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Hall D. Simulating biological surface dynamics in high-speed atomic force microscopy experiments. Biophys Rev 2023; 15:2069-2079. [PMID: 38192349 PMCID: PMC10771409 DOI: 10.1007/s12551-023-01169-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 01/10/2024] Open
Abstract
High-speed atomic force microscopy (HSAFM) is an important tool for studying the dynamic behavior of large biomolecular assemblies at surfaces. However, unlike light microscopy techniques, which visualize each point in the field of view at the same time, in HSAFM, the surface is literally imaged pixel-by-pixel with a variable extent of time separation existing between recordings made at one pixel and all others within the surface image. Such "temporal asynchronicity" in the recording of the spatial information can introduce distortions into the image when the surface components move at a rate comparable to that at which the surface is imaged. This Letter describes recently released software developments that are able to predict the likely form of these distortions and estimate confidence levels when assigning the identity of observed structures. These described approaches may facilitate both the design and optimization of future HSAFM experimental protocols. Further to this, they may assist in the interpretation of results from already published HSAFM studies.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
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2
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Kiss B, Mudra D, Török G, Mártonfalvi Z, Csík G, Herényi L, Kellermayer M. Single-particle virology. Biophys Rev 2020; 12:1141-1154. [PMID: 32880826 PMCID: PMC7471434 DOI: 10.1007/s12551-020-00747-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - György Török
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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3
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Hall D, Takagi J, Nakamura H. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday. Biophys Rev 2018; 10:105-129. [PMID: 29500796 PMCID: PMC5899743 DOI: 10.1007/s12551-018-0401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.
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Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
- Research School of Chemistry, Australian National University, Acton, ACT 2601 Australia
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
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Sharma S, Grintsevich E, Woo J, Gurel PS, Higgs HN, Reisler E, Gimzewski JK. Nanostructured self-assembly of inverted formin 2 (INF2) and F-actin-INF2 complexes revealed by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7533-7539. [PMID: 24915113 PMCID: PMC4082382 DOI: 10.1021/la501748x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/08/2014] [Indexed: 06/03/2023]
Abstract
Self-organization of cytoskeletal proteins such as actin and tubulin into filaments and microtubules is frequently assisted by the proteins binding to them. Formins are regulatory proteins that nucleate the formation of new filaments and are essential for a wide range of cellular functions. The vertebrate inverted formin 2 (INF2) has both actin filament nucleating and severing/depolymerizing activities connected to its ability to encircle actin filaments. Using atomic force microscopy, we report that a formin homology 2 (FH2) domain-containing construct of INF2 (INF2-FH1-FH2-C or INF2-FFC) self-assembles into nanoscale ringlike oligomeric structures in the absence of actin filaments, demonstrating an inherent ability to reorganize from a dimeric to an oligomeric state. A construct lacking the C-terminal region (INF2-FH1-FH2 or INF2-FF) also oligomerizes, confirming the dominant role of FH2-mediated interactions. Moreover, INF2-FFC domains were observed to organize into ringlike structures around single actin filaments. This is the first demonstration that formin FH2 domains can self-assemble into oligomers in the absence of filaments and has important implications for observing unaveraged decoration and/or remodeling of filaments by actin binding proteins.
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Affiliation(s)
- Shivani Sharma
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Elena
E. Grintsevich
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - JungReem Woo
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Pinar S. Gurel
- Department
of Biochemistry, Geisel School of Medicine
at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Henry N. Higgs
- Department
of Biochemistry, Geisel School of Medicine
at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Emil Reisler
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- Molecular
Biology Institute, University of California, Los Angeles, California 90095, United States
| | - James K. Gimzewski
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, University
of California, Los Angeles, California 90095, United States
- International
Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
- Centre for
Nanoscience and Quantum Information, University
of Bristol, Bristol BS8 1TH, U.K.
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5
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Sharma S, Zhu H, Grintsevich EE, Reisler E, Gimzewski JK. Correlative nanoscale imaging of actin filaments and their complexes. NANOSCALE 2013; 5:5692-702. [PMID: 23727693 PMCID: PMC4030708 DOI: 10.1039/c3nr01039b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.
