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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
Akira R Kinjo
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are used for both parameter optimization of the model and production runs to explore the sequence subspace around a given protein family. In this Note, I describe the details of the MC algorithm as well as some preliminary results of MC simulations with various temperatures and chemical potentials, and compare them with the mean-field approximation...
2017: Biophysics and Physicobiology
Kotomi Shibata, Tsubasa Koyama, Shohei Inde, Sosuke Iwai, Shigeru Chaen
The myosin II SH1 helix is a joint that links the converter subdomain to the rest of the myosin motor domain and possibly plays a key role in the arrangement of the converter/lever arm. Several point mutations within the SH1 helix in human myosin IIs have been shown to cause diseases. To reveal whether these SH1 helix mutations affect not only motile activities but also thermal properties of myosin II, here we introduced the E683K or R686C point mutation into the SH1 helix in Dictyostelium myosin II. Thermal inactivation as well as thermal aggregation rates of these mutant proteins demonstrated that these mutations decreased the thermal stability of myosin II...
2017: Biophysics and Physicobiology
Yumeka Yamauchi, Masae Konno, Shota Ito, Satoshi P Tsunoda, Keiichi Inoue, Hideki Kandori
Microbial rhodopsins are membrane proteins found widely in archaea, eubacteria and eukaryotes (fungal and algal species). They have various functions, such as light-driven ion pumps, light-gated ion channels, light sensors and light-activated enzymes. A light-driven proton pump bacteriorhodopsin (BR) contains a DTD motif at positions 85, 89, and 96, which is unique to archaeal proton pumps. Recently, channelrhodopsins (ChRs) containing the DTD motif, whose sequential identity is ~20% similar to BR and to cation ChRs in Chlamydomonas reinhardtii (CrCCRs), were found...
2017: Biophysics and Physicobiology
Jun Tamogami, Takashi Kikukawa, Toshifumi Nara, Makoto Demura, Tomomi Kimura-Someya, Mikako Shirouzu, Shigeyuki Yokoyama, Seiji Miyauchi, Kazumi Shimono, Naoki Kamo
A spectrally silent change is often observed in the photocycle of microbial rhodopsins. Here, we suggest the presence of two O intermediates in the photocycle of Acetabularia rhodopsin II (ARII or also called Ace2), a light-driven algal proton pump from Acetabularia acetabulum. ARII exhibits a photocycle including a quasi-equilibrium state of M, N, and O (M⇄N⇄O→) at near neutral and above pH values. However, acidification of the medium below pH ~5.5 causes no accumulation of N, resulting in that the photocycle of ARII can be described as an irreversible scheme (M→O→)...
2017: Biophysics and Physicobiology
Noriyo Mitome, Hiroki Sato, Taishi Tomiyama, Katsuya Shimabukuro, Takuya Matsunishi, Kohei Hamada, Toshiharu Suzuki
The Fo-a subunit of the Na(+)-transporting FoF1 ATP synthase from Propionigenium modestum plays a key role in Na(+) transport. It forms half channels that allow Na(+) to enter and leave the buried carboxyl group on Fo-c subunits. The essential Arg residue R226, which faces the carboxyl group of Fo-c subunits in the middle of transmembrane helix 5 of the Fo-a subunit, separates the cytoplasmic side and periplasmic half-channels. To elucidate contributions of other amino acid residues of transmembrane helix 5 using hybrid FoF1 (Fo from P...
2017: Biophysics and Physicobiology
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
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
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
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
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
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
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
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
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
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