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Biophysics and Physicobiology

Keisuke Arikawa
We propose methods for directly analyzing structural compliance (SC) properties of elastic network models of proteins, and we also propose methods for extracting information about motion properties from the SC properties. The analysis of SC properties involves describing the relationships between the applied forces and the deformations. When decomposing the motion according to the magnitude of SC (SC mode decomposition), we can obtain information about the motion properties under the assumption that the lower SC mode motions or the softer motions occur easily...
2018: Biophysics and Physicobiology
Ken H Nagai
Self-propelled rods, which propel by themselves in the direction from the tail to the head and align nematically through collision, have been well-investigated theoretically. Various phenomena including true long-range ordered phase with the Giant number fluctuations, and the collective motion composed of many vorices were predicted using the minimal mathematical models of self-propelled rods. Using filamentous bacteria and running microtubules, we found that the predicted phenomena by the minimal models occur in the real world...
2018: Biophysics and Physicobiology
Hiroki Nagashima, Mizue Asada, Hiroyuki Mino
The electronic structure of manganese (Mn) cluster in photosystem II was investigated by electron paramagnetic resonance (EPR) spectroscopy. In order to determine the spin density distribution in magnetically coupled Mn in the S2 state Mn cluster, pulsed electron-electron double resonance (PELDOR) measurement was performed. The local environment of the Mn cluster was investigated by electron-nuclear double resonance (ENDOR). Using spin projections determined by PELDOR, ENDOR signals were assigned to the water molecules ligated to the Mn cluster...
2018: Biophysics and Physicobiology
Mitsuhiko Odera, Tadaomi Furuta, Yoshiro Sohma, Minoru Sakurai
Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that belongs to the ATP binding cassette protein superfamily. Deletion of phenylalanine at position 508 (ΔF508) is the most common CF-associated mutation and is present in nearly 90% of CF patients. Currently, atomistic level studies are insufficient for understanding the mechanism by which the deletion of a single amino acid causes greatly reduced folding as well as trafficking and gating defects. To clarify this mechanism, we first constructed an atomic model of the inward-facing ΔF508-CFTR and performed allatom molecular dynamics (MD) simulations of the protein in a membrane environment...
2018: Biophysics and Physicobiology
Takashi Fujii, Hideyuki Matsunami, Yumi Inoue, Keiichi Namba
The bacterial flagellar hook is a short, highly curved tubular structure connecting the basal body as a rotary motor and the filament as a helical propeller to function as a universal joint to transmit motor torque to the filament regardless of its orientation. This highly curved form is known to be part of a supercoil as observed in the polyhook structure. The subunit packing interactions in the Salmonella hook structure solved in the straight form gave clear insights into the mechanisms of its bending flexibility and twisting rigidity...
2018: Biophysics and Physicobiology
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
Photolyases (PHRs) and cryptochromes (CRYs) belong to the same family known as blue-light photoreceptors. Although their amino acid sequences and corresponding structures are similar to each other, they exert different functions. PHRs function as an enzyme to repair UV-induced deoxyribonucleic acid (DNA) lesions such as a cyclobutane pyrimidine dimer (CPD) and a (6-4) photoproduct ((6-4)pp), whereas CRYs are a circadian photoreceptor in plants and animals and at the same time they control the photoperiodic induction of flowering in plants...
2018: Biophysics and Physicobiology
Yoichi Nakatani, Osamu Hisatomi
Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida . Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light-oxygen-voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states...
2018: Biophysics and Physicobiology
Akira Kitamura, Masataka Kinjo
Fluorescence recovery after photobleaching (FRAP) enables characterization of quantitative dynamic properties such as diffusion coefficients of fluorescent molecules in living cells by analyzing the recovery of fluorescence intensity after photobleaching in a specific cellular compartment or area. To quantitatively determine high intracellular diffusion coefficients, a suitable optical system as well as an appropriate model for fast diffusion analysis is necessary. Here, we propose a procedure to quantify the diffusion coefficient of rapidly-diffusing fluorescent molecules that makes use of an epi-fluorescence microscope with a photobleaching laser in combination with established models for diffusion analysis...
2018: Biophysics and Physicobiology
Daisuke Miyashiro, Misato Ohtsuki, Yuta Shimamoto, Jun'ichi Wakayama, Yuki Kunioka, Takakazu Kobayashi, Shin'ichi Ishiwata, Takenori Yamada
We have studied the stiffness of myofilament lattice in sarcomeres in the pre-force generating state, which was realized by a relaxing reagent, BDM (butane dione monoxime). First, the radial stiffness for the overlap regions of sarcomeres of isolated single myofibrils was estimated from the resulting decreases in diameter by osmotic pressure applied with the addition of Dextran. Then, the radial stiffness was also estimated from force-distance curve measurements with AFM technology. The radial stiffness for the overlap regions thus obtained was composed of a soft and a rigid component...
