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Biophysics and Physicobiology

Hiroyuki Kitahata, Masanobu Tanaka
Spiral waves are observed in wide variety of reaction-diffusion systems. Those observed in cardiac tissues are important since they are related to serious disease that threatens human lives, such as atrial or ventricular fibrillation. We consider the unpinning of spiral waves anchored to a circular obstacle on excitable media using high-frequency pacing. Here, we consider two types of the obstacle; i.e. , that without any diffusive interaction with the environment, and that with diffusive interaction. We found that the threshold frequency for success in unpinning is lower for the obstacle with diffusive interaction than for the one without it...
2018: Biophysics and Physicobiology
Kazuhiro Maeshima, Sachiko Tamura, Yuta Shimamoto
The nucleus in eukaryotic cells is the site for genomic functions such as RNA transcription, DNA replication, and DNA repair/recombination. However, the nucleus is subjected to various mechanical forces associated with diverse cellular activities, including contraction, migration, and adhesion. Although it has long been assumed that the lamina structure, underlying filamentous mesh-work of the nuclear envelope, plays an important role in resisting mechanical forces, the involvement of compact chromatin in mechanical resistance has also recently been suggested...
2018: Biophysics and Physicobiology
Keiichi Kojima, Hiroshi C Watanabe, Satoko Doi, Natsuki Miyoshi, Misaki Kato, Hiroshi Ishikita, Yuki Sudo
Anion channelrhodopsin-2 (ACR2), a light-gated channel recently identified from the cryptophyte alga Guillardia theta , exhibits anion channel activity with exclusive selectivity. In addition to its novel function, ACR2 has become a focus of interest as a powerful tool for optogenetics. Here we combined experimental and computational approaches to investigate the roles of conserved carboxylates on the anion transport activity of ACR2 in Escherichia coli membrane. First, we replaced six conserved carboxylates with a neutral residue (i...
2018: Biophysics and Physicobiology
Hiroyuki Terashima, Katsumi Imada
Type III secretion system (T3SS) is a protein translocator complex family including pathogenic injectisome or bacterial flagellum. The inejectisomal T3SS serves to deliver virulence proteins into host cell and the flagellar T3SS constructs the flagellar axial structure. Although earlier studies have provided many findings on the molecular mechanism of the Type III protein export, they were not sufficient to reveal energy transduction mechanism due to difficulties in controlling measurement conditions in vivo ...
2018: Biophysics and Physicobiology
Ryosuke Iwai, Kota Kasahara, Takuya Takahashi
The replica-exchange molecular dynamics (REMD) method has been used for conformational sampling of various biomolecular systems. To maximize sampling efficiency, some adjustable parameters must be optimized. Although it is agreed that shorter intervals between the replica-exchange attempts enhance traversals in the temperature space, details regarding the artifacts caused by these short intervals are controversial. In this study, we revisit this problem by performing REMD simulations on an alanine octapeptide in an implicit solvent...
2018: Biophysics and Physicobiology
Tadashi Nakashima, Hajime Mushiake, Kazuhiro Sakamoto
An individual's personality develops through a combination of experiences and parental inheritance. When faced with a conflict, will an individual take an innate behavior or a learned one? In such situations, individuality will manifest itself. Here, we focused on turn alternation behavior, which is a habitual tendency to turn in the direction opposite the preceding turn, in earthworms ( Eisenia fetida ) and examined how this behavior is affected by an aversive stimulus. Of 10 earthworms, 3 were affected by the stimulus...
2018: Biophysics and Physicobiology
Fumio Oosawa
An enormous amount of research has been performed to characterize actin dynamics. Structural biology investigations have determined the localization of main chains and their changes coupled with G (Globular)-F (Filamentous) transformation of actin, whereas local thermal fluctuations that may be caused by free rotations of the tips of side chains are not yet fully investigated. This paper argues if the entropy change of actin accompanied by the G-F transformation is simply attributable to the changes in hydration...
2018: Biophysics and Physicobiology
Sumita Das, Tomoki P Terada, Masaki Sasai
When three cyanobacterial proteins, KaiA, KaiB, and KaiC, are incubated with ATP in vitro, the phosphorylation level of KaiC hexamers shows stable oscillation with approximately 24 h period. In order to understand this KaiABC clockwork, we need to analyze both the macroscopic synchronization of a large number of KaiC hexamers and the microscopic reactions and structural changes in individual KaiC molecules. In the present paper, we explain two coarse-grained theoretical models, the many-molecule (MM) model and the single-molecule (SM) model, to bridge the gap between macroscopic and microscopic understandings...
