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Biophysics (Nagoya-Shi, Japan)

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https://www.readbyqxmd.com/read/27493522/revealing-the-peptide-presenting-process-of-human-leukocyte-antigen-through-the-analysis-of-fluctuation
#1
REVIEW
Saeko Yanaka, Takamasa Ueno, Kouhei Tsumoto, Kenji Sugase
Structural fluctuation on microsecond to millisecond time scales has been reported to play an important role in proteins that undergo significant structural change during their expression of function. In these proteins, the structural change was obvious in the crystal structures. However, protein motions in solution could contribute to the function of proteins, even if no significant structural difference is observed in crystal structure of different states while they function. In this review, we introduce our recent report on the stabilization mechanism of human leukocyte antigen, and the possibility of fluctuation contributing to several biophysical properties of proteins...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493521/how-do-chaperonins-fold-protein
#2
REVIEW
Fumihiro Motojima
Protein folding is a biological process that is essential for the proper functioning of proteins in all living organisms. In cells, many proteins require the assistance of molecular chaperones for their folding. Chaperonins belong to a class of molecular chaperones that have been extensively studied. However, the mechanism by which a chaperonin mediates the folding of proteins is still controversial. Denatured proteins are folded in the closed chaperonin cage, leading to the assumption that denatured proteins are completely encapsulated inside the chaperonin cage...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493520/experimental-and-theoretical-bases-for-mechanisms-of-antigen-discrimination-by-t-cells
#3
REVIEW
Masashi K Kajita, Ryo Yokota, Kazuyuki Aihara, Tetsuya J Kobayashi
Interaction only within specific molecules is a requisite for accurate operations of a biochemical reaction in a cell where bulk of background molecules exist. While structural specificity is a well-established mechanism for specific interaction, biophysical and biochemical experiments indicate that the mechanism is not sufficient for accounting for the antigen discrimination by T cells. In addition, the antigen discrimination by T cells also accompanies three intriguing properties other than the specificity: sensitivity, speed, and concentration compensation...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493519/a-protocol-for-preparing-nucleotide-free-kaic-monomer
#4
Atsushi Mukaiyama, Masato Osako, Takaaki Hikima, Takao Kondo, Shuji Akiyama
The hexameric form of the KaiC protein is a core of the cyanobacterial biological clock, and its enzymatic activities exhibit circadian periodicity. The instability of the monomeric form of nucleotide-free KaiC has precluded its storage and detailed analyses of the activities of the reassembled hexamer. Here, we provide a protocol for preparing nucleotide-free KaiC monomer that is stable in solution and for triggering its reassembly into intact KaiC hexamer by the addition of ATP. A phosphate buffer containing glutamic acid and arginine enhanced the stability of KaiC monomer considerably...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493518/a-new-antigenic-marker-specifically-labels-a-subpopulation-of-the-class-ii-kenyon-cells-in-the-brain-of-the-european-honeybee-apis-mellifera
#5
Takayuki Watanabe, Takeo Kubo
The mushroom bodies are the higher-order integration center in the insect brain and are involved in higher brain functions such as learning and memory. In the social hymenopteran insects such as honeybees, the mushroom bodies are the prominent brain structures. The mushroom bodies are composed of lobed neuropils formed by thousands of parallel-projecting axons of intrinsic neurons, and the lobes are divided into parallel subdivisions. In the present paper, we report a new antigenic marker to label a single layer in the vertical lobes of the European honeybee Apis mellifera...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493517/in-vitro-directed-evolution-of-alpha-hemolysin-by-liposome-display
#6
REVIEW
Satoshi Fujii, Tomoaki Matsuura, Tetsuya Yomo
We have developed a method to enable in vitro directed evolution that can be applied to membrane proteins. This method, termed liposome display, uses liposomes as compartments in which membrane proteins are synthesized and as scaffolds for membrane protein integration. Thus, the synthesized membrane proteins are displayed on the surface of the liposome and exhibit their functions. A randomly mutated DNA library of the membrane protein was generated, encapsulated in the liposomes at the single-molecule level, and used to generate a liposome library...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493516/ftir-study-of-primate-color-visual-pigments
#7
REVIEW
Kota Katayama, Hideki Kandori
How do we distinguish colors? Humans possess three color pigments; red-, green-, and blue-sensitive proteins, which have maximum absorbance (λmax) at 560, 530, and 420 nm, respectively, and contribute to normal human trichromatic vision (RGB). Each color pigments consists of a different opsin protein bound to a common chromophore molecule, 11-cis-retinal, whereas different chromophore-protein interactions allow preferential absorption of different colors. However, detailed experimental structural data to explain the molecular basis of spectral tuning of color pigments are lacking, mainly because of the difficulty in sample preparation...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493515/the-activity-of-isolated-snail-neurons-controlling-locomotion-is-affected-by-glucose
#8
Varvara Dyakonova, László Hernádi, Etsuro Ito, Taisia Dyakonova, Igor Zakharov, Dmitri Sakharov