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Affiliation(s)
- Shivani Sharma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Huanqi Zhu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Elena E. Grintsevich
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - James K. Gimzewski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
- International Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
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6
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Kuznetsov YG, Chang SC, McPherson A. Investigation of bacteriophage T4 by atomic force microscopy. BACTERIOPHAGE 2011; 1:165-173. [PMID: 22164350 PMCID: PMC3225781 DOI: 10.4161/bact.1.3.17650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/16/2011] [Accepted: 08/06/2011] [Indexed: 11/19/2022]
Abstract
Bacteriophage T4 was visualized using atomic force microscopy (AFM). The images were consistent with, and complementary to electron microscopy images. Head heights of dried particles containing DNA were about 75 nm in length and 60 nm in width, or about 100 nm and 85 nm respectively when scanned in fluid. The diameter of hydrated tail assemblies was 28 nm and their lengths about 130 nm. Seven to eight pronounced, right-handed helical turns with a pitch of 15 nm were evident on the tail assemblies. At the distal end of the tail was a knob shaped mass, presumably the baseplate. The opposite end, where the tail assembly joins the head, was tapered and connected to the portal complex, which was also visible. Phage that had ejected their DNA revealed the internal injection tube of the tail assembly. Heads disrupted by osmotic shock yielded boluses of closely packed DNA that unraveled slowly to expose threads composed of multiple twisted strands of nucleic acid. Assembly errors resulted in the appearance of several percent of the phage exhibiting two rather than one tail assemblies that were consistently oriented at about 72° to one another. No pattern of capsomeres was visible on native T4 heads. A mutant that is negative for the surface proteins hoc and soc, however, clearly revealed the icosahedral arrangement of ring shaped capsomeres on the surface. The hexameric rings have an outside diameter of about 14 nm, a pronounced central depression, and a center-to-center distance of 15 nm. Phage collapsed on cell surfaces appeared to be dissolving, possibly into the cell membrane.
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Affiliation(s)
- Yuri G Kuznetsov
- Department of Molecular Biology and Biochemistry; University of California Irvine; Irvine, CA USA
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7
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Wu H, Williams K, Singh SR, Scissum-Gunn K, Singh NK, Teresa D, Giambrone JJ. Integrity of a recombinant hemagglutinin protein of an avian influenza virus. Biotechnol Lett 2009; 31:1511-7. [DOI: 10.1007/s10529-009-0047-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/19/2009] [Accepted: 05/21/2009] [Indexed: 11/24/2022]
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8
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Dubrovin EV, Voloshin AG, Kraevsky SV, Ignatyuk TE, Abramchuk SS, Yaminsky IV, Ignatov SG. Atomic force microscopy investigation of phage infection of bacteria. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:13068-13074. [PMID: 18850726 DOI: 10.1021/la8022612] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Atomic force microscopy (AFM) was used to study the process of infection of bacterial cells by bacteriophages, for which purpose experimental protocols were elaborated. Three types of bacteriophages were characterized with AFM and transmission electron microscopy (TEM). Bacteriophage interaction with cells was studied for three bacterial hosts: Gram-negative Escherichia coli 057 and Salmonella enteritidis 89 and Gram-positive Bacillus thuringiensis 393. Depending on the phase of lytic cycle, different cell surface changes are observed in AFM images of infected cells in comparison with intact cells: from phage adsorption on the cells and flagella to complete lysis of the cells, accompanied by the release of a large number of newly formed phages. Control experiments (cells without phages and cells with nonspecific phages) did not reveal any surface changes. Penetration of phages inside obligate aerobe Bacillus thuringiensis was shown to be oxygen-dependent and required aeration in laboratory conditions. Our results show great potential of using AFM for numerous fundamental and applied tasks connected with pathogen-host interaction.
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Affiliation(s)
- Evgeniy V Dubrovin
- Department of Physics of Polymers and Crystals, Faculty of Physics, Moscow State University, Moscow, Russian Federation.
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9
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Arkhangelsky E, Gitis V. Effect of transmembrane pressure on rejection of viruses by ultrafiltration membranes. Sep Purif Technol 2008. [DOI: 10.1016/j.seppur.2008.03.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Johnson JC, Nettikadan SR, Vengasandra SG, Henderson E. Analysis of solid-phase immobilized antibodies by atomic force microscopy. ACTA ACUST UNITED AC 2004; 59:167-80. [PMID: 15163528 DOI: 10.1016/j.jbbm.2003.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 12/05/2003] [Accepted: 12/28/2003] [Indexed: 10/26/2022]
Abstract
Antibody adsorption to solid surfaces creates a number of constraints that may interfere with epitope recognition and ligand-antibody interaction. By optimizing the conditions of adsorption, one may minimize these constraints. We have studied several factors that affect the antibody adsorption using atomic force microscopy (AFM) as a readout mechanism. AFM provides a highly sensitive, label-free method for detecting and analyzing molecular interactions. In this report, AFM was used to study antibody properties, the efficiency of particle capture and ligand-antibody interaction using anti-bacteriophage fd antibodies in a solid phase assay format. The capture efficiencies of anti-fd preparations adsorbed onto gold surfaces under various conditions including pH and antibody concentration were determined and compared. The relative sensitivities of each antibody for the capture of phage fd as a function of applied phage concentrations was evaluated. The collective data indicates that AFM is effective as an analytical instrument for studying the functionality of surface adsorbed antibodies in particle capture assays. This method of analysis can be extended to rapidly screen and select antibodies or other ligands with a specific set of characteristics. As the number and complexity of chip-based analytical platforms in proteomics increases, rapid selection/screening processes such as that described here will become invaluable.
