Article
Biochemistry & Molecular Biology
Pauline Cornette, Ilhem Lilia Jaabar, Vincent Dupres, Jean-David Werthel, Francis Berenbaum, Xavier Houard, Jessem Landoulsi, Geoffroy Nourissat
Summary: The study investigated the effect of crosslinking treatment on the structure and mechanical properties of diseased human shoulder capsules. The results showed that the crosslinking procedure changed the biomechanics of the capsules while keeping their structural organization unchanged at the single fibril level. This procedure may be a promising way to preserve the functions of collagen-based tissues and tune their elasticity for clinically relevant treatments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Biomedical
Yan Han, Joel Gomez, Rui Hua, Pengwei Xiao, Wei Gao, Jean X. Jiang, Xiaodu Wang
Summary: Research shows that removal of GAGs from bone tissues increases the elastic modulus and reduces plastic energy dissipation, particularly in wet conditions. GAGs not only affect the capacity of EFM, but may also impact the elastic modulus of MCFs.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2021)
Article
Neurosciences
Elise Santorella, Jeremy L. Balsbaugh, Shujun Ge, Parisa Saboori, David Baker, Joel S. Pachter
Summary: This study investigated the protein composition and structural organization of the meninges surrounding the brain and spinal cord. The results revealed regional differences in the protein makeup of the meninges, which may play a role in protective and neuroimmune functions.
FLUIDS AND BARRIERS OF THE CNS
(2023)
Article
Engineering, Biomedical
Marouane El Mouss, Tarek Merzouki, Amna Rekik, Ridha Hambli
Summary: In this paper, a novel hybrid multiscale model for cortical bone incorporating the tropocollagen molecule based on the combination of finite element method and different homogenization techniques was developed. The objective was to investigate the influence of age-related structural alterations that occur at the molecular level on mechanical properties of the bone tissue.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2022)
Article
Biochemical Research Methods
Sebastian Freidank, Alfred Vogel, Norbert Linz
Summary: This study investigates the mechanisms of laser dissection in cornea using ultra-high-speed photography and finds that the cutting process relies on crack propagation along the bubble lobes. These insights are important for improving the cutting mechanisms in refractive surgery.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Chemistry, Physical
Miki Hoshi, Tomofumi Sawada, Wataru Hatakeyama, Masayuki Taira, Yuki Hachinohe, Kyoko Takafuji, Hidemichi Kihara, Shinji Takemoto, Hisatomo Kondo
Summary: This study characterized five clinically applied collagenous biomaterials using four different methods and found that membrane-type materials have longer biodegradation time and higher durability due to their higher cross-link degree. These findings are valuable for the selection and development of fibrous collagenous biomaterials.
Article
Zoology
Stanislav Stukalyuk, Mykola Kozyr, Ascar Akhmedov
Summary: This study compared the speed of movement of three species of ants on different substrate types. It found that larger ant species moved faster than smaller ones, and ants preferred logs on highways. Additionally, ants moved faster on logs than on the ground and transported more food.
TURKISH JOURNAL OF ZOOLOGY
(2023)
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)
Article
Microscopy
Kenichi Umeda, Steven J. McArthur, Noriyuki Kodera
Summary: High-speed atomic force microscopy (HS-AFM) is a unique technique that allows real-time visualization of biological macromolecules in action without chemical labeling. It has sub-100 ms temporal resolution, 2-3 nm lateral resolution, and 0.1 nm vertical resolution. HS-AFM has provided valuable mechanistic insights into biomolecular function, but the level of detail depends on the spatiotemporal resolution. This review article discusses the principles of HS-AFM, resolution determination, and recent efforts to improve resolution.
Article
Chemistry, Multidisciplinary
Leonardo Puppulin, Junichiro Ishikawa, Ayumi Sumino, Arin Marchesi, Holger Flechsig, Kenichi Umeda, Noriyuki Kodera, Hiroshi Nishimasu, Mikihiro Shibata
Summary: High-speed atomic force microscopy (HS-AFM) is used to study the dynamics of DNA binding and cleavage by Staphylococcus aureus Cas9 (SaCas9). SaCas9 forms a close bilobed structure upon binding to single-guide RNA (sgRNA), which transiently adopts an open configuration. SaCas9-mediated DNA cleavage involves the release of cleaved DNA and immediate dissociation, indicating its function as a multiple turnover endonuclease. HS-AFM experiments reveal a potential long-range attractive interaction between SaCas9-sgRNA and its target DNA, preceding the formation of the stable ternary complex.
