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Biophysics and Physicobiology

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https://read.qxmd.com/read/30775200/uncovering-dehydration-in-cytochrome-c-refolding-from-urea-and-guanidine-hydrochloride-denatured-unfolded-state-by-high-pressure-spectroscopy
#1
Shohei Konno, Kentaro Doi, Koichiro Ishimori
To investigate the dehydration associated with protein folding, the partial molar volume changes for protein unfolding (Δ V u ) in cytochrome c (Cyt c ) were determined using high pressure absorption spectroscopy. Δ V u values for the unfolding to urea- and guanidine hydrochloride (GdnHCl)-denatured Cyt c were estimated to be 56±5 and 29±1 mL mol-1 , respectively. Considering that the volume change for hydration of hydrophobic groups is positive and that Cyt c has a covalently bonded heme, a positive Δ V u reflects the primary contribution of the hydration of heme...
2019: Biophysics and Physicobiology
https://read.qxmd.com/read/30775199/dynamic-and-static-analyses-of-glass-like-properties-of-three-dimensional-tissues
#2
Hironobu Nogucci
The mechanical properties of tissues are influenced by those of constituent cells in various ways. For instance, it has been theoretically demonstrated that two-dimensional confluent tissues comprising mechanically uniform cells can undergo density-independent rigidity transitions, and analysis of the dynamical behavior of tissues near the critical point revealed that the transitions are geometrically controlled by the so-called cell shape parameter. To investigate whether three-dimensional tissues behave similarly to two-dimensional ones, we herein extend the previously developed model to three dimensions both dynamically and statically, demonstrating that two mechanical states similar to those of glassy materials exist in the three-dimensional case...
2019: Biophysics and Physicobiology
https://read.qxmd.com/read/30775198/millimeter-sized-belt-like-pattern-formation-of-actin-filaments-in-solution-by-interacting-with-surface-myosin-in-vitro
#3
Kentaro Ozawa, Hirotaka Taomori, Masayuki Hoshida, Ituki Kunita, Sigeru Sakurazawa, Hajime Honda
The movements of single actin filaments along a myosin-fixed glass surface were observed under a conventional fluorescence microscope. Although random at a low concentration, moving directions of filaments were aligned by the presence of over 1.0 mg/mL of unlabeled filaments. We found that actin filaments when at the intermediate concentrations ranging from 0.1 to 1.0 mg/mL, formed winding belt-like patterns and moved in a two-directional manner along the belts. These patterns were spread over a millimeter range and found to have bulged on the glass in a three-dimensional manner...
2019: Biophysics and Physicobiology
https://read.qxmd.com/read/30713826/forced-diffusion-of-water-molecules-through-aquaporin-5-biomembrane-a-molecular-dynamics-study
#4
Marzieh Alishahi, Reza Kamali
Aquaporins (AQPs) are protein channels located across the cell membrane which conduct the water permeation through the cell membrane. Different types of AQPs exist in human organs and play vital roles, as the malfunction of such protein membranes can lead to life-threatening conditions. A specific type of AQP, identified as AQP5, is particularly essential to the generation of saliva, tears and pulmonary secretions. We have adopted Molecular Dynamics (MD) simulation to analyze the water permeation and diffusion in AQP5 structure in a 0...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30713825/crystallographic-analysis-of-the-overlapping-dinucleosome-as-a-novel-chromatin-unit
#5
REVIEW
Masahiro Nishimura, Kayo Nozawa, Hitoshi Kurumizaka
Recent evidence has suggested that chromatin is not simply repeats of the canonical nucleosome, called the "octasome", but may include diverse repertoires of basic structural units. During the transcription process, a nucleosome is repositioned by a chromatin remodeler and collides with a neighboring nucleosome, thus creating an unusual nucleosome substructure termed the "overlapping dinucleosome". We previously developed a method for the large-scale preparation of the overlapping dinucleosome...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30713824/data-analytic-study-of-the-homothermal-maintenance-mechanism-of-skunk-cabbage-capturing-pre-equilibrium-characteristics-using-extended-poisson-model
#6
Shuji Kawasaki, Kikukatsu Ito
A wild plant called Skunk Cabbage is known to heat itself and keep its body warm before spring. We study its homothermal maintenance mechanism from a mesoscopic point of view. We take the increment process of the temperature time series and consider it as 'elastic' force that always tries to backlash its temperature to an intrinsic target temperature. We then propose a kind of extended Poisson distribution for the model of the 'elastic' force. The hypothesis testing result by Kolmogorov-Smirnov test suggests that the proposed distribution is a plausible candidate of the model for the 'elastic' force, on the temperature range in which the system is in equillibrium...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30450272/fluorescent-nanodiamonds-as-a-robust-temperature-sensor-inside-a-single-cell
