaging applications that require high resolution over large areas.
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47
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Otieno LO, Alunda BO, Kim J, Lee YJ. Design and Fabrication of a High-Speed Atomic Force Microscope Scan-Head. SENSORS 2021; 21:s21020362. [PMID: 33430315 PMCID: PMC7825750 DOI: 10.3390/s21020362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/02/2022]
Abstract
A high-speed atomic force microscope (HS-AFM) requires a specialized set of hardware and software and therefore improving video-rate HS-AFMs for general applications is an ongoing process. To improve the imaging rate of an AFM, all components have to be carefully redesigned since the slowest component determines the overall bandwidth of the instrument. In this work, we present a design of a compact HS-AFM scan-head featuring minimal loading on the Z-scanner. Using a custom-programmed controller and a high-speed lateral scanner, we demonstrate its working by obtaining topographic images of Blu-ray disk data tracks in contact- and tapping-modes. Images acquired using a contact-mode cantilever with a natural frequency of 60 kHz in constant deflection mode show good tracking of topography at 400 Hz. In constant height mode, tracking of topography is demonstrated at rates up to 1.9 kHz for the scan size of 1μm×1μm with 100×100 pixels.
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Affiliation(s)
- Luke Oduor Otieno
- Department of Mechanical Engineering, Kyungpook National University, Daegu 41566, Korea;
| | - Bernard Ouma Alunda
- School of Mines and Engineering, Taita Taveta University, P.O. Box 635, Voi 80300, Kenya;
| | - Jaehyun Kim
- Department of Mechanical and Design Engineering, Hongik University, Sejong 30016, Korea;
| | - Yong Joong Lee
- Department of Mechanical Engineering, Kyungpook National University, Daegu 41566, Korea;
- Correspondence:
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48
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Direct visualization of translational GTPase factor pool formed around the archaeal ribosomal P-stalk by high-speed AFM. Proc Natl Acad Sci U S A 2020; 117:32386-32394. [PMID: 33288716 PMCID: PMC7768734 DOI: 10.1073/pnas.2018975117] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Translation of genetic information by the ribosome is a core biological process in all organisms. The ribosomal stalk is a multimeric ribosomal protein complex which plays an essential role in translation elongation. However, the working mechanism of the ribosomal stalk still remains unclear. In this study, we applied HS-AFM to investigate the working mechanism of the archaeal ribosomal P-stalk. HS-AFM movies demonstrate that the P-stalk collects two translational GTPase factors (trGTPases), aEF1A and aEF2, and increases their local concentration near the ribosome. These direct visual evidences show that the multiple arms of the ribosomal P-stalk catch the trGTPases for efficient protein synthesis in the crowded intracellular environment. In translation elongation, two translational guanosine triphosphatase (trGTPase) factors EF1A and EF2 alternately bind to the ribosome and promote polypeptide elongation. The ribosomal stalk is a multimeric ribosomal protein complex which plays an essential role in the recruitment of EF1A and EF2 to the ribosome and their GTP hydrolysis for efficient and accurate translation elongation. However, due to the flexible nature of the ribosomal stalk, its structural dynamics and mechanism of action remain unclear. Here, we applied high-speed atomic force microscopy (HS-AFM) to directly visualize the action of the archaeal ribosomal heptameric stalk complex, aP0•(aP1•aP1)3 (P-stalk). HS-AFM movies clearly demonstrated the wobbling motion of the P-stalk on the large ribosomal subunit where the stalk base adopted two conformational states, a predicted canonical state, and a newly identified flipped state. Moreover, we showed that up to seven molecules of archaeal EF1A (aEF1A) and archaeal EF2 (aEF2) assembled around the ribosomal P-stalk, corresponding to the copy number of the common C-terminal factor-binding site of the P-stalk. These results provide visual evidence for the factor-pooling mechanism by the P-stalk within the ribosome and reveal that the ribosomal P-stalk promotes translation elongation by increasing the local concentration of translational GTPase factors.
