A5059101377- Force Microscopy Techniques and Applications
- Protein Structure and Dynamics
- Advanced Electron Microscopy Techniques and Applications
- RNA and protein synthesis mechanisms
- Lipid Membrane Structure and Behavior
- Ion channel regulation and function
- Neuroscience and Neuropharmacology Research
- Enzyme Structure and Function
- Hepatitis C virus research
- Microtubule and mitosis dynamics
- Integrated Circuits and Semiconductor Failure Analysis
- Cardiomyopathy and Myosin Studies
- Ubiquitin and proteasome pathways
- Cancer-related Molecular Pathways
- Molecular Junctions and Nanostructures
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Cold Atom Physics and Bose-Einstein Condensates
- Advanced Fluorescence Microscopy Techniques
- RNA Interference and Gene Delivery
- stochastic dynamics and bifurcation
- Advanced Chemical Physics Studies
- Quantum and electron transport phenomena
- Biochemical and Molecular Research
- HIV Research and Treatment
Life Science Institute
2018-2024
Kanazawa University
2018-2024
Hiroshima University
2014-2017
Fritz Haber Institute of the Max Planck Society
2007-2016
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, scanning tip probes only molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework reconstruct 3D atomistic structures AFM scans, employing simulation and automatized fitting experimental images. We provide applications images ranging...
We provide a stand-alone software, the BioAFMviewer, which transforms biomolecular structures into graphical representation corresponding to outcome of atomic force microscopy (AFM) experiments. The AFM graphics is obtained by performing simulated scanning over molecular structure encoded in PDB file. A versatile viewer integrates visualization and control their orientation, while synchronized with variable spatial resolution tip-shape geometry produces graphics. demonstrate applicability...
Abstract Transmembrane protein 16 F (TMEM16F) is a Ca 2+ -activated homodimer which functions as an ion channel and phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, mechanism activation substrate translocation remains controversial, possibly due to restrictions in accessible conformational space. In this study, we use atomic force under physiological conditions reveal range structurally mechanically diverse assemblies,...
Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting in silico synthetic structures, which, as principal element allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar coarse-grained models real proteins. A strategy evolutionary optimization was...
High-speed atomic force microscopy (HS-AFM) is a powerful tool for visualizing the dynamics of individual biomolecules. However, in single-molecule HS-AFM imaging applications, x,y-scanner ranges are typically restricted to few hundred nanometers, preventing overview observation larger molecular assemblies, such as 2-dimensional protein crystal growth or fibrillar aggregation. Previous advances scanner design using mechanical amplification piezo-driven x,y-positioning system have extended...
While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks calculations on supercomputers. Surprisingly, many aspects operation can be however already reproduced by using very simple mechanical models elastic networks. The analysis suggests that, similar other self-organized systems, functional collective dynamics in such proteins is effectively reduced low-dimensional attractive manifold.
Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) plays a pivotal role in synaptic plasticity. It is dodecameric serine/threonine that has been highly conserved across metazoans for over million years. Despite the extensive knowledge of mechanisms underlying CaMKII activation, its behavior at molecular level remained unobserved. In this study, we used high-speed atomic force microscopy to visualize activity-dependent structural dynamics rat/hydra/ C. elegans with nanometer resolution....
Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with and ATP, constructed. Using such mechanical model, entire operation cycles an important protein machine could be followed in structurally resolved simulations. Ratcheting inchworm translocation spring-loaded unwinding, suggested by experimental data, were reproduced. Thus, feasibility...
Overexpression of the vitamin D3-inactivating enzyme CYP24A1 (cytochrome P450 family 24 subfamily and hereafter referred to as CYP24) can cause chronic kidney diseases, osteoporosis, several types cancers. Therefore, CYP24 inhibition has been considered a potential therapeutic approach. Vitamin D3 mimetics small molecule inhibitors have shown be effective, but nonspecific binding, drug resistance, toxicity limit their effectiveness. We identified novel 70-nt DNA aptamer-based inhibitor by...
α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid glutamate receptors (AMPARs) enable rapid excitatory synaptic transmission by localizing to the postsynaptic density of glutamatergic spines. AMPARs possess large extracellular N-terminal domains (NTDs), which are crucial for AMPAR clustering at sites. However, dynamics NTDs and molecular mechanism governing their remain elusive. Here, we employed high-speed atomic force microscopy (HS-AFM) directly visualize conformational in GluA2...
Laminins are trimeric glycoproteins with important roles in cell-matrix adhesion and tissue organization. The laminin α, ß, γ-chains have short N-terminal arms, while their C-termini connected via a triple coiled-coil domain, giving the molecule well-characterized cross-shaped morphology as result. C-terminus of alpha chains contains additional globular G-like (LG) domains mediating cell adhesion. Dynamic conformational changes different been implicated regulating function, but so far not...
Helicases are motor proteins that play a central role in the metabolism of DNA and RNA biological cells. Using energy ATP molecules, they able to translocate along nucleic acids unwind their duplex structure. They have been extensively characterized past grouped into superfamilies based on structural similarities sequential motifs. However, functional aspects mechanism operation not yet well understood. Here, we consider three helicases from major superfamily 2--Hef, Hel308 XPD--and study...
Ubiquitin (Ub) ligases E3 are important factors in selecting target proteins for ubiquitination and determining the type of polyubiquitin chains on proteins. In HECT (homologous to E6AP C-terminus)-type ligases, domain is composed an N-lobe a C-lobe that connected by flexible hinge loop. The large conformational rearrangement via loop essential HECT-type E3-mediated Ub transfer from E2 protein. However, detailed insights into structural dynamics remain unclear. Here, we provide first direct...
Transcription activator-like effectors (TALEs) are DNA-related proteins that recognise and bind specific target sequences to manipulate gene expression. Recently determined crystal structures show their common architecture reveals a superhelical overall structure may undergo drastic conformational changes. To establish link between dynamics in TALE we have employed coarse-grained elastic-network modelling of currently available structural data implemented force-probe setup allowed us...
ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding their activity is still hampered since conformational dynamics underlying operation such cannot yet be resolved in detailed molecular studies. Here a coarse grained model allows to mimic binding nucleotides and follow subsequent motions full-length transporter structures computer simulations proposed implemented....
Abstract Transcription activator-like effector (TALE) nuclease (TALEN) is widely used as a tool in genome editing. The DNA binding part of TALEN consists tandem array TAL-repeats that form right-handed superhelix. Each TAL-repeat recognises specific base by the repeat variable diresidue (RVD) at positions 12 and 13. comprising with periodic mutations to residues 4 32 (non-RVD sites) each (VT-TALE) exhibits increased efficacy editing compared counterpart without (CT-TALE). molecular basis for...
Protein molecular motors play a fundamental role in biological cells and development of their synthetic counterparts is major challenge. Here, we show how model motor system with the operation mechanism resembling that muscle myosin can be designed at concept level, without addressing implementation aspects. The constructed as an elastic network, similar to coarse-grained descriptions used for real proteins. We by numerical simulations operate deterministic or Brownian ratchet there...
Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, off-target observed in sequences with some homology to target still represents a major limitation for more widespread use of Cas9 biology medicine. For this reason, complete understanding dynamics binding, interrogation is crucial improve efficiency genome editing. Here, we high-speed atomic force microscopy (HS-AFM) investigate Staphylococcus aureus (SaCas9) its cleavage. Upon single-guide...