journal
https://read.qxmd.com/read/38362318/introduction-of-session-2-advanced-methods-for-retinal-proteins
#21
JOURNAL ARTICLE
Takayuki Uchihashi, Hideki Kandori
No abstract text is available yet for this article.
March 21, 2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38362317/dieter-oesterhelt-1940-2022-life-with-light-and-color-pioneer-of-membrane-protein-research
#22
Peter Hegemann, Hartmut Michel
No abstract text is available yet for this article.
March 21, 2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38362316/optogenetics-ii-sponsored-by-jst-report-for-the-session-13
#23
JOURNAL ARTICLE
Hiroo Imai, Hideki Kandori
No abstract text is available yet for this article.
March 21, 2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38362315/from-activation-dynamics-to-functional-diversity-of-retinal-proteins-report-for-the-session-3-at-the-19-th-international-conference-on-retinal-proteins
#24
JOURNAL ARTICLE
Chii-Shen Yang, Mikio Kataoka
No abstract text is available yet for this article.
March 21, 2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38362314/recent-advances-in-signaling-and-activation-mechanism-in-microbial-rhodopsins-report-for-the-session-6-at-the-19-th-international-conference-on-retinal-proteins
#25
JOURNAL ARTICLE
Kazumi Shimono, Norbert A Dencher
No abstract text is available yet for this article.
March 21, 2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496247/calculations-of-the-binding-free-energies-of-the-comprehensive-in-vitro-proarrhythmia-assay-cipa-reference-drugs-to-cardiac-ion-channels
#26
JOURNAL ARTICLE
Tatsuki Negami, Tohru Terada
The evaluation of the inhibitory activities of drugs on multiple cardiac ion channels is required for the accurate assessment of proarrhythmic risks. Moreover, the in silico prediction of such inhibitory activities of drugs on cardiac channels can improve the efficiency of the drug-development process. Here, we performed molecular docking simulations to predict the complex structures of 25 reference drugs that were proposed by the Comprehensive in vitro Proarrhythmia Assay consortium using two cardiac ion channels, the human ether-a-go-go-related gene (hERG) potassium channel and human NaV 1...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496246/identification-and-structural-basis-of-an-enzyme-that-degrades-oligosaccharides-in-caramel
#27
JOURNAL ARTICLE
Toma Kashima, Akihiro Ishiwata, Kiyotaka Fujita, Shinya Fushinobu
Cooking with fire produces foods containing carbohydrates that are not naturally occurring, such as α-d-fructofuranoside found in caramel. Each of the hundreds of compounds produced by caramelization reactions is considered to possess its own characteristics. Various studies from the viewpoints of biology and biochemistry have been conducted to elucidate some of the scientific characteristics. Here, we review the composition of caramelized sugars and then describe the enzymatic studies that have been conducted and the physiological functions of the caramelized sugar components that have been elucidated...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496245/ring-formation-by-vibrio-fusion-protein-composed-of-flif-and-flig-ms-ring-and-c-ring-component-of-bacterial-flagellar-motor-in-membrane
#28
JOURNAL ARTICLE
Kanji Takahashi, Tatsuro Nishikino, Hiroki Kajino, Seiji Kojima, Takayuki Uchihashi, Michio Homma
The marine bacterium Vibrio alginolyticus has a single flagellum as a locomotory organ at the cell pole, which is rotated by the Na+ -motive force to swim in a liquid. The base of the flagella has a motor composed of a stator and rotor, which serves as a power engine to generate torque through the rotor-stator interaction coupled to Na+ influx through the stator channel. The MS-ring, which is embedded in the membrane at the base of the flagella as part of the rotor, is the initial structure required for flagellum assembly...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496244/controlling-complex-dynamical-systems-based-on-the-structure-of-the-networks
#29
JOURNAL ARTICLE
Atsushi Mochizuki
Progress of molecular biology resulted in the accumulation of information on biomolecular interactions, which are complex enough to be termed as networks. Dynamical behavior generated by complex network systems is considered to be the origin of the biological functions. One of the largest missions in modern life science is to obtain logical understanding for the dynamics of complex systems based on experimentally identified networks. However, a network does not provide sufficient information to specify dynamics explicitly, i...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496243/quantitative-analysis-of-protein-dynamics-using-a-deep-learning-technique-combined-with-experimental-cryo-em-density-data-and-md-simulations
#30
JOURNAL ARTICLE
Shigeyuki Matsumoto, Shoichi Ishida, Kei Terayama, Yasuhshi Okuno
Protein functions associated with biological activity are precisely regulated by both tertiary structure and dynamic behavior. Thus, elucidating the high-resolution structures and quantitative information on in-solution dynamics is essential for understanding the molecular mechanisms. The main experimental approaches for determining tertiary structures include nuclear magnetic resonance (NMR), X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Among these procedures, recent remarkable advances in the hardware and analytical techniques of cryo-EM have increasingly determined novel atomic structures of macromolecules, especially those with large molecular weights and complex assemblies...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496242/phone2sas-3d-scanning-by-smartphone-aids-the-realization-of-small-angle-scattering
#31
JOURNAL ARTICLE
Hiroshi Imamura