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49
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Koebley SR, Mikheikin A, Leslie K, Guest D, McConnell-Wells W, Lehman JH, Al Juhaishi T, Zhang X, Roberts CH, Picco L, Toor A, Chesney A, Reed J. Digital Polymerase Chain Reaction Paired with High-Speed Atomic Force Microscopy for Quantitation and Length Analysis of DNA Length Polymorphisms. ACS NANO 2020; 14:15385-15393. [PMID: 33169971 DOI: 10.1021/acsnano.0c05897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA length polymorphisms are found in many serious diseases, and assessment of their length and abundance is often critical for accurate diagnosis. However, measuring their length and frequency in a mostly wild-type background, as occurs in many situations, remains challenging due to their variable and repetitive nature. To overcome these hurdles, we combined two powerful techniques, digital polymerase chain reaction (dPCR) and high-speed atomic force microscopy (HSAFM), to create a simple, rapid, and flexible method for quantifying both the size and proportion of DNA length polymorphisms. In our approach, individual amplicons from each dPCR partition are imaged and sized directly. We focused on internal tandem duplications (ITDs) located within the FLT3 gene, which are associated with acute myeloid leukemia and often indicative of a poor prognosis. In an analysis of over 1.5 million HSAFM-imaged amplicons from cell line and clinical samples containing FLT3-ITDs, dPCR-HSAFM returned the expected variant length and variant allele frequency, down to 5% variant samples. As a high-throughput method with single-molecule resolution, dPCR-HSAFM thus represents an advance in HSAFM analysis and a powerful tool for the diagnosis of length polymorphisms.
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Affiliation(s)
- Sean R Koebley
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Andrey Mikheikin
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kevin Leslie
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Daniel Guest
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Wendy McConnell-Wells
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joshua H Lehman
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Taha Al Juhaishi
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Xiaojie Zhang
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Catherine H Roberts
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Loren Picco
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Amir Toor
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Alden Chesney
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Jason Reed
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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50
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Amyot R, Flechsig H. BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics. PLoS Comput Biol 2020; 16:e1008444. [PMID: 33206646 PMCID: PMC7710046 DOI: 10.1371/journal.pcbi.1008444] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/02/2020] [Accepted: 10/15/2020] [Indexed: 11/28/2022] Open
Abstract
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into the graphical representation corresponding to the outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over the molecular structure encoded in the corresponding PDB file. A versatile molecular viewer integrates the visualization of PDB structures and control over their orientation, while synchronized simulated scanning with variable spatial resolution and tip-shape geometry produces the corresponding AFM graphics. We demonstrate the applicability of the BioAFMviewer by comparing simulated AFM graphics to high-speed AFM observations of proteins. The software can furthermore process molecular movies of conformational motions, e.g. those obtained from servers which model functional transitions within a protein, and produce the corresponding simulated AFM movie. The BioAFMviewer software provides the platform to employ the plethora of structural and dynamical data of proteins in order to help in the interpretation of biomolecular AFM experiments. Nowadays nanotechnology allows to observe single proteins at work. Under atomic force microscopy (AFM), e.g., their surface can be rapidly scanned and functional motions monitored, which is of great importance for applications in all fields of Life science. The analysis and interpretation of experimental results remains however challenging, because the resolution of obtained images or molecular movies is far from perfect. On the other side, high-resolution static structures of most proteins are known and their conformational dynamics can be computed in molecular simulations. This enormous amount of available data offers a great opportunity to better understand the outcome of resolution-limited scanning experiments. Our software provides the computational package towards this goal. The BioAFMviewer computationally emulates the scanning of any biomolecular structure to produce graphical images that mimic the outcome of AFM experiments. This makes the comparison of all available structural data and computational molecular movies to AFM results possible. We demonstrate that simulated AFM images are of great value to facilitate the interpretation of high-speed AFM observations. With its versatile interactive interface and rich functionality, the BioAFMviewer provides a convenient platform for the broad Bio-AFM community to better understand experiments.
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Affiliation(s)
- Romain Amyot
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
- * E-mail:
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