1
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Kong SG, Yamazaki Y, Shimada A, Kijima ST, Hirose K, Katoh K, Ahn J, Song HG, Han JW, Higa T, Takano A, Nakamura Y, Suetsugu N, Kohda D, Uyeda TQP, Wada M. CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement. THE PLANT CELL 2024; 36:1159-1181. [PMID: 38134410 PMCID: PMC10980345 DOI: 10.1093/plcell/koad320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/09/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Plants have unique responses to fluctuating light conditions. One such response involves chloroplast photorelocation movement, which optimizes photosynthesis under weak light by the accumulation of chloroplasts along the periclinal side of the cell, which prevents photodamage under strong light by avoiding chloroplast positioning toward the anticlinal side of the cell. This light-responsive chloroplast movement relies on the reorganization of chloroplast actin (cp-actin) filaments. Previous studies have suggested that CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) is essential for chloroplast photorelocation movement as a regulator of cp-actin filaments. In this study, we conducted comprehensive analyses to understand CHUP1 function. Functional, fluorescently tagged CHUP1 colocalized with and was coordinately reorganized with cp-actin filaments on the chloroplast outer envelope during chloroplast movement in Arabidopsis thaliana. CHUP1 distribution was reversibly regulated in a blue light- and phototropin-dependent manner. X-ray crystallography revealed that the CHUP1-C-terminal domain shares structural homology with the formin homology 2 (FH2) domain, despite lacking sequence similarity. Furthermore, the CHUP1-C-terminal domain promoted actin polymerization in the presence of profilin in vitro. Taken together, our findings indicate that CHUP1 is a plant-specific actin polymerization factor that has convergently evolved to assemble cp-actin filaments and enables chloroplast photorelocation movement.
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Affiliation(s)
- Sam-Geun Kong
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Chungnam 32588, Korea
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Yosuke Yamazaki
- Department of Physics, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Atsushi Shimada
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Saku T Kijima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan
| | - Keiko Hirose
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan
| | - Kaoru Katoh
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan
| | - Jeongsu Ahn
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Chungnam 32588, Korea
| | - Hyun-Geun Song
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Chungnam 32588, Korea
| | - Jae-Woo Han
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Chungnam 32588, Korea
| | - Takeshi Higa
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Akira Takano
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuki Nakamura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Noriyuki Suetsugu
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8562, Japan
| | - Masamitsu Wada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812-8581, Japan
- Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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2
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Nishide G, Lim K, Tamura M, Kobayashi A, Zhao Q, Hazawa M, Ando T, Nishida N, Wong RW. Nanoscopic Elucidation of Spontaneous Self-Assembly of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Open Reading Frame 6 (ORF6) Protein. J Phys Chem Lett 2023; 14:8385-8396. [PMID: 37707320 PMCID: PMC10544025 DOI: 10.1021/acs.jpclett.3c01440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
Open reading frame 6 (ORF6), the accessory protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that suppresses host type-I interferon signaling, possesses amyloidogenic sequences. ORF6 amyloidogenic peptides self-assemble to produce cytotoxic amyloid fibrils. Currently, the molecular properties of the ORF6 remain elusive. Here, we investigate the structural dynamics of the full-length ORF6 protein in a near-physiological environment using high-speed atomic force microscopy. ORF6 oligomers were ellipsoidal and readily assembled into ORF6 protofilaments in either a circular or a linear pattern. The formation of ORF6 protofilaments was enhanced at higher temperatures or on a lipid substrate. ORF6 filaments were sensitive to aliphatic alcohols, urea, and SDS, indicating that the filaments were predominantly maintained by hydrophobic interactions. In summary, ORF6 self-assembly could be necessary to sequester host factors and causes collateral damage to cells via amyloid aggregates. Nanoscopic imaging unveiled the innate molecular behavior of ORF6 and provides insight into drug repurposing to treat amyloid-related coronavirus disease 2019 complications.
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Affiliation(s)
- Goro Nishide
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative,
WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Keesiang Lim
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Maiki Tamura
- Graduate
School of Pharmaceutical Sciences, Chiba
University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Akiko Kobayashi
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Qingci Zhao
- Graduate
School of Pharmaceutical Sciences, Chiba
University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Masaharu Hazawa
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noritaka Nishida
- Graduate
School of Pharmaceutical Sciences, Chiba
University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Richard W. Wong
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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3
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Chan FY, Kurosaki R, Ganser C, Takeda T, Uchihashi T. Tip-scan high-speed atomic force microscopy with a uniaxial substrate stretching device for studying dynamics of biomolecules under mechanical stress. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:113703. [PMID: 36461522 DOI: 10.1063/5.0111017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/09/2022] [Indexed: 06/17/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) is a powerful tool for studying the dynamics of biomolecules in vitro because of its high temporal and spatial resolution. However, multi-functionalization, such as combination with complementary measurement methods, environment control, and large-scale mechanical manipulation of samples, is still a complex endeavor due to the inherent design and the compact sample scanning stage. Emerging tip-scan HS-AFM overcame this design hindrance and opened a door for additional functionalities. In this study, we designed a motor-driven stretching device to manipulate elastic substrates for HS-AFM imaging of biomolecules under controllable mechanical stimulation. To demonstrate the applicability of the substrate stretching device, we observed a microtubule buckling by straining the substrate and actin filaments linked by α-actinin on a curved surface. In addition, a BAR domain protein BIN1 that senses substrate curvature was observed while dynamically controlling the surface curvature. Our results clearly prove that large-scale mechanical manipulation can be coupled with nanometer-scale imaging to observe biophysical effects otherwise obscured.