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Affiliation(s)
- James C Johnson
- BioForce Nanosciences Inc., 2901 South Loop Drive, Suite 3400, Ames, IA 50010, USA
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11
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Nettikadan SR, Johnson JC, Mosher C, Henderson E. Virus particle detection by solid phase immunocapture and atomic force microscopy. Biochem Biophys Res Commun 2004; 311:540-5. [PMID: 14592450 DOI: 10.1016/j.bbrc.2003.10.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel application of atomic force microscopy (AFM) in the rapid, label-free detection and identification of viruses is described. Multiplexed, miniaturized antibody domains were constructed using "ink-jet" protein arraying technology. The solid-phase affinity substrate termed the "ViriChip" was used in the immunocapture of bacteriophage fd, canine parvoviruses, and coxsackieviruses and analyzed by AFM. Immunocapture was found to be antibody-specific with a sensitivity of 10(8)pfu/ml in 30min. Virus binding was found to be linear for concentration between 10(8) and 10(10)pfu/ml and did not reach saturation through 4h.
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Affiliation(s)
- Saju R Nettikadan
- BioForce Nanosciences, 2901 S. Loop Drive, Suite 3400, Ames, IA 50010, USA.
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Yamada T, Arakawa H, Okajima T, Shimada T, Ikai A. Use of AFM for imaging and measurement of the mechanical properties of light-convertible organelles in plants. Ultramicroscopy 2002; 91:261-8. [PMID: 12211477 DOI: 10.1016/s0304-3991(02)00107-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We obtained topographic images of etioplasts and chloroplasts and measured their elasticity in a physiological buffer using an atomic force microscope (AFM) and found a possible correlation between the morphological and mechanical properties during the light conversion of etioplasts to chloroplasts. Alcian blue 8GX dye was found to be effective for immobilizing the plant organelles stably on a glass surface for AFM experiments. We employed the tapping-mode AFM with a cantilever soft enough to measure the elasticity of the organelles in a liquid solution. The best images of soft, spherical organelles were obtained using the tapping-mode AFM with oscillation at the thermal vibration frequency of the cantilever of around 3 kHz. Whereas etioplasts were found to be smooth-surfaced and stiff against compression by the AFM tip, before light conversion to chloroplasts, they became rough-surfaced and mechanically soft after exposure to light. The elasticity of etioplasts was 20 times higher than that of chloroplasts, probably reflecting changes in their inner structures.
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Affiliation(s)
- Takafumi Yamada
- Laboratory of Biodynamics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Osada T, Arakawa H, Ichikawa M, Ikai A. Atomic force microscopy of histological sections using a new electron beam etching method. J Microsc 1998; 189:43-9. [PMID: 9503657 DOI: 10.1046/j.1365-2818.1998.00269.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to examine histological sections of the rat vomeronasal epithelium with the atomic force microscope (AFM), we developed an electron beam etching method that improves the resolution of AFM images. This method results in AFM images comparable to those obtained with the transmission electron microscope (TEM). Ultrathin tissue sections embedded in epoxy resin were observed before and after the treatment with electron beam radiation. Before electron beam treatment, epithelial structures such as the microvilli surface, dendritic processes, the supporting cell layers and the neuronal cell layers were all visible using the AFM. However, only a few subcellular structures could also be resolved. The AFM images were not as clear as those obtained with the TEM. After electron beam treatment, however, the resolution of AFM images was greatly improved. Most of the subcellular structures observed in TEM images, including the inner membrane of mitochondria, ciliary-structure precursor body, junctional complexes between the neurons and supporting cells, and individual microvilli were now visible in the AFM images. The electron beam treatment appeared to melt the embedding resin, bringing subcellular structures into high relief. The result of this study suggests that electron beam etching of histological samples may provide a new method for the study of subcellular structure using the AFM.
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Affiliation(s)
- T Osada
- Department of Biological Sciences, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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14
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�sterberg R, Mortensen K, Ikai A. Direct observation of humic acid clusters, a nonequilibrium system with a fractal structure. Naturwissenschaften 1995. [DOI: 10.1007/bf01177274] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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