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Biophysics and Physicobiology

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https://www.readbyqxmd.com/read/28409086/kinetic-characteristics-of-chimeric-channelrhodopsins-implicate-the-molecular-identity-involved-in-desensitization
#1
Alemeh Zamani, Shigeo Sakuragi, Toru Ishizuka, Hiromu Yawo
Channelrhodopsin (ChR)-1 and ChR2 were the first-identified members of ChRs which are a growing subfamily of microbial-type rhodopsins. Light absorption drives the generation of a photocurrent in cell membranes expressing ChR2. However, the photocurrent amplitude attenuates and becomes steady-state during prolonged irradiation. This process, called desensitization or inactivation, has been attributed to the accumulation of intermediates less conductive to cations. Here we provided evidence that the dark-adapted (DA) photocurrent before desensitization is kinetically different from the light-adapted (LA) one after desensitization, that is, the deceleration of both basal-to-conductive and conductive-to-basal transitions...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409085/mechanical-properties-of-spindle-poles-are-symmetrically-balanced
#2
Kazuya Suzuki, Takeshi Itabashi, Shin'ichi Ishiwata
The metaphase spindle is organized for accurate chromosome segregation. One of the fundamental features of the spindle across the species is its symmetrical shape; the spindle consists of two polar arrays of microtubules at both ends. Although it has been suggested that the formation of the bipolar shape requires force balance coordination by molecular motors, i.e., kinesins and dyneins, quantitative analysis for the pole mechanics has not been conducted. Here, we demonstrate that it is not only the shape but also the stiffness and microtubule density of the pairs of pole regions are symmetrically balanced in single spindles self-assembled in Xenopus egg extracts...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28275530/model-based-control-of-the-temporal-patterns-of-intracellular-signaling-in-silico
#3
Yohei Murakami, Masanori Koyama, Shigeyuki Oba, Shinya Kuroda, Shin Ishii
The functions of intracellular signal transduction systems are determined by the temporal behavior of intracellular molecules and their interactions. Of the many dynamical properties of the system, the relationship between the dynamics of upstream molecules and downstream molecules is particularly important. A useful tool in understanding this relationship is a methodology to control the dynamics of intracellular molecules with an extracellular stimulus. However, this is a difficult task because the relationship between the levels of upstream molecules and those of downstream molecules is often not only stochastic, but also time-inhomogeneous, nonlinear, and not one-to-one...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28275529/enhanced-mrna-protein-fusion-efficiency-of-a-single-domain-antibody-by-selection-of-mrna-display-with-additional-random-sequences-in-the-terminal-translated-regions
#4
Kazuki Takahashi, Masato Sunohara, Takuya Terai, Shigefumi Kumachi, Naoto Nemoto
In vitro display technologies such as mRNA and cDNA display are powerful tools to create and select functional peptides. However, in some cases, efficiency of mRNA-protein fusion is very low, which results in decreased library size and lower chance of successful selection. In this study, to improve mRNA-protein fusion efficiency, we prepared an mRNA display library of a protein with random N- and C-terminal coding regions consisting of 12 nucleotides (i.e. four amino acids), and performed an electrophoresis mobility shift assay (EMSA)-based selection of successfully formed mRNA display molecules...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409084/actin-binding-domain-of-filamin-distinguishes-posterior-from-anterior-actin-filaments-in-migrating-dictyostelium-cells
#5
Keitaro Shibata, Akira Nagasaki, Hiroyuki Adachi, Taro Q P Uyeda
Actin filaments in different parts of a cell interact with specific actin binding proteins (ABPs) and perform different functions in a spatially regulated manner. However, the mechanisms of those spatially-defined interactions have not been fully elucidated. If the structures of actin filaments differ in different parts of a cell, as suggested by previous in vitro structural studies, ABPs may distinguish these structural differences and interact with specific actin filaments in the cell. To test this hypothesis, we followed the translocation of the actin binding domain of filamin (ABDFLN) fused with photoswitchable fluorescent protein (mKikGR) in polarized Dictyostelium cells...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409083/theoretical-analyses-on-a-flipping-mechanism-of-uv-induced-dna-damage
#6
Ryuma Sato, Ryuhei Harada, Yasuteru Shigeta
As for UV-induced DNA damage, which may induce skin cancer in animals and growth inhibition in plants, there are two types of photoproducts, namely cis-sin cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts. When they are to be repaired, base-flipping occurs, and they bind to enzymes. However, this process remains relatively unknown at a molecular level. We analyze conformation and interaction energy changes upon base-flipping using classical molecular dynamics (CMD) simulations and ab initio electronic structure calculations...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409082/what-parameters-characterize-life
#7
Shigeki Mitaku, Ryusuke Sawada
"Life" is a particular state of matter, and matter is composed of various molecules. The state corresponding to "life" is ultimately determined by the genome sequence, and this sequence determines the conditions necessary for survival of the organism. In order to elucidate one parameter characterizing the state of "life", we analyzed the amino acid sequences encoded in the total genomes of 557 prokaryotes and 40 eukaryotes using a membrane protein prediction online tool called SOSUI. SOSUI uses only the physical parameters of the encoded amino acid sequences to make its predictions...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409081/itinerary-profiling-to-analyze-a-large-number-of-protein-folding-trajectories
#8
Motonori Ota, Mitsunori Ikeguchi, Akinori Kidera