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Affiliation(s)
- Feng-Yueh Chan
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryo Kurosaki
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Christian Ganser
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Tetsuya Takeda
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita-Ku, Okayama 700-8558, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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4
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Kodera N, Ando T. Guide to studying intrinsically disordered proteins by high-speed atomic force microscopy. Methods 2022; 207:44-56. [PMID: 36055623 DOI: 10.1016/j.ymeth.2022.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are partially or entirely disordered. Their intrinsically disordered regions (IDRs) dynamically explore a wide range of structural space by their highly flexible nature. Due to this distinct feature largely different from structured proteins, conventional structural analyses relying on ensemble averaging is unsuitable for characterizing the dynamic structure of IDPs. Therefore, single-molecule measurement tools have been desired in IDP studies. High-speed atomic force microscopy (HS-AFM) is a unique tool that allows us to directly visualize single biomolecules at 2-3 nm lateral and ∼ 0.1 nm vertical spatial resolution, and at sub-100 ms temporal resolution under near physiological conditions, without any chemical labeling. HS-AFM has been successfully used not only to characterize the shape and motion of IDP molecules but also to visualize their function-related dynamics. In this article, after reviewing the principle and current performances of HS-AFM, we describe experimental considerations in the HS-AFM imaging of IDPs and methods to quantify molecular features from captured images. Finally, we outline recent HS-AFM imaging studies of IDPs.
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Affiliation(s)
- Noriyuki Kodera
- 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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5
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Yoshimi K, Takeshita K, Kodera N, Shibumura S, Yamauchi Y, Omatsu M, Umeda K, Kunihiro Y, Yamamoto M, Mashimo T. Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3. Nat Commun 2022; 13:4917. [PMID: 36042215 PMCID: PMC9427990 DOI: 10.1038/s41467-022-32618-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Type I CRISPR-Cas3 uses an RNA-guided multi Cas-protein complex, Cascade, which detects and degrades foreign nucleic acids via the helicase-nuclease Cas3 protein. Despite many studies using cryoEM and smFRET, the precise mechanism of Cas3-mediated cleavage and degradation of target DNA remains elusive. Here we reconstitute the CRISPR-Cas3 system in vitro to show how the Escherichia coli Cas3 (EcoCas3) with EcoCascade exhibits collateral non-specific single-stranded DNA (ssDNA) cleavage and target specific DNA degradation. Partial binding of EcoCascade to target DNA with tolerated mismatches within the spacer sequence, but not the PAM, elicits collateral ssDNA cleavage activity of recruited EcoCas3. Conversely, stable binding with complete R-loop formation drives EcoCas3 to nick the non-target strand (NTS) in the bound DNA. Helicase-dependent unwinding then combines with trans ssDNA cleavage of the target strand and repetitive cis cleavage of the NTS to degrade the target double-stranded DNA (dsDNA) substrate. High-speed atomic force microscopy demonstrates that EcoCas3 bound to EcoCascade repeatedly reels and releases the target DNA, followed by target fragmentation. Together, these results provide a revised model for collateral ssDNA cleavage and target dsDNA degradation by CRISPR-Cas3, furthering understanding of type I CRISPR priming and interference and informing future genome editing tools.
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Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Kohei Takeshita
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Mine Omatsu
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Masaki Yamamoto
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan. .,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
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6
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Lim K, Nishide G, Yoshida T, Watanabe‐Nakayama T, Kobayashi A, Hazawa M, Hanayama R, Ando T, Wong RW. Millisecond dynamic of SARS-CoV-2 spike and its interaction with ACE2 receptor and small extracellular vesicles. J Extracell Vesicles 2021; 10:e12170. [PMID: 34874124 PMCID: PMC8650025 DOI: 10.1002/jev2.12170] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 spike protein (S) binds to human angiotensin-converting enzyme 2 (hACE2), allowing virus to dock on cell membrane follow by viral entry. Here, we use high-speed atomic force microscopy (HS-AFM) for real-time visualization of S, and its interaction with hACE2 and small extracellular vesicles (sEVs). Results show conformational heterogeneity of S, flexibility of S stalk and receptor-binding domain (RBD), and pH/temperature-induced conformational change of S. S in an S-ACE2 complex appears as an all-RBD up conformation. The complex acquires a distinct topology upon acidification. S and S2 subunit demonstrate different membrane docking mechanisms on sEVs. S-hACE2 interaction facilitates S to dock on sEVs, implying the feasibility of ACE2-expressing sEVs for viral neutralization. In contrary, S2 subunit docks on lipid layer and enters sEV using its fusion peptide, mimicking the viral entry scenario. Altogether, our study provides a platform that is suitable for real-time visualization of various entry inhibitors, neutralizing antibodies, and sEV-based decoy in blocking viral entry. Teaser: Comprehensive observation of SARS-CoV-2 spike and its interaction with receptor ACE2 and sEV-based decoy in real time using HS-AFM.