The involvement of serotonin in mediating hunger-related changes in behavioral state has been described in many invertebrates. However, the mechanisms by which hunger signals to serotonergic cells remain unknown. We tested the hypothesis that serotonergic neurons can directly sense the concentration of glucose, a metabolic indicator of nutritional state. In the snail Lymnaea stagnalis, we demonstrate that completely isolated pedal serotonergic neurons that control locomotion changed their biophysical characteristics in response to glucose application by lowering membrane potential and decreasing the firing rate...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493514/lever-arm-extension-of-myosin-vi-is-unnecessary-for-the-adjacent-binding-state
#9
REVIEW
Keigo Ikezaki, Tomotaka Komori, Yoshiyuki Arai, Toshio Yanagida
Myosin VI is a processive myosin that has a unique stepping motion, which includes three kinds of steps: a large forward step, a small forward step and a backward step. Recently, we proposed the parallel lever arms model to explain the adjacent binding state, which is necessary for the unique motion. In this model, both lever arms are directed the same direction. However, experimental evidence has not refuted the possibility that the adjacent binding state emerges from myosin VI folding its lever arm extension (LAE)...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493513/ftir-study-of-cpd-photolyase-with-substrate-in-single-strand-dna
#10
I M Mahaputra Wijaya, Tatsuya Iwata, Junpei Yamamoto, Kenichi Hitomi, Shigenori Iwai, Elizabeth D Getzoff, Hideki Kandori
Photolyases (PHRs) utilize near UV/blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer (CPD)-PHR binds flavin adenine dinucleotide (FAD) as a cofactor and repairs CPD lesions in double-stranded DNA. To understand the activation and repair mechanism of CPD-PHR, we applied light-induced difference Fourier transform infrared (FTIR) spectroscopy to CPD-PHR, whose signals were identified by use of isotope-labeling. To further investigate the enzymatic function, here we study the activation and repair mechanism of CPD-PHR with the substrate in single strand DNA, and the obtained FTIR spectra are compared with those in double-stranded DNA, the natural substrate...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493512/thermodynamic-implications-of-high-q-10-of-thermo-trp-channels-in-living-cells
#11
Etsuro Ito, Yusuke Ikemoto, Tohru Yoshioka
The activity of thermo-transient receptor potential (TRP) channels is highly dependent on temperature, and thus thermo-TRP reactions have a high temperature coefficient Q 10. In thermodynamics, a high value of Q 10 indicates the existence of a large activation energy (i.e., a large enthalpy) over a short period during the transition process between the closed and open states of the channels. The Gibbs free energy equation shows that a large entropy is required to compensate for this large enthalpy and permit activation of the channels, suggesting a large conformational change of the channels...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493511/role-of-trp-channels-in-the-induction-of-heat-shock-proteins-hsps-by-heating-skin
#12
REVIEW
Wen-Li Hsu, Tohru Yoshioka
Transient receptor potential (TRP) channels in skin are crucial for achieving temperature sensitivity to maintain internal temperature balance and thermal homeostasis, as well as to protect skin cells from environmental stresses such as infrared (IR) or near-infrared (NIR) radiation via heat shock protein (Hsp) production. However, the mechanisms by which IR and NIR activate TRP channels and produce Hsps intracellularly have been independently reported. In this review, we discuss the relationship between TRP channel activation and Hsp production, and introduce the roles of several skin TRP channels in the regulation of HSP production by IR and NIR exposure...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493510/trp-channels-in-skin-from-physiological-implications-to-clinical-significances
#13
REVIEW
Ji-Chen Ho, Chih-Hung Lee
TRP channels are expressed in various cells in skin. As an organ system to border the host and environment, many nonneuronal cells, including epidermal keratinocytes and melanocytes, express several TRP channels functionally distinct from sensory processing. TRPV1 and TRPV3 in keratinocytes of the epidermis and hair apparatus inhibit proliferation, induce terminal differentiation, induce apoptosis, and promote inflammation. Activation of TRPV4, 6, and TRPA1 promotes regeneration of the severed skin barriers...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493509/electrophysiological-characteristics-of-ib4-negative-trpv1-expressing-muscle-afferent-drg-neurons
#14
Yi-Wen Lin, Chih-Cheng Chen
Muscle afferent neurons that express transient receptor potential vanilloid type I (TRPV1) are responsible for muscle pain associated with tissue acidosis. We have previously found that TRPV1 of isolectin B4 (IB4)-negative muscle nociceptors plays an important role in the acid-induced hyperalgesic priming and the development of chronic hyperalgesia in a mouse model of fibromyalgia. To understand the electrophysiological properties of the TRPV1-expressing muscle afferent neurons, we used whole-cell patch clamp recording to study the acid responsiveness and action potential (AP) configuration of capsaicin-sensitive neurons innervating to gastrocnemius muscle...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493508/preface-of-special-issue-trp-channels-their-functional-roles-in-medical-sciences
#15
Etsuro Ito
No abstract text is available yet for this article.
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493507/effects-of-serotonin-on-the-heartbeat-of-pond-snails-in-a-hunger-state
#16
Miki Yamagishi, Takayuki Watanabe, Dai Hatakeyama, Etsuro Ito
Serotonin (5-hydroxytryptamine: 5-HT) is a multimodal transmitter that controls both feeding response and heartbeat in snails. However, the effects of 5-HT on the hunger state are still unknown. We therefore examined the relation among the hunger state, the heartbeat rate and the 5-HT action in food-starved snails. We found that the hunger state was significantly distinguished by the heartbeat rate in snails. The heartbeat rate was high in the food-satiated snails, whereas it was low in the food-starved snails...
2015: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493506/electrophysiological-characteristics-of-feeding-related-neurons-after-taste