2017: Biophysics and Physicobiology
Hiroshi Hashimoto, Asami Hishiki, Kodai Hara, Sotaro Kikuchi
DNA damage tolerance (DDT) is a cell function to avoid replication arrest by DNA damage during DNA replication. DDT includes two pathways, translesion DNA synthesis (TLS) and template-switched DNA synthesis (TS). DDT is regulated by ubiquitination of proliferating cell nuclear antigen that binds to double-stranded DNA and functions as scaffold protein for DNA metabolism. TLS is transient DNA synthesis using damaged DNA as a template by error-prone DNA polymerases termed TLS polymerases specialized for DNA damage...
2017: Biophysics and Physicobiology
Hiroyuki Terashima, Akihiro Kawamoto, Yusuke V Morimoto, Katsumi Imada, Tohru Minamino
The bacterial flagellum is a supramolecular motility machine consisting of the basal body as a rotary motor, the hook as a universal joint, and the filament as a helical propeller. Intact structures of the bacterial flagella have been observed for different bacterial species by electron cryotomography and subtomogram averaging. The core structures of the basal body consisting of the C ring, the MS ring, the rod and the protein export apparatus, and their organization are well conserved, but novel and divergent structures have also been visualized to surround the conserved structure of the basal body...
2017: Biophysics and Physicobiology
Kazuho Yoshida, Takahiro Yamashita, Kengo Sasaki, Keiichi Inoue, Yoshinori Shichida, Hideki Kandori
We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template...
2017: Biophysics and Physicobiology
Shota Kondo, Michio Homma, Seiji Kojima
Vibrio alginolyticus normally has a single polar flagellum whose number and placement are regulated positively by FlhF. FlhF is a GTPase and homolog of a signal recognition particle (SRP) protein called Ffh and SRP receptor FtsY. FlhF is located at the cell pole and directs formation of the flagellum. To study the mechanism of FlhF localization, we introduced random mutations into flhF by means of hydroxylamine and isolated mutants that could not generate the flagellum at the cell pole. The novel mutations were only mapped to the GTPase motif of FlhF...
2017: Biophysics and Physicobiology
Naoki Arai, Tadaomi Furuta, Minoru Sakurai
Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces...
2017: Biophysics and Physicobiology
Eiji Yamamoto
Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes...
2017: Biophysics and Physicobiology
Toshifumi Kumai
It is established knowledge that the action potential event of nerves is formed by the combination of a phasic inward Na(+) current and a following outward K(+) current which increases gradually. These changes in current are commonly referred to as conductance changes of channels for Na(+) and K(+) with time. On the other hand, electric requirements for action potential generation in phenomena such as anode break excitation, hyperpolarizing break stimulation and accommodation, strongly suggest an existence of an inductance factor in the plasma membrane of nerves...
2017: Biophysics and Physicobiology
Ayumi Hashimoto, Toyohiro Sawada, Kiyohisa Natsume
The study aimed to determine whether and how the activation of the acetylcholine receptor affects epileptiform discharges in the CA3 region in a rat hippocampus. Picrotoxin (100 μM), a GABAA receptor antagonist, was applied to a hippocampal slice to induce epileptiform discharges. The effects of the cholinergic agonist, carbachol, on the discharges were examined at the several concentrations (1-30 μM). Carbachol had different impacts on epileptiform discharges at the different concentrations. Relatively low concentrations of carbachol (<10 μM) increased the frequency but decreased the amplitude of the discharges...
2017: Biophysics and Physicobiology
Mikihiro Shibata, Hiroki Watanabe, Takayuki Uchihashi, Toshio Ando, Ryohei Yasuda
Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell...
2017: Biophysics and Physicobiology
Hiroaki Machiyama, Takamitsu J Morikawa, Kazuko Okamoto, Tomonobu M Watanabe, Hideaki Fujita
We evaluated usability of a previously developed genetically encoded molecular crowding sensor in various biological phenomena. Molecular crowding refers to intracellular regions that are occupied more by proteins and nucleotides than by water molecules and is thought to have a strong effect on protein function. To evaluate intracellular molecular crowding, usually the diffusion coefficient of a probe is used because it is related to mobility of the surrounding molecular crowding agents. Recently, genetically encoded molecular crowding sensors based on Förster resonance energy transfer were reported...
2017: Biophysics and Physicobiology
Yutaro Yamada, Hiroki Konno, Katsuya Shimabukuro
In this study, we present a new technique called correlative atomic force and transmission electron microscopy (correlative AFM/TEM) in which a targeted region of a sample can be observed under AFM and TEM. The ultimate goal of developing this new technique is to provide a technical platform to expand the fields of AFM application to complex biological systems such as cell extracts. Recent advances in the time resolution of AFM have enabled detailed observation of the dynamic nature of biomolecules. However, specifying molecular species, by AFM alone, remains a challenge...
2017: Biophysics and Physicobiology
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