Small-angle scattering (SAS) is a powerful tool for the detailed structural analysis of objects at the nanometer scale. In contrast to techniques such as electron microscopy, SAS data are presented as reciprocal space information, which hinders the intuitive interpretation of SAS data. This study presents a workflow: (1) creating objects, (2) 3D scanning, (3) the representation of the object as point clouds on a laptop, (4) computation of a distance distribution function, and (5) computation of SAS, executed via the computer program Phone2SAS...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496241/mathematical-model-of-structural-changes-in-nuclear-speckle
#32
JOURNAL ARTICLE
Shingo Wakao, Noriko Saitoh, Akinori Awazu
Nuclear speckles are nuclear bodies consisting of populations of small and irregularly shaped droplet-like molecular condensates that contain various splicing factors. Recent experiments have revealed the following structural features of nuclear speckles: (I) Each molecular condensate contains SON and SRRM2 proteins, and MALAT 1 non-coding RNA surrounds these condensates; (II) During normal interphase of the cell cycle in multicellular organisms, these condensates are broadly distributed throughout the nucleus...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496240/guideline-for-design-of-substrate-stiffness-for-mesenchymal-stem-cell-culture-based-on-heterogeneity-of-yap-and-runx2-responses
#33
JOURNAL ARTICLE
Hiromi Miyoshi, Masashi Yamazaki, Hiromichi Fujie, Satoru Kidoaki
Mesenchymal stem cells (MSCs) have the potential for self-renewal and multipotency to differentiate into various lineages. Thus, they are of great interest in regenerative medicine as a cell source for tissue engineering. Substrate stiffness is one of the most extensively studied exogenous physical factors; however, consistent results have not always been reported for controlling MSCs. Conventionally used stiff culture substrates, such as tissue-culture polystyrene and glass, enhance nuclear localization of a mechanotransducer YAP and a pre-osteogenic transcription factor RUNX2, and bias MSCs towards the osteogenic lineage, even without osteogenic-inducing soluble factors...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496239/why-we-are-made-of-proteins-and-nucleic-acids-structural-biology-views-on-extraterrestrial-life
#34
JOURNAL ARTICLE
Shunsuke Tagami
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496238/mathematical-model-for-promotion-of-wound-closure-with-atp-release
#35
JOURNAL ARTICLE
Kenta Odagiri, Hiroshi Fujisaki, Hiroya Takada, Rei Ogawa
To computationally investigate the recent experimental finding such that extracellular ATP release caused by exogeneous mechanical forces promote wound closure, we introduce a mathematical model, the Cellular Potts Model (CPM), which is a popular discretized model on a lattice, where the movement of a "cell" is determined by a Monte Carlo procedure. In the experiment, it was observed that there is mechanosensitive ATP release from the leading cells facing the wound gap and the subsequent extracellular Ca2+ influx...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496237/methods-to-spontaneously-generate-three-dimensionally-arrayed-microdroplets-triggered-by-capillarity-for-bioassays-and-bioengineering
#36
JOURNAL ARTICLE
Hiroki Yasuga
Herein, I review our recent work toward developing methods for generating three-dimensional (3D) droplet arrays driven by capillarity. Microdroplet array-based systems are useful for bioassays and bioengineering because they require only small amounts of samples and reagents and provide the high throughput. Various methods have been developed for preparing droplet arrays, among which methods based on capillarity have attracted considerable attention owing to their simplicity. I and collaborators have developed such methods based on capillary flow, including a method for preparing droplet arrays via oil-water replacement...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496236/lov2-based-photoactivatable-camkii-and-its-application-to-single-synapses-local-optogenetics
#37
JOURNAL ARTICLE
Yutaro Nagasawa, Hiromi H Ueda, Haruka Kawabata, Hideji Murakoshi
Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the "high spatial resolution" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38496235/general-anesthetic-binding-mode-via-hydration-with-weak-affinity-and-molecular-discrimination-general-anesthetic-dissolution-in-interfacial-water-of-the-common-binding-site-of-gaba-a-receptor
#38
JOURNAL ARTICLE
Tomoyoshi Seto
The GABAA receptor (GABAA R) is a target channel for the loss of awareness of general anesthesia. General anesthetic (GA) spans a wide range of chemical structures, such as monatomic molecules, barbital acids, phenols, ethers, and alkanes. GA has a weak binding affinity, and the affinity has a characteristic that correlates with the solubility in olive oil rather than the molecular shape. The GA binding site of GABAA R is common to GAs and exists in the transmembrane domain of the GABAA R intersubunit. In this study, the mechanism of GA binding, which allows binding of various GAs with intersubunit selectivity, was elucidated from the hydration analysis of the binding site...
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38344038/announcement-of-bppb-paper-awards-2023
#39
JOURNAL ARTICLE
Haruki Nakamura
No abstract text is available yet for this article.
2023: Biophysics and Physicobiology
https://read.qxmd.com/read/38344037/bottom-up-creation-of-cell-free-molecular-systems-basic-research-toward-social-implementation
#40
JOURNAL ARTICLE
Izuru Kawamura, Ryuji Kawano, Tomoaki Matsuura
No abstract text is available yet for this article.
2023: Biophysics and Physicobiology
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