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Affiliation(s)
- Keesiang Lim
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Goro Nishide
- Division of Nano Life Science in the Graduate School of Frontier Science InitiativeWISE Program for Nano‐Precision MedicineScience and TechnologyKanazawa UniversityKanazawaIshikawaJapan
| | - Takeshi Yoshida
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | | | - Akiko Kobayashi
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Masaharu Hazawa
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Rikinari Hanayama
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | - Toshio Ando
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Richard W. Wong
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
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7
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Puppulin L, Kanayama D, Terasaka N, Sakai K, Kodera N, Umeda K, Sumino A, Marchesi A, Weilin W, Tanaka H, Fukuma T, Suga H, Matsumoto K, Shibata M. Macrocyclic Peptide-Conjugated Tip for Fast and Selective Molecular Recognition Imaging by High-Speed Atomic Force Microscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:54817-54829. [PMID: 34766499 DOI: 10.1021/acsami.1c17708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fast and selective recognition of molecules at the nanometer scale without labeling is a much desired but still challenging goal to achieve. Here, we show the use of high-speed atomic force microscopy (HS-AFM) for real-time and real-space recognition of unlabeled membrane receptors using tips conjugated with small synthetic macrocyclic peptides. The single-molecule recognition method is validated by experiments on the human hepatocyte growth factor receptor (hMET), which selectively binds to the macrocyclic peptide aMD4. By testing and comparing aMD4 synthesized with linkers of different lengths and rigidities, we maximize the interaction between the functionalized tip and hMET added to both a mica surface and supported lipid bilayers. Phase contrast imaging by HS-AFM enables us to discriminate nonlabeled hMET against the murine MET homologue, which does not bind to aMD4. Moreover, using ligands and linkers of small size, we achieve minimal deterioration of the spatial resolution in simultaneous topographic imaging. The versatility of macrocyclic peptides in detecting unlimited types of membrane receptors with high selectivity and the fast imaging by HS-AFM broaden the range of future applications of this method for molecular recognition without labeling.
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Affiliation(s)
- Leonardo Puppulin
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kajii-cho, Kawaramachi-Hirokoji, Kyoto 602-8566, Japan
| | - Daiki Kanayama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Katsuya Sakai
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Ayumi Sumino
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Arin Marchesi
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Wei Weilin
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hideo Tanaka
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kajii-cho, Kawaramachi-Hirokoji, Kyoto 602-8566, Japan
| | - Takeshi Fukuma
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kunio Matsumoto
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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8
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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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9
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Gudzenko T, Franz CM. Controlling Fibronectin Fibrillogenesis Using Visible Light. Front Mol Biosci 2020; 7:149. [PMID: 32733919 PMCID: PMC7360794 DOI: 10.3389/fmolb.2020.00149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/15/2020] [Indexed: 01/04/2023] Open
Abstract
We previously developed a surface-assisted assay to image early steps of cell-induced plasma fibronectin (FN) fibrillogenesis by timelapse atomic force microscopy (AFM). Unexpectedly, complementary attempts to visualize FN fibrillogenesis using fluorescently labeled FN (Alexa Fluor 488 or 568) and live-cell light microscopy initially failed consistently. Further analysis revealed that fibrillar remodeling was inhibited efficiently in the focal area illuminated during fluorescence imaging, but progressed normally elsewhere on the substrate, suggesting photo sensitivity of the FN fibrillogenesis process. In agreement, active cell-driven fibrillar extension of FN could be stopped by transient illumination with visible light during AFM timelapse scanning. Phototoxic effects on the cells could be ruled out, because pre-illuminating the FN layer before cell seeding also blocked subsequent fibrillar formation. Varying the illumination wavelength range between 400 and 640 nm revealed strong inhibition across the visible spectrum up to 560 nm, and a decreasing inhibitory effect at longer wavelengths. The photo effect also affected unlabeled FN, but was enhanced by fluorophore labeling of FN. The inhibitory effect could be reduced when reactive oxygen species (ROS) were removed for the cell imaging medium. Based on these findings, FN fibrillogenesis could be imaged successfully using a labeling dye with a long excitation wavelength (Alexa Fluor 633, excitation at 632 nm) and ROS scavengers, such as oxyrase, in the imaging medium. Fibrillar remodeling of exposed cell-free FN layers by AFM scanning required higher scan forces compared to non-exposed FN, consisting with mechanical stiffing of the FN layer after illumination. In agreement with changes in FN mechanics, cells spreading on pre-exposed FN showed reduced migration speeds, altered focal adhesion arrangement, and changes in mechanosensitive signaling pathways, including reduced FAK (Y397) and paxillin (Y118) phosphorylation. Pre-exposure of FN to visible light prior to cell seeding thus provides a useful tool to delineate mechanosensitive signaling pathway related to FN fibrillogenesis. When using FN-coated cell adhesion substrates, care should be taken when comparing experimental results obtained on non-exposed FN layers in cell culture incubators, or during live-cell fluorescence imaging, as FN fibrillogenesis and mechanosensitive cellular signaling pathways may be affected differently.
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Affiliation(s)
- Tetyana Gudzenko
- DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Clemens M Franz
- DFG-Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany.,WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
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10
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BEDNARIKOVA Z, GAZOVA Z, VALLE F, BYSTRENOVA E. Atomic force microscopy as an imaging tool to study the bio/nonbio complexes. J Microsc 2020; 280:241-251. [DOI: 10.1111/jmi.12936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Z. BEDNARIKOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
| | - Z. GAZOVA
- Slovak Academy of Science Institute of Experimental Physics Kosice Slovakia
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11
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Kodera N, Ando T. High-Speed Atomic Force Microscopy to Study Myosin Motility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1239:127-152. [PMID: 32451858 DOI: 10.1007/978-3-030-38062-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
High-speed atomic force microscopy (HS-AFM) is a unique tool that enables imaging of protein molecules during their functional activity at sub-100 ms temporal and submolecular spatial resolution. HS-AFM is suited for the study of highly dynamic proteins, including myosin motors. HS-AFM images of myosin V walking on actin filaments provide irrefutable evidence for the swinging lever arm motion propelling the molecule forward. Moreover, molecular behaviors that have not been noticed before are also displayed on the AFM movies. This chapter describes the principle, underlying techniques and performance of HS-AFM, filmed images of myosin V, and mechanistic insights into myosin motility provided from the filmed images.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan.