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
Chemistry, Multidisciplinary
Takahiro Watanabe-Nakayama, Mayumi Tsuji, Kenichi Umeda, Tatsunori Oguchi, Hiroki Konno, Moeko Noguchi-Shinohara, Yuji Kiuchi, Noriyuki Kodera, David B. Teplow, Kenjiro Ono
Summary: This study used high-speed atomic force microscopy to observe the structural dynamics of Afl42 PF at the single-molecule level and the effect of lecanemab, an anti-Afl PF antibody. It was found that PF had a curved nodal structure and underwent intramolecular cleavage. Lecanemab remained stable in binding to PFs and globular oligomers, inhibiting the formation of large aggregates. These results provide direct evidence for the mechanism by which antibody drugs interfere with the Afl aggregation process.
Article
Chemistry, Multidisciplinary
Shin Morioka, Shoko Sato, Naoki Horikoshi, Tomoya Kujirai, Takuya Tomita, Yudai Baba, Takahiro Kakuta, Tomoki Ogoshi, Leonardo Puppulin, Ayumi Sumino, Kenichi Umeda, Noriyuki Kodera, Hitoshi Kurumizaka, Mikihiro Shibata
Summary: This study used high-speed atomic force microscopy to directly observe the subsecond dynamics of human H2A.Z.1-nucleosomes. The results showed that the nucleosomes can slide along 4 nm of DNA within 0.3 s in any direction. The interaction between the N-terminal region of H2A.Z.1 and the DNA was found to be responsible for nucleosome sliding.
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)
Article
Biochemistry & Molecular Biology
Tomoko Hirano, Kazuo Ebine, Takashi Ueda, Takumi Higaki, Takahiro Watanabe-Nakayama, Hiroki Konno, Hisako Takigawa-Imamura, Masa H. Sato
Summary: This study demonstrates that the SYP123-VAMP727-dependent secretion pathway plays a crucial role in delivering secondary cell wall components for the hardening of the subapical zone and shank of Arabidopsis root hairs. The localization of SYP123 at the plasma membrane is dependent on the production of phosphatidylinositol (PtdIns)(3,5)P2, and this pathway is involved in maintaining the tubular morphology of root hairs by transporting secondary cell wall components. The study highlights the importance of SYP123-VAMP727-mediated secretion in root hair elongation and maintenance.
Review
Biochemistry & Molecular Biology
Romain Amyot, Noriyuki Kodera, Holger Flechsig
Summary: Atomic force microscopy (AFM) and high-speed scanning have revolutionized real time observation of biomolecular dynamics, while post-experimental computational analysis has become increasingly important for interpreting resolution-limited imaging. The BioAFMviewer software provides an interactive user-friendly interface for simulation AFM, enabling researchers to infer the underlying 3D atomistic structures and advance molecular understanding beyond topographic imaging.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2023)
Article
Biophysics
Shintaroh Kubo, Kenichi Umeda, Noriyuki Kodera, Shoji Takada
Summary: The high-speed atomic force microscopy (HS-AFM) is a unique and prominent method to observe structural dynamics of biomolecules at single molecule level at near-physiological condition. In this study, a computational method was developed to detect and remove the parachuting artifact in HS-AFM images using the two-way scanning data.
BIOPHYSICS AND PHYSICOBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Akihito Nishiyama, Masahiro Shimizu, Tomoyuki Narita, Noriyuki Kodera, Yuriko Ozeki, Akira Yokoyama, Kouta Mayanagi, Takehiro Yamaguchi, Mariko Hakamata, Amina Kaboso Shaban, Yoshitaka Tateishi, Kosuke Ito, Sohkichi Matsumoto
Summary: The DNA-binding protein 1 (MDP1) of mycobacteria induces dormancy phenotypes by compacting DNA through reversible cross-linking of adjacent DNA strands using the intrinsically disordered region (IDR). This IDR-mediated DNA compaction model helps in understanding the molecular mechanism of MDP1 suppression of genomic function in non-replicating dormant mycobacteria.
NUCLEIC ACIDS RESEARCH
(2023)