2018: Biophysics and Physicobiology
Hitoshi Aonuma, Yuki Totani, Manabu Sakakibara, Ken Lukowiak, Etsuro Ito
To find a causal mechanism of learning and memory is a heuristically important topic in neuroscience. In the pond snail Lymnaea stagnalis , the following experimental facts have accrued regarding a classical conditioning procedure known as conditioned taste aversion (CTA): (1) one-day food-deprived Dutch snails have superior CTA memory formation; (2) the one-day food-deprived snails have a low monoamine content (e.g., serotonin, dopamine, octopamine) in their central nervous system (CNS); (3) fed or five-day food-deprived snails have poorer CTA memory and a higher monoamine content; (4) the Dutch snails form better CTA memory than the Canadian TC1 strain; and, (5) the F1 cross snails between the Dutch and Canadian TC1 strains also form poor CTA memory...
2018: Biophysics and Physicobiology
Yoshiaki Kinosita, Takayuki Nishizaka
In many microorganisms helical structures are important for motility, e.g., bacterial flagella and kink propagation in Spiroplasma eriocheiris . Motile archaea also form a helical-shaped filament called the 'archaellum' that is functionally equivalent to the bacterial flagellum, but structurally resembles type IV pili. The archaellum motor consists of 6-8 proteins called fla accessory genes, and the filament assembly is driven by ATP hydrolysis at catalytic sites in FlaI. Remarkably, previous research using a dark-field microscopy showed that right-handed filaments propelled archaeal cells forwards or backwards by clockwise or counterclockwise rotation, respectively...
2018: Biophysics and Physicobiology
Kei Yura
No abstract text is available yet for this article.
2018: Biophysics and Physicobiology
Hiroyuki Iwamoto
We studied the effect of myosin inhibitors, N-benzyl-p-toluenesulfonamide (BTS), blebbistatin, and butanedione monoxime (BDM) on X-ray diffraction patterns from rabbit psoas fibers under relaxing and contracting conditions. The first two inhibitors suppressed the contractile force almost completely at a 100 μM concentration, and a similar effect was obtained at 50 mM for BDM. However, still substantial changes were observed in the diffraction patterns upon calcium-activation of inhibited muscle fibers. (1) The 2nd actin layer-line reflection was enhanced normally, indicating that calcium binding to troponin and the subsequent movement of tropomyosin are not inhibited, (2) the myosin layer-line reflections became much weaker, and (3) the 1,1/1,0 intensity ratio of the equatorial reflections was increased...
2018: Biophysics and Physicobiology
Masami Ikeda, Minoru Sugihara, Makiko Suwa
We report the development of the SEVENS database, which contains information on G-protein coupled receptor (GPCR) genes that are identified with high confidence levels (A, B, C, and D) from various eukaryotic genomes, by using a pipeline comprising bioinformatics softwares, including a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS compiles detailed information on GPCR genes, such as chromosomal mapping position, phylogenetic tree, sequence similarity to known genes, and protein function described by motif/domain and transmembrane helices...
2018: Biophysics and Physicobiology
Akiko Higuchi, Naoki Nonaka, Kei Yura
Membrane transporter proteins play important roles in transport of nutrients into the cell, in transport of waste out of the cell, in maintenance of homeostasis, and in signal transduction. Solute carrier (SLC) transporter is the superfamily, which has the largest number of genes (>400 in humans) in membrane transporter and consists of 52 families. SLC transporters carry a wide variety of substrates such as amino acids, peptides, saccharides, ions, neurotransmitters, lipids, hormones and related materials...
2018: Biophysics and Physicobiology
Miki H Maeda, Tomoki Yonezawa, Tomomi Komaba
We have developed a three-dimensional structure database of natural metabolites (3DMET). Early development of the 3DMET database relied on content auto-generated from 2D-structures of other chemical databases. From 2009, we began manual curation, obtaining new compounds from published works. In the process of curation, problems of digitizing 3D-structures from structure drawings of documents were accumulated. As the same as auto-generation, structure drawings should be also payed attention about stereochemistry...
2018: Biophysics and Physicobiology
Shigeki Mitaku, Ryusuke Sawada
Organisms generally display two contrasting properties: large biodiversity and a uniform state of "life". In this study, we focused on the question of how genome sequences describe "life" where a large number of biomolecules are harmonized. We analyzed the whole genome sequence of 2664 organisms, paying attention to the nucleotide composition which is an intensive parameter from the genome sequence. The results showed that all organisms were plotted in narrow regions of the nucleotide composition space of the first and second letters of the codon...
2018: 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
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