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12
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Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. J Mol Biol 2020; 432:2846-2860. [DOI: 10.1016/j.jmb.2020.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
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Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 2019; 1864:129420. [PMID: 31472175 DOI: 10.1016/j.bbagen.2019.129420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial. METHOD We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image. RESULTS The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations. CONCLUSIONS The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail. GENERAL SIGNIFICANCE High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.
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Affiliation(s)
- Bhaskar Dasgupta
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Florence Tama
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, 464-8601, Japan.
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14
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Kodera N, Ando T. Direct Imaging of Walking Myosin V by High-Speed Atomic Force Microscopy. Methods Mol Biol 2019; 1805:103-122. [PMID: 29971715 DOI: 10.1007/978-1-4939-8556-2_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
High-speed atomic force microscopy allows for directly observing biological molecules in dynamic action at submolecular and sub-100 ms spatiotemporal resolution, without disturbing their function. This microscopy has recently been applied to various proteins with great success. Here, we describe methods to image myosin V molecules walking on actin filaments with high-speed atomic force microscopy.
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Affiliation(s)
- Noriyuki Kodera
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Toshio Ando
- Nano Life Science Institute (WPI NanoLSI), Kanazawa University, Kanazawa, Japan.
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15
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Optimum Substrates for Imaging Biological Molecules with High-Speed Atomic Force Microscopy. Methods Mol Biol 2018; 1814:159-179. [PMID: 29956232 DOI: 10.1007/978-1-4939-8591-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent progresses in high-speed atomic force microscopy (HS-AFM) have enabled us to directly visualize dynamic processes of various proteins in liquid conditions. One of the key factors leading to successful HS-AFM observations is the selection of an appropriate substrate depending on molecules to be observed. For the HS-AFM imaging, a target molecule must be absorbed on a substrate by controlling its orientation without impairing the dynamics or physiological function of the molecule. In this chapter, we describe protocols for preparation of substrates that have been used for HS-AFM and then introduce observation examples on dynamic processes of biological molecules.
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16
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Watanabe-Nakayama T, Ono K. High-Speed Atomic Force Microscopy of Individual Amyloidogenic Protein Assemblies. Methods Mol Biol 2018; 1814:201-212. [PMID: 29956234 DOI: 10.1007/978-1-4939-8591-3_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) with high spatiotemporal resolution allows for the video imaging of the conformational changes of individual molecules in an observation area in liquid at nanometer-scale spatial resolution. This method verifies the molecular mechanism and reveals the structural dynamics of relevant biomolecules for various biological phenomena. Here, we describe the methods for HS-AFM observation and the analysis of the structural dynamics of individual amyloidogenic protein assemblies using amyloid β 1-42 as an example.
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Affiliation(s)
| | - Kenjiro Ono
- Department of Neurology, School of Medicine, Showa University, Tokyo, Japan
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17
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Benning FMC, Sakiyama Y, Mazur A, Bukhari HST, Lim RYH, Maier T. High-Speed Atomic Force Microscopy Visualization of the Dynamics of the Multienzyme Fatty Acid Synthase. ACS NANO 2017; 11:10852-10859. [PMID: 29023094 DOI: 10.1021/acsnano.7b04216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Multienzymes, such as the protein metazoan fatty acid synthase (FAS), are giant and highly dynamic molecular machines for critical biosynthetic processes. The molecular architecture of FAS was elucidated by static high-resolution crystallographic analysis, while electron microscopy revealed large-scale conformational variability in FAS with some correlation to functional states in catalysis. However, little is known about time scales of conformational dynamics, the trajectory of motions in individual FAS molecules, and the extent of coupling between catalysis and structural changes. Here, we present an experimental single-molecule approach to film immobilized or selectively tethered FAS in solution at different viewing angles and high spatiotemporal resolution using high-speed atomic force microscopy. Mobility of individual regions of the multienzyme is recognized in video sequences, and correlation of shape features implies a convergence of temporal resolution and velocity of FAS dynamics. Conformational variety can be identified and grouped by reference-free 2D class averaging, enabling the tracking of conformational transitions in movies. The approach presented here is suited for comprehensive studies of the dynamics of FAS and other multienzymes in aqueous solution at the single-molecule level.
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Affiliation(s)
- Friederike M C Benning
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Yusuke Sakiyama
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Adam Mazur
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Habib S T Bukhari
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Timm Maier
- Biozentrum, ‡Swiss Nanoscience Institute, and §Research IT, Biozentrum, University of Basel , Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Ando T. Directly watching biomolecules in action by high-speed atomic force microscopy. Biophys Rev 2017; 9:421-429. [PMID: 28762198 DOI: 10.1007/s12551-017-0281-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/14/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, high-speed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions. The molecular movies have provided insights that could not have been reached in other ways. Moreover, the cantilever tip can be used to manipulate molecules during successive imaging. This capability allows us to observe changes in molecules resulting from dissection or perturbation. This mode of imaging has been successfully applied to myosin V, peroxiredoxin and doublet microtubules, leading to new discoveries. Since HS-AFM can be combined with other techniques, such as super-resolution optical microscopy and optical tweezers, the usefulness of HS-AFM will be further expanded in the near future.
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Affiliation(s)
- Toshio Ando
- Bio-AFM Frontier Research Center, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan. .,CREST, Japan Science and Technology Agency, Tokyo, 102-0075, Japan.
