Article
Chemistry, Physical
Francisco J. Solis, Monica Olvera de la Cruz
Summary: This article discusses the interactions between charged particles and induced polarization charge on solid-liquid or liquid-liquid interfaces with dielectric contrast, as well as the self-energy of charged particles near rough surfaces. Results show that the local convexity and concavity of the surface affect the repulsion of ions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Sourav Maity, Gianluca Trinco, Pedro Buzon, Zaid R. Anshari, Noriyuki Kodera, Kien Xuan Ngo, Toshio Ando, Dirk J. Slotboom, Wouter H. Roos
Summary: This study used high-speed atomic force microscopy to visualize the transport cycle of the CitS protein in real time. It revealed the presence of three distinguishable states and independent movement of the protein subunits. These findings provide insights into the transport mechanism of the CitS protein.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Shuji Fujisawa, Kazuho Daicho, Ayhan Yurtsever, Takeshi Fukuma, Tsuguyuki Saito
Summary: All-atom molecular dynamics simulations and atomic force microscopy were used to study the structural dynamics of single nanocellulose during drying. It was discovered that the twist morphology of nanocellulose becomes localized along the fibril axis in the final stage of drying. Conformational changes at C6 hydroxymethyl groups and glycoside bond were also observed, indicating an increase in crystallinity during the drying process. These insights provide valuable information for understanding the nanocellulose structures in material processing and designing materials with advanced functionalities.
Article
Biochemical Research Methods
Alfred Nguyen, Matthias Brandt, Till M. Muenker, Timo Betz
Summary: A novel method for frequency-dependent microrheology on cells using acoustic forces is presented, allowing multiplexed measurements of several cells in parallel and continuous measurement of complex shear modulus G*(omega). The experimental results are consistent with fractional viscoelastic models, showing the correlation between power-law shear moduli and cellular structures. Thorough calibration and careful data analysis are crucial for performing viscoelastic measurements with acoustic force spectroscopy (AFS), with protocols and guidelines provided.
Article
Multidisciplinary Sciences
Ryusei Yamada, Tran Ngoc Trang, Holger Flechsig, Toshiki Takeda, Noriyuki Kodera, Hiroki Konno
Summary: The N-terminal of annexin V has significant influence on 2D crystal formation, as observed using high-speed atomic force microscopy (HS-AFM). Furthermore, a quick purification method is presented to purify recombinant annexin V without any residual affinity tag after protein purification in approximately 3 hours.
Article
Chemistry, Physical
G. C. Savulescu, M. Rucker, A. Scanziani, R. Pini, A. Georgiadis, P. F. Luckham
Summary: This study investigates the potential of using atomic force microscopy to characterize wetting behavior at the nanoscale, successfully observing an attraction phenomenon on the water droplet surface in experiments and obtaining parameters such as contact angle and contact angle distribution.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Rashad Kariuki, Rowan Penman, Saffron J. Bryant, Rebecca Orrell-Trigg, Nastaran Meftahi, Russell J. Crawford, Chris F. McConville, Gary Bryant, Kislon Voitchovsky, Charlotte E. Conn, Andrew J. Christofferson, Aaron Elbourne
Summary: Nanomaterials have the potential to revolutionize biological and biomedical research, and this study provides detailed insights into how gold nanoparticles interact with phospholipid membranes. The study shows that the nanoparticles can be absorbed and internalized by fluid-phase membranes, and partially embed into gel-phase membranes, causing perturbations throughout the bilayers.