#7
Takeharu Sekiguchi, Shingo Sotoma, Yoshie Harada
Thermometers play an important role to study the biological significance of temperature. Fluorescent nanodiamonds (FNDs) with negatively-charged nitrogen-vacancy centers, a novel type of fluorescence-based temperature sensor, have physicochemical inertness, low cytotoxicity, extremely stable fluorescence, and unique magneto-optical properties that allow us to measure the temperature at the nanoscale level inside single cells. Here, we demonstrate that the thermosensing ability of FNDs is hardly influenced by environmental factors, such as pH, ion concentration, viscosity, molecular interaction, and organic solvent...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30450271/verification-of-the-effect-of-the-axon-fluid-as-a-highly-dielectric-medium-in-the-high-speed-conduction-of-action-potentials-using-a-novel-axon-equivalent-circuit
#8
Takayoshi Tsubo, Makoto Kurokawa
Both sensory neurons and motor neurons transfer signals rapidly through long pathways. Such signals propagate as action potentials through neurons. In myelinated neurons, high conduction velocities of 120 m/s have been reported, even for axons of just 20 μm in diameter. Such a high conduction velocity is enabled by the characteristic morphology of a myelinated axon: repeated regions encased by long uniform myelin sheaths alternating with extremely short exposed regions of the axon called nodes of Ranvier, which generate extremely sharp action potentials...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30450270/inhibition-of-crude-viper-venom-action-by-silver-nanoparticles-a-biophysical-and-biochemical-study
#9
Vrushali C Hingane, Dhanashri Pangam, Prabhakar M Dongre
This investigation understands the interaction between lyophilized crude Viper snake venom ( Doboia russellie ) and Silver nanoparticles (SNPs) using biophysical and biochemical approaches. SNPs were synthesized by chemical reduction method and characterized using UV-Visible spectroscopy, Dynamic Light Scattering (DLS) and Transmission electron microscope (TEM). The average hydrodynamic size of SNPs was found to be 52 nm with 0.261 PDI. TEM image revealed the spherical shape of SNP. Interaction of SNPs and viper venom was resulted in the formation of complex which was confirmed by using DLS technique...
2018: Biophysics and Physicobiology
https://read.qxmd.com/read/30349804/mathematical-approach-to-unpinning-of-spiral-waves-anchored-to-an-obstacle-with-high-frequency-pacing
#10
REVIEW
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
https://read.qxmd.com/read/30349803/chromatin-as-a-nuclear-spring
#11
REVIEW
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
https://read.qxmd.com/read/30349802/mutational-analysis-of-the-conserved-carboxylates-of-anion-channelrhodopsin-2-acr2-expressed-in-escherichia-coli-and-their-roles-in-anion-transport
#12
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
https://read.qxmd.com/read/30250776/novel-insight-into-an-energy-transduction-mechanism-of-the-bacterial-flagellar-type-iii-protein-export
#13
REVIEW
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
https://read.qxmd.com/read/30250775/influence-of-various-parameters-in-the-replica-exchange-molecular-dynamics-method-number-of-replicas-replica-exchange-frequency-and-thermostat-coupling-time-constant
#14
REVIEW
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
https://read.qxmd.com/read/30105176/earthworm-individualities-when-facing-a-conflict-between-turn-alternation-and-aversive-learning
#15
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
https://read.qxmd.com/read/30105175/my-various-thoughts-on-actin
#16
REVIEW
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
https://read.qxmd.com/read/29955565/single-molecular-and-ensemble-level-oscillations-of-cyanobacterial-circadian-clock
#17
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://read.qxmd.com/read/29955564/comparison-of-brain-monoamine-content-in-three-populations-of-lymnaea-that-correlates-with-taste-aversive-learning-ability
#18
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://read.qxmd.com/read/29955563/cross-kymography-analysis-to-simultaneously-quantify-the-function-and-morphology-of-the-archaellum
#19
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://read.qxmd.com/read/29904620/preface-of-special-issue-databases
#20
EDITORIAL
Kei Yura
No abstract text is available yet for this article.
2018: Biophysics and Physicobiology
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