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19
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Karner A, Nimmervoll B, Plochberger B, Klotzsch E, Horner A, Knyazev DG, Kuttner R, Winkler K, Winter L, Siligan C, Ollinger N, Pohl P, Preiner J. Tuning membrane protein mobility by confinement into nanodomains. NATURE NANOTECHNOLOGY 2017; 12:260-266. [PMID: 27842062 PMCID: PMC5734611 DOI: 10.1038/nnano.2016.236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/30/2016] [Indexed: 05/04/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) can be used to visualize function-related conformational changes of single soluble proteins. Similar studies of single membrane proteins are, however, hampered by a lack of suitable flat, non-interacting membrane supports and by high protein mobility. Here we show that streptavidin crystals grown on mica-supported lipid bilayers can be used as porous supports for membranes containing biotinylated lipids. Using SecYEG (protein translocation channel) and GlpF (aquaglyceroporin), we demonstrate that the platform can be used to tune the lateral mobility of transmembrane proteins to any value within the dynamic range accessible to HS-AFM imaging through glutaraldehyde-cross-linking of the streptavidin. This allows HS-AFM to study the conformation or docking of spatially confined proteins, which we illustrate by imaging GlpF at sub-molecular resolution and by observing the motor protein SecA binding to SecYEG.
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Affiliation(s)
- Andreas Karner
- Center for Advanced Bioanalysis GmbH, Gruberstr. 40-42, 4020 Linz, Austria
| | | | - Birgit Plochberger
- Upper Austria University of Applied Sciences, Campus Linz, Garnisonstrasse 21, 4020 Linz, Austria
| | - Enrico Klotzsch
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Roland Kuttner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Klemens Winkler
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Lukas Winter
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Nicole Ollinger
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, 4020 Linz, Austria
| | - Johannes Preiner
- Center for Advanced Bioanalysis GmbH, Gruberstr. 40-42, 4020 Linz, Austria
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20
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Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy. SENSORS 2017; 17:s17010200. [PMID: 28117741 PMCID: PMC5298773 DOI: 10.3390/s17010200] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 12/23/2022]
Abstract
The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.
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21
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Abstract
Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC)
- Brussels
- Belgium
- Vrije Universiteit Brussel
- Brussels
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22
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. [AFM-based technologies as the way towards the reverse Avogadro number]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:239-53. [PMID: 25978390 DOI: 10.18097/pbmc20156102239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.
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Affiliation(s)
| | - I D Shumov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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23
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. AFM-based technologies as the way towards the reverse Avogadro number. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815030063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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A comparison of the surface nanostructure from two different types of gram-negative cells: Escherichia coli and Rhodobacter sphaeroides. Micron 2015; 72:8-14. [PMID: 25725215 DOI: 10.1016/j.micron.2015.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/26/2015] [Accepted: 02/04/2015] [Indexed: 11/20/2022]
Abstract
Bacteria have been studied using different microscopy methods for many years. Recently, the developments of high-speed atomic force microscopy have opened the doors to study bacteria in new ways due to the fact that it uses much less force on the sample while imaging. This makes the high-speed atomic force microscope an indispensable technique for imaging the surface of living bacterial cells because it allows for the high-resolution visualization of surface proteins in their natural condition without disrupting the cell or the activity of the proteins. Previous work examining living cells of Magnetospirillum magneticum AMB-1 demonstrated that the surface of these bacteria was covered with a net-like structure that is mainly composed of porin molecules. However, it was unclear whether or not this feature was unique to other living bacteria. In this study we used the high-speed atomic force microscope to examine the surface of living cells of Escherichia coli and Rhodobacter sphaeroides to compare their structure with that of M. magneticum. Our research clearly demonstrated that both of these types of cells have an outer surface that is covered in a network of nanometer-sized holes similar to M. magneticum. The diameter of the holes was 8.0±1.5 nm for E. coli and 6.6±1.1 nm for R. sphaeroides. The results in this paper confirm that this type of outer surface structure exists in other types of bacteria and it is not unique to Magnetospirillum.
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26
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Ngo KX, Kodera N, Katayama E, Ando T, Uyeda TQP. Cofilin-induced unidirectional cooperative conformational changes in actin filaments revealed by high-speed atomic force microscopy. eLife 2015; 4. [PMID: 25642645 PMCID: PMC4337605 DOI: 10.7554/elife.04806] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/02/2015] [Indexed: 01/12/2023] Open
Abstract
High-speed atomic force microscopy was employed to observe structural changes in actin filaments induced by cofilin binding. Consistent with previous electron and fluorescence microscopic studies, cofilin formed clusters along actin filaments, where the filaments were 2-nm thicker and the helical pitch was ∼25% shorter, compared to control filaments. Interestingly, the shortened helical pitch was propagated to the neighboring bare zone on the pointed-end side of the cluster, while the pitch on the barbed-end side was similar to the control. Thus, cofilin clusters induce distinctively asymmetric conformational changes in filaments. Consistent with the idea that cofilin favors actin structures with a shorter helical pitch, cofilin clusters grew unidirectionally toward the pointed-end of the filament. Severing was often observed near the boundaries between bare zones and clusters, but not necessarily at the boundaries. DOI:http://dx.doi.org/10.7554/eLife.04806.001 Actin is one of the most abundant proteins found inside all eukaryotic cells including plant, animal, and fungal cells. This protein is involved in a wide range of biological processes that are essential for an organism's survival. Actin proteins form long filaments that help cells to maintain their shape and also provide the force required for cells to divide and/or move. Actin filaments are helical in shape and are made up of many actin subunits joined together. Actin filaments are changeable structures that continuously grow and shrink as new actin subunits are added to or removed from the ends of the filaments. One end of an actin filament grows faster than the other; the fast-growing