Article
Multidisciplinary Sciences
Rita dos Santos Natividade, Melanie Koehler, Priscila S. F. C. Gomes, Joshua D. Simpson, Sydni Caet Smith, Diego E. B. Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S. Dermody, Rafael C. Bernardi, Kristen M. Ogden, David Alsteens
Summary: This study investigates the nanomechanical properties of viral attachment proteins and their impact on virus-binding capacity and infectivity. The research reveals that conformational changes in the viral protein a1 significantly increase its affinity for JAM-A, leading to enhanced infectivity. The study also demonstrates how GM2 enhances the a1-JAM-A interaction. These findings provide important insights for the development of antiviral drugs and improved oncolytic vectors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
Keivan Asadi, Junghoon Yeom, Hanna Cho
Summary: Investigating internal resonance (IR) mechanisms in micro/nanoresonators reveals that intermodal coupling between second and third flexural modes in asymmetric structures provides an optimal condition for strong IR, with high energy transfer to the resonated mode. This study introduces design strategies that can be easily integrated into typical micro/nanoelectromechanical systems, offering potential for paradigm-shifting applications in micro/nanosystems.
MICROSYSTEMS & NANOENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Xiangxiang Sun, Yumei Yu, Ahmed S. M. Saleh, Xinyu Yang, Jiale Ma, Wenhao Li, Dequan Zhang, Zhenyu Wang
Summary: This study investigated the influence of constant heating treatment on the structural and adsorption properties of chicken myofibrillar proteins (MPs). The results showed that heat treatment increased the exposure of sulfhydryl groups and improved the hydrophobicity of MPs' surface. The particle size distribution, alpha-helix and beta-sheet structures, as well as the formation of aggregates, viscosity, surface roughness, and zeta potential of MPs were significantly affected by heat treatments. Additionally, the binding interactions between MPs and flavors of spices varied depending on the nature of MPs, flavor compounds, and heat treatment duration.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Editorial Material
Multidisciplinary Sciences
Telmo O. Paiva, Albertus Viljoen, Yves F. Dufrene
Summary: Advancements in atomic force microscopy (AFM) techniques and methodologies in microbiology have enhanced our understanding of microbial cell surfaces. Recent studies have shown that AFM imaging of cells and membranes at or near molecular resolution enables detailed visualization of membrane-drug interactions.
NATURE COMMUNICATIONS
(2022)
Article
Environmental Sciences
Amanda Pacholak, Wojciech Juzwa, Agnieszka Zgola-Grzeskowiak, Ewa Kaczorek
Summary: The excessive presence of antibiotics and their residues can pose a danger to the natural environment. This study aimed to explore the potential of bacterial strains in degrading nitrofurantoin (NFT) and reducing its negative impact. Single strains isolated from contaminated areas were utilized, and their degradation efficiency and dynamic changes in NFT biodegradation were investigated. Serratia marcescens ODW152 showed the highest performance in NFT removal, with significant modifications observed in cell shape and surface structure. The study suggests that nitrofurantoin biodegradation produces stable transformation products that significantly affect bacterial cell physiology and structure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Hai Lei, Junsheng Zhang, Ying Li, Xin Wang, Meng Qin, Wei Wang, Yi Cao
Summary: In this study, a histidine-specific phosphorylation strategy was developed to covalently anchor proteins to an atomic force microscopy. This method improved the data quality of single-molecule force spectroscopy experiments and was successfully applied to investigate the mechanical stability and unfolding process of proteins.