Understanding how proteins fold through a vast number of unfolded states is a major subject in the study of protein folding. Herein, we present itinerary profiling as a simple method to analyze molecular dynamics trajectories, and apply this method to Trp-cage. In itinerary profiling, structural clusters included in a trajectory are represented by a bit sequence, and a number of trajectories, as well as the structural clusters, can be compared and classified. As a consequence, the structural clusters that characterize the foldability of trajectories were able to be identified...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409080/cooperativity-and-modularity-in-protein-folding
#9
REVIEW
Masaki Sasai, George Chikenji, Tomoki P Terada
A simple statistical mechanical model proposed by Wako and Saitô has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Muñoz and Eaton and has since been referred to as the Wako-Saitô-Muñoz-Eaton (WSME) model. The success of the WSME model in explaining the folding of many proteins has verified the hypothesis that the folding is dominated by native interactions, which makes the energy landscape globally biased toward native conformation...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409079/characterization-of-protein-folding-by-a-%C3%AE-value-calculation-with-a-statistical-mechanical-model
#10
Hiroshi Wako, Haruo Abe
The Φ-value analysis approach provides information about transition-state structures along the folding pathway of a protein by measuring the effects of an amino acid mutation on folding kinetics. Here we compared the theoretically calculated Φ values of 27 proteins with their experimentally observed Φ values; the theoretical values were calculated using a simple statistical-mechanical model of protein folding. The theoretically calculated Φ values reflected the corresponding experimentally observed Φ values with reasonable accuracy for many of the proteins, but not for all...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409078/statistical-mechanics-of-protein-structural-transitions-insights-from-the-island-model
#11
REVIEW
Yukio Kobayashi
The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô's views on the hierarchic structure of science...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409077/professor-nobuhiko-sait%C3%A3-s-contribution-to-statistical-mechanics-of-biopolymers
#12
Mitiko Go
No abstract text is available yet for this article.
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28409076/memorial-issue-for-professor-nobuhiko-sait%C3%A3
#13
Kei Yura, Hiroshi Wako
No abstract text is available yet for this article.
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924279/accelerating-in-vitro-studies-on-circadian-clock-systems-using-an-automated-sampling-device
#14
Yoshihiko Furuike, Jun Abe, Atsushi Mukaiyama, Shuji Akiyama
KaiC, a core protein of the cyanobacterial circadian clock, is rhythmically autophosphorylated and autodephosphorylated with a period of approximately 24 h in the presence of two other Kai proteins, KaiA and KaiB. In vitro experiments to investigate the KaiC phosphorylation cycle consume considerable time and effort. To automate the fractionation, quantification, and evaluation steps, we developed a suite consisting of an automated sampling device equipped with an 8-channel temperature controller and accompanying analysis software...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924278/domain-based-biophysical-characterization-of-the-structural-and-thermal-stability-of-flig-an-essential-rotor-component-of-the-na-driven-flagellar-motor
#15
Yasuhiro Onoue, Rei Abe-Yoshizumi, Mizuki Gohara, Yuuki Nishino, Shiori Kobayashi, Yasuo Asami, Michio Homma
Many bacteria move using their flagellar motor, which generates torque through the interaction between the stator and rotor. The most important component of the rotor for torque generation is FliG. FliG consists of three domains: FliGN, FliGM, and FliGC. FliGC contains a site(s) that interacts with the stator. In this study, we examined the physical properties of three FliG constructs, FliGFull, FliGMC, and FliGC, derived from sodium-driven polar flagella of marine Vibrio. Size exclusion chromatography revealed that FliG changes conformational states under two different pH conditions...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924277/model-simulation-of-the-spoc-wave-in-a-bundle-of-striated-myofibrils
#16
Koutaro Nakagome, Katsuhiko Sato, Seine A Shintani, Shin'ichi Ishiwata
SPOC (spontaneous oscillatory contraction) is a phenomenon observed in striated muscle under intermediate activation conditions. Recently, we constructed a theoretical model of SPOC for a sarcomere, a unit sarcomere model, which explains the behavior of SPOC at each sarcomere level. We also constructed a single myofibril model, which visco-elastically connects the unit model in series, and explains the behaviors of SPOC at the myofibril level. In the present study, to understand the SPOC properties in a bundle of myofibrils, we extended the single myofibril model to a two-dimensional (2D) model and a three-dimensional (3D) model, in which myofibrils were elastically connected side-by-side through cross-linkers between the Z-lines and M-lines...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924276/mypresto-omegagene-a-gpu-accelerated-molecular-dynamics-simulator-tailored-for-enhanced-conformational-sampling-methods-with-a-non-ewald-electrostatic-scheme
#17
Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura
Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g., the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924275/erratum
#18
(no author information available yet)
[This corrects the article on p. 173 in vol. 13.].
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924274/metabolic-pathway-reconstruction-strategies-for-central-metabolism-and-natural-product-biosynthesis
#19
REVIEW
Masaaki Kotera, Susumu Goto
Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924273/molecular-dynamics-analysis-to-evaluate-docking-pose-prediction
#20
Takako Sakano, Md Iqbal Mahamood, Takefumi Yamashita, Hideaki Fujitani
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position...
2016: Biophysics and Physicobiology
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