end is known as the barbed-end, while the slow-growing end is referred to as the pointed-end. Over 100 other proteins are known to bind to and work with actin to regulate its roles in cells and how it forms into filaments. Cofilin is one such protein that binds to and forms clusters on actin filaments and it can also sever actin filaments. Severing an actin filament can encourage the filament to disassemble, or it can help produce new barbed ends that can then grow into new filaments. Previous work had suggested that cofilin severs actin filaments at the junction between regions on the filament that are coated with cofilin and those that are not. It was also known that cofilin binding to a filament causes the filament to change shape, and that the shape change is propagated to neighboring sections of the filaments not coated with cofilin. However, the details of where cofilin binds and how changes in shape are propagated along an actin filament were not known. Furthermore, the findings of these previous studies were largely based on examining still images of actin filaments, which are unlike the constantly changing filaments of living cells. Ngo, Kodera et al. have now analyzed what happens when cofilin binds to and forms clusters along actin filaments using a recently developed imaging technique called high-speed atomic force microscopy. This technique can be used to directly visualize individual proteins in action. Consistent with previous findings, Ngo, Kodera et al. observed that filaments coated with cofilin are thicker than those filaments without cofilin; and that cofilin binding also substantially reduces the helical twist of the filament. Ngo, Kodera et al. also found that these changes in shape are propagated along the filament but in only one direction—towards the pointed-end. Moreover, cofilin clusters also only grew towards the pointed-end of the actin filament—and the filaments were often severed near, but not exactly at, the junctions between cofilin-coated and uncoated regions. Such one-directional changes in shape of the actin filaments presumably help to regulate how other actin binding proteins can interact with the filament and consequently regulate the roles of the filaments themselves. DOI:http://dx.doi.org/10.7554/eLife.04806.002
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Affiliation(s)
- Kien Xuan Ngo
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Noriyuki Kodera
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Japan
| | - Eisaku Katayama
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Japan
| | - Taro Q P Uyeda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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27
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Deleu M, Crowet JM, Nasir MN, Lins L. Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3171-3190. [DOI: 10.1016/j.bbamem.2014.08.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
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28
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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29
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Sugiyama H. Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame. Nucleic Acids Res 2013; 41:8738-47. [PMID: 23863846 PMCID: PMC3794576 DOI: 10.1093/nar/gkt592] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Guanine-rich oligonucleotides often show a strong tendency to form supramolecular architecture, the so-called G-quadruplex structure. Because of the biological significance, it is now considered to be one of the most important conformations of DNA. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G-G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands. In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time. The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan, Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan, CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan and University of Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
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Fukuda S, Uchihashi T, Iino R, Okazaki Y, Yoshida M, Igarashi K, Ando T. High-speed atomic force microscope combined with single-molecule fluorescence microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:073706. [PMID: 23902075 DOI: 10.1063/1.4813280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) and total internal reflection fluorescence microscopy (TIRFM) have mutually complementary capabilities. Here, we report techniques to combine these microscopy systems so that both microscopy capabilities can be simultaneously used in the full extent. To combine the two systems, we have developed a tip-scan type HS-AFM instrument equipped with a device by which the laser beam from the optical lever detector can track the cantilever motion in the X- and Y-directions. This stand-alone HS-AFM system is mounted on an inverted optical microscope stage with a wide-area scanner. The capability of this combined system is demonstrated by simultaneous HS-AFM∕TIRFM imaging of chitinase A moving on a chitin crystalline fiber and myosin V walking on an actin filament.
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Affiliation(s)
- Shingo Fukuda
- Department of Physics, College of Science and Engineering, Kanazawa University, Ishikawa 920-1192, Japan
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31
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Abstract
Directly observing individual protein molecules in action at high spatiotemporal resolution has long been a holy grail for biological science. This is because we long have had to infer how proteins function from the static snapshots of their structures and dynamic behavior of optical makers attached to the molecules. This limitation has recently been removed to a large extent by the materialization of high-speed atomic force microscopy (HS-AFM). HS-AFM allows us to directly visualize the structure dynamics and dynamic processes of biological molecules in physiological solutions, at subsecond to sub-100-ms temporal resolution, without disturbing their function. In fact, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. In this review, we first describe theoretical considerations for the highest possible imaging rate of this new microscope, and then highlight recent imaging studies. Finally, the current limitation and future challenges to explore are described.
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Affiliation(s)
- Toshio Ando
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan.
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32
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Molecular machines directly observed by high-speed atomic force microscopy. FEBS Lett 2013; 587:997-1007. [PMID: 23318713 DOI: 10.1016/j.febslet.2012.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 11/22/2022]
Abstract
Molecular machines made of proteins are highly dynamic and carry out sophisticated biological functions. The direct and dynamic high-resolution visualization of molecular machines in action is considered to be the most straightforward approach to understanding how they function but this has long been infeasible until recently. High-speed atomic force microscopy has recently been realized, making such visualization possible. The captured images of myosin V, F1-ATPase, and bacteriorhodopsin have enabled their dynamic processes and structure dynamics to be revealed in great detail, giving unique and deep insights into their functional mechanisms.
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Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and Real-Time Observation of Rotary Movement of a DNA Nanomechanical Device. J Am Chem Soc 2013; 135:1117-23. [DOI: 10.1021/ja310454k] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku,
Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku,
Tokyo 102-0075, Japan
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34
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Abstract
High-speed atomic force microscopy (HS-AFM) has been developed as a nano-dynamics visualization technique. This microscopy permits direct observation of structure dynamics and dynamic processes of biological molecules in physiological solutions, at a subsecond to sub-100 ms temporal resolution and an ∼2 nm lateral and a 0.1 nm vertical resolution. Importantly, tip-sample interactions do not disturb the biomolecules' functions. Various functioning proteins including myosin V walking on an actin filament and bacteriorhodopsin responding to light have been successfully visualized with HS-AFM. In the quest for understanding the functional mechanisms of proteins, inferences no longer have to be made from static snapshots of molecular structures and dynamic behavior of optical markers attached to proteins. High-resolution molecular movies obtained from HS-AFM observations reveal the details of molecules' dynamic behavior in action, without the need for intricate analyses and interpretations. In this review, I first describe the fundamentals behind the achieved high imaging rate and low invasiveness to samples, and then highlight recent imaging studies. Finally, future studies are briefly described.
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Affiliation(s)
- Toshio Ando
- Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa, Japan.
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35
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Yamashita H, Taoka A, Uchihashi T, Asano T, Ando T, Fukumori Y. Single-Molecule Imaging on Living Bacterial Cell Surface by High-Speed AFM. J Mol Biol 2012; 422:300-9. [DOI: 10.1016/j.jmb.2012.05.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/14/2012] [Indexed: 11/27/2022]
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36
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Atomic force microscopy for the study of membrane proteins. Curr Opin Biotechnol 2012; 23:510-5. [DOI: 10.1016/j.copbio.2011.11.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 11/08/2011] [Accepted: 11/25/2011] [Indexed: 11/19/2022]
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37
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Shlyakhtenko LS, Lushnikov AY, Miyagi A, Li M, Harris RS, Lyubchenko YL. Nanoscale structure and dynamics of ABOBEC3G complexes with single-stranded DNA. Biochemistry 2012; 51:6432-40. [PMID: 22809226 DOI: 10.1021/bi300733d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA cytosine deaminase APOBEC3G (A3G) is capable of blocking retrovirus replication by editing viral cDNA and impairing reverse transcription. However, the biophysical details of this host-pathogen interaction are unclear. We applied atomic force microscopy (AFM) and hybrid DNA substrates to investigate properties of A3G bound to single-stranded DNA (ssDNA). Hybrid DNA substrates included ssDNA with 5' or 3' ends attached to DNA duplexes (tail-DNA) and gap-DNA substrates, in which ssDNA is flanked by two double-stranded fragments. We found that A3G binds with similar efficiency to the 5' and 3' substrates, suggesting that ssDNA polarity is not an important factor. Additionally, we observed that A3G binds the single-stranded region of the gap-DNA substrates with the same efficiency as tail-DNA. These results demonstrate that single-stranded DNA ends are not needed for A3G binding. The protein stoichiometry does not depend on the ssDNA substrate type, but the ssDNA length modulates the stoichiometry of A3G in the complex. We applied single-molecule high-speed AFM to directly visualize the dynamics of A3G in the complexes. We were able to visualize A3G sliding and protein association-dissociation events. During sliding, A3G translocated over a 69-nucleotide ssDNA segment in <1 s. Association-dissociation events were more complex, as dimeric A3G could dissociate from the template as a whole or undergo a two-step process with monomers capable of sequential dissociation. We conclude that A3G monomers, dimers, and higher-order oligomers can bind ssDNA substrates in a manner independent of strand polarity and availability of free ssDNA ends.
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Affiliation(s)
- Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Endo M, Tatsumi K, Terushima K, Katsuda Y, Hidaka K, Harada Y, Sugiyama H. Direct Visualization of the Movement of a Single T7 RNA Polymerase and Transcription on a DNA Nanostructure. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Endo M, Tatsumi K, Terushima K, Katsuda Y, Hidaka K, Harada Y, Sugiyama H. Direct visualization of the movement of a single T7 RNA polymerase and transcription on a DNA nanostructure. Angew Chem Int Ed Engl 2012; 51:8778-82. [PMID: 22848002 DOI: 10.1002/anie.201201890] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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40
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Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy. Nat Protoc 2012; 7:1193-206. [DOI: 10.1038/nprot.2012.047] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Abstract
High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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42
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Igarashi K, Uchihashi T, Koivula A, Wada M, Kimura S, Penttilä M, Ando T, Samejima M. Visualization of cellobiohydrolase I from Trichoderma reesei moving on crystalline cellulose using high-speed atomic force microscopy. Methods Enzymol 2012; 510:169-82. [PMID: 22608726 DOI: 10.1016/b978-0-12-415931-0.00009-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cellulases hydrolyze β-1,4-glucosidic linkages of insoluble cellulose at the solid/liquid interface, generating soluble cellooligosaccharides. We describe here our method for real-time observation of the behavior of cellulase molecules on the substrate, using high-speed atomic force microscopy (HS-AFM). When glycoside hydrolase family 7 cellobiohydrolase from Trichoderma reesei (TrCel7A) was incubated with crystalline cellulose, many enzyme molecules were observed to move unidirectionally on the surface of the substrate by HS-AFM. The velocity of the moving molecules of TrCel7A on cellulose I crystals was estimated by means of image analysis.
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Affiliation(s)
- Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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43
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Abstract
Intrinsically disordered regions (IDRs) of proteins are very thin and hence hard to be visualized by electron microscopy. Thus far, only high-speed atomic force microscopy (HS-AFM) can visualize them. The molecular movies identify the alignment of IDRs and ordered regions in an intrinsically disordered protein (IDP) and show undulation motion of the IDRs. The visualized tail-like structures contain the information of mechanical properties of the IDRs. Here, we describe methods of HS-AFM visualization of IDPs and methods of analyzing the obtained images to characterize IDRs.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Japan.