Article
Multidisciplinary Sciences
Devin T. Edwards, Marc-Andre Leblanc, Thomas T. Perkins
Summary: Single-molecule force spectroscopy was used to study protein folding dynamics, revealing intrinsic changes in protein folding dynamics and transition state height under different pH conditions. Despite differences in destabilization mechanisms, constant-force landscapes showed minimal differences in transition state height, while force-dependent rates increased as pH decreased. This study provides insights for future AFM-based studies of mechanoresponsive proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Carolina Paba, Virginia Dorigo, Beatrice Senigagliesi, Nicola Tormena, Pietro Parisse, Kislon Voitchovsky, Loredana Casalis
Summary: This study investigates the interaction between small extracellular vesicles (sEVs) released from triple-negative breast cancer cells and synthetic model membranes. The results show that the fluidity of the membranes plays a crucial role in the uptake of sEVs, with stronger interaction and fusion occurring in less fluid regions.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Noriyuki Kodera, Toshio Ando
Summary: High-speed atomic force microscopy (HS-AFM) is a powerful tool for studying the dynamic properties of both structured and intrinsically disordered proteins under near-physiological conditions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bikash R. Sahoo, Christopher L. Souders, Takahiro Watanabe-Nakayama, Zhou Deng, Hunter Linton, Saba Suladze, Magdalena I. Ivanova, Bernd Reif, Toshio Ando, Christopher J. Martyniuk, Ayyalusamy Ramamoorthy
Summary: This study demonstrates that synthetic copolymer derivatives can alter amylin aggregation and modulate its conformation, providing insights into the mechanism of amylin pathogenic formation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Sourav Maity, Gianluca Trinco, Pedro Buzon, Zaid R. Anshari, Noriyuki Kodera, Kien Xuan Ngo, Toshio Ando, Dirk J. Slotboom, Wouter H. Roos
Summary: This study used high-speed atomic force microscopy to visualize the transport cycle of the CitS protein in real time. It revealed the presence of three distinguishable states and independent movement of the protein subunits. These findings provide insights into the transport mechanism of the CitS protein.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Instruments & Instrumentation
Masahiro Shimizu, Chihiro Okamoto, Kenichi Umeda, Shinji Watanabe, Toshio Ando, Noriyuki Kodera
Summary: The article presents an ultrafast piezoelectric Z-scanner with a high resonance frequency and response time, which allows for imaging of biological polymers in a buffer solution.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Biochemistry & Molecular Biology
Hirotaka Ariyama
Summary: Pore-forming proteins are important structures produced by various organisms, including pathogenic bacteria, and play a vital role in their function. By using high-speed atomic force microscopy, the transition process for pore formation is observed, revealing the mechanism of transition in a subunit and the collaboration between subunits.
JOURNAL OF MEMBRANE BIOLOGY
(2023)
Article
Biochemical Research Methods
Noriyuki Kodera, Toshio Ando
Summary: Intrinsically disordered proteins (IDPs) are proteins that are partially or entirely disordered, and their intrinsically disordered regions (IDRs) explore a wide range of structural space due to their highly flexible nature. Conventional structural analyses are not suitable for studying the dynamic structure of IDPs, so single-molecule measurement tools are needed. High-speed atomic force microscopy (HS-AFM) is a unique tool that allows direct visualization of the shape and motion of individual biomolecules under near physiological conditions, without any chemical labeling.
Article
Cell Biology
Elma Sakinatus Sajidah, Keesiang Lim, Tomoyoshi Yamano, Goro Nishide, Yujia Qiu, Takeshi Yoshida, Hanbo Wang, Akiko Kobayashi, Masaharu Hazawa, Firli R. P. Dewi, Rikinari Hanayama, Toshio Ando, Richard W. Wong
Summary: Small extracellular vesicles (sEVs) play a crucial role in cell communication and can be used for drug delivery and structural characterization of nanoparticles. The high-speed atomic force microscopy (HS-AFM) can evaluate the structural changes of sEVs under different physicochemical stresses.
JOURNAL OF EXTRACELLULAR VESICLES
(2022)
Article
Biology
Yuuki Hayakawa, Masak Takaine, Kien Xuan Ngo, Taiga Imai, Masafumi D. Yamada, Arash Badami Behjat, Kenichi Umeda, Keiko Hirose, Ayhan Yurtsever, Noriyuki Kodera, Kiyotaka Tokuraku, Osamu Numata, Takeshi Fukuma, Toshio Ando, Kentaro Nakano, Taro Q. P. Uyeda
Summary: Sub-stoichiometric binding of an actin-binding protein can induce structural changes in actin filaments and inhibit their movement, affecting actomyosin interactions and force generation.
