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Biophysics and Physicobiology

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https://www.readbyqxmd.com/read/29955565/single-molecular-and-ensemble-level-oscillations-of-cyanobacterial-circadian-clock
#1
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
https://www.readbyqxmd.com/read/29955564/comparison-of-brain-monoamine-content-in-three-populations-of-lymnaea-that-correlates-with-taste-aversive-learning-ability
#2
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
https://www.readbyqxmd.com/read/29955563/cross-kymography-analysis-to-simultaneously-quantify-the-function-and-morphology-of-the-archaellum
#3
REVIEW
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
https://www.readbyqxmd.com/read/29904620/preface-of-special-issue-databases
#4
EDITORIAL
Kei Yura
No abstract text is available yet for this article.
2018: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/29892517/effects-of-myosin-inhibitors-on-the-x-ray-diffraction-patterns-of-relaxed-and-calcium-activated-rabbit-skeletal-muscle-fibers
#5
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
https://www.readbyqxmd.com/read/29892516/sevens-a-database-for-comprehensive-gpcr-genes-obtained-from-genomes-update-to-68-eukaryotes
#6
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
https://www.readbyqxmd.com/read/29892515/imusta4slc-database-for-the-structural-property-and-variations-of-solute-carrier-transporters
#7
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
https://www.readbyqxmd.com/read/29892514/chemical-curation-to-improve-data-accuracy-recent-development-of-the-3dmet-database
#8
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
https://www.readbyqxmd.com/read/29892513/biological-meaning-of-habitable-zone-in-nucleotide-composition-space
#9
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
https://www.readbyqxmd.com/read/29607281/theoretical-framework-for-analyzing-structural-compliance-properties-of-proteins
#10
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
https://www.readbyqxmd.com/read/29607280/collective-motion-of-rod-shaped-self-propelled-particles-through-collision
#11
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
https://www.readbyqxmd.com/read/29607279/magnetic-structure-of-manganese-cluster-in-photosystem-ii-investigated-by-electron-paramagnetic-resonance
#12
REVIEW
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
https://www.readbyqxmd.com/read/29607278/molecular-dynamics-simulation-study-on-the-structural-instability-of-the-most-common-cystic-fibrosis-associated-mutant-%C3%AE-f508-cftr
#13
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
https://www.readbyqxmd.com/read/29607277/evidence-for-the-hook-supercoiling-mechanism-of-the-bacterial-flagellum
#14
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
https://www.readbyqxmd.com/read/29450111/the-binding-structure-and-affinity-of-photodamaged-duplex-dna-with-members-of-the-photolyase-cryptochrome-family-a-computational-study
#15
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
https://www.readbyqxmd.com/read/29450110/quantitative-analyses-of-the-equilibria-among-dna-complexes-of-a-blue-light-regulated-bzip-module-photozipper
#16
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
https://www.readbyqxmd.com/read/29450109/determination-of-diffusion-coefficients-in-live-cells-using-fluorescence-recovery-after-photobleaching-with-wide-field-fluorescence-microscopy
#17
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
https://www.readbyqxmd.com/read/29362706/radial-stiffness-characteristics-of-the-overlap-regions-of-sarcomeres-in-isolated-skeletal-myofibrils-in-pre-force-generating-state
#18
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
https://www.readbyqxmd.com/read/29362705/structural-basis-for-the-molecular-interactions-in-dna-damage-tolerances
#19
REVIEW
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
https://www.readbyqxmd.com/read/29362704/structural-differences-in-the-bacterial-flagellar-motor-among-bacterial-species
#20
REVIEW
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
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