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44
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Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy. Methods Mol Biol 2012; 931:295-312. [PMID: 23027008 DOI: 10.1007/978-1-62703-056-4_14] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface preparation is a key step for reliable and reproducible imaging of DNA and protein-DNA complexes with atomic force microscopy (AFM). This article describes the approaches for chemical functionalization of the mica surface. One approach utilizes 3-aminopropyl-trietoxy silane (APTES), enabling one to obtain a smooth surface termed AP-mica. This surface binds nucleic acids and nucleoprotein complexes in a wide range of ionic strengths, in the absence of divalent cations and in a broad range of pH. Another method utilizes aminopropyl silatrane (APS) to yield an APS-mica surface. The advantage of APS-mica compared with AP-mica is the ability to obtain reliable and reproducible time-lapse images in aqueous solutions. The chapter describes the methodologies for the preparation of AP-mica and APS-mica surfaces and the preparation of samples for AFM imaging. The protocol for synthesis and purification of APS is also provided. The applications are illustrated with a number of examples.
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45
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Grossman M, Sela-Passwell N, Sagi I. Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches. Curr Opin Struct Biol 2011; 21:678-85. [PMID: 21945040 DOI: 10.1016/j.sbi.2011.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/21/2011] [Accepted: 07/31/2011] [Indexed: 11/30/2022]
Abstract
A network of dynamic protein interactions with their protein partners, substrates, and ligands is known to be crucial for biological function. Revealing molecular and structural-based mechanisms at atomic resolution and in real-time is fundamental for achieving a basic understanding of cellular processes. These technically challenging goals may be achieved by combining time-resolved spectroscopic and structural-kinetic tools, thus providing broad insights into specific molecular events over a wide range of timescales. Here we review representative studies utilizing such an integrated real-time structural approach designed to reveal molecular mechanisms underlying protein interactions at atomic resolution.
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Affiliation(s)
- Moran Grossman
- Departments of Structural Biology and Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
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46
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Igarashi K, Uchihashi T, Koivula A, Wada M, Kimura S, Okamoto T, Penttilä M, Ando T, Samejima M. Traffic jams reduce hydrolytic efficiency of cellulase on cellulose surface. Science 2011; 333:1279-82. [PMID: 21885779 DOI: 10.1126/science.1208386] [Citation(s) in RCA: 346] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A deeper mechanistic understanding of the saccharification of cellulosic biomass could enhance the efficiency of biofuels development. We report here the real-time visualization of crystalline cellulose degradation by individual cellulase enzymes through use of an advanced version of high-speed atomic force microscopy. Trichoderma reesei cellobiohydrolase I (TrCel7A) molecules were observed to slide unidirectionally along the crystalline cellulose surface but at one point exhibited collective halting analogous to a traffic jam. Changing the crystalline polymorphic form of cellulose by means of an ammonia treatment increased the apparent number of accessible lanes on the crystalline surface and consequently the number of moving cellulase molecules. Treatment of this bulky crystalline cellulose simultaneously or separately with T. reesei cellobiohydrolase II (TrCel6A) resulted in a remarkable increase in the proportion of mobile enzyme molecules on the surface. Cellulose was completely degraded by the synergistic action between the two enzymes.
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Affiliation(s)
- Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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47
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Tompa P. Unstructural biology coming of age. Curr Opin Struct Biol 2011; 21:419-25. [PMID: 21514142 DOI: 10.1016/j.sbi.2011.03.012] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/28/2011] [Accepted: 03/24/2011] [Indexed: 12/19/2022]
Abstract
It is now generally accepted that many proteins or protein domains (intrinsically disordered proteins, IDPs) lack a well-defined tertiary structure under functional conditions. Due to recent concerted activity, a critical transition in this field is gaining momentum, in which qualitative observations are turned into quantitative structural models of IDPs. Here, it is suggested that the transition is set up by the synergy of: (i) more advanced bioinformatic tools for the prediction of disorder and function of IDPs, (ii) ensemble description of their structure and dynamics in both free and bound states, down to the single molecule level, (iii) advent of in-cell approaches for characterizing their structure and function in vivo, and (iv) generation of small-molecule inhibitors both against their binding partners and IDPs themselves. In all, we suggest that due to steady advance in these areas, the field of 'unstructural' biology is rapidly maturing to a state where it can provide quantitative models of proteins functioning without well-defined three-dimensional structures.
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Affiliation(s)
- Peter Tompa
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.
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48
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Video imaging of walking myosin V by high-speed atomic force microscopy. Nature 2010; 468:72-6. [PMID: 20935627 DOI: 10.1038/nature09450] [Citation(s) in RCA: 508] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 08/24/2010] [Indexed: 11/08/2022]
Abstract
The dynamic behaviour of myosin V molecules translocating along actin filaments has been mainly studied by optical microscopy. The processive hand-over-hand movement coupled with hydrolysis of adenosine triphosphate was thereby demonstrated. However, the protein molecules themselves are invisible in the observations and have therefore been visualized by electron microscopy in the stationary states. The concomitant assessment of structure and dynamics has been unfeasible, a situation prevailing throughout biological research. Here we directly visualize myosin V molecules walking along actin tracks, using high-speed atomic force microscopy. The high-resolution movies not only provide corroborative 'visual evidence' for previously speculated or demonstrated molecular behaviours, including lever-arm swing, but also reveal more detailed behaviours of the molecules, leading to a comprehensive understanding of the motor mechanism. Our direct and dynamic high-resolution visualization is a powerful new approach to studying the structure and dynamics of biomolecules in action.
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