LIFE SCIENCE ALLIANCE
(2022)
Article
Chemistry, Multidisciplinary
Keesiang Lim, Goro Nishide, Elma Sakinatus Sajidah, Tomoyoshi Yamano, Yujia Qiu, Takeshi Yoshida, Akiko Kobayashi, Masaharu Hazawa, Toshio Ando, Rikinari Hanayama, Richard W. Wong
Summary: In this study, high-speed atomic force microscopy (HS-AFM) was used to investigate the molecular properties and interactions between spike proteins and S NAbs. The results showed that S NAbs existed as monomers in a Y conformation at low density and formed hexameric oligomers at high density. The dynamic interaction between S NAbs and spike proteins did not induce RBD opening or S1 subunit shedding, and the interaction remained stable at endosomal pH. Additionally, the movement of spike proteins on small extracellular vesicles (S sEV) resembled that on SARS-CoV-2, and the sensitivity of variant S sEVs to S NAbs could be evaluated using HS-AFM. Overall, this study provides a nanoscopic assessment platform for evaluating the binding properties of S NAbs.
Article
Biochemical Research Methods
Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga
Summary: High-speed atomic force microscopy (HS-AFM) is a powerful technique for capturing the time-resolved behavior of biomolecules. However, the structural information obtained from HS-AFM images is limited to the surface geometry, so it is important to infer the latent three-dimensional structures.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Holger Flechsig, Toshio Ando
Summary: High-speed atomic force microscopy (HS-AFM) allows direct observation of biological molecules in dynamic action, but it lacks atomic resolution. This article reviews recent progress in computational methods for inferring high-resolution information, such as the construction of 3D atomic structures, from experimentally acquired resolution-limited HS-AFM images.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ryo Ikeda, Daisuke Noshiro, Hideaki Morishita, Shuhei Takada, Shun Kageyama, Yuko Fujioka, Tomoko Funakoshi, Satoko Komatsu-Hirota, Ritsuko Arai, Elena Ryzhii, Manabu Abe, Tomoaki Koga, Hozumi Motohashi, Mitsuyoshi Nakao, Kenji Sakimura, Arata Horii, Satoshi Waguri, Yoshinobu Ichimura, Nobuo N. Noda, Masaaki Komatsu
Summary: ULK1 is a kinase responsible for the phosphorylation of p62, which activates NRF2. p62(S351E/+) mice, with phosphorylation-mimicking mutation, exhibit NRF2 hyperactivation and growth retardation.
Article
Chemistry, Physical
Goro Nishide, Keesiang Lim, Maiki Tamura, Akiko Kobayashi, Qingci Zhao, Masaharu Hazawa, Toshio Ando, Noritaka Nishida, Richard W. Wong
Summary: The accessory protein of SARS-CoV-2, ORF6, has amyloidogenic sequences and can self-assemble into cytotoxic amyloid fibrils. This study used high-speed atomic force microscopy to investigate the structural dynamics of the full-length ORF6 protein in a near-physiological environment. The findings reveal the molecular behavior of ORF6 and provide insights for drug repurposing in the treatment of amyloid-related complications of COVID-19.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Chemistry, Multidisciplinary
Mu-Yueh Chang, Hirotaka Ariyama, Wilhelm T. S. Huck, Nan-Nan Deng
Summary: The bottom-up construction of a living cell using non-living materials is a major challenge in science and technology. Reproduction of cells into similar offspring is crucial for life, and therefore, building a synthetic cell that can autonomously divide is a fundamental task in bottom-up synthetic biology. In this review, we summarize the strategies of inducing synthetic division using physical, chemical, and biological stimuli, and highlight the future challenges in constructing autonomous synthetic cell division.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Multidisciplinary
Azusa Miyata, Sohei Ito, Daisuke Fujinami
Summary: Post-translational prenylations play crucial roles in biomolecular interactions. The prenyltransferase PalQ was identified, which can transfer extended prenyl chains to the indole C3 position. This prenylation introduces structural diversity to the tryptophan side chain and alters the conformational dynamics of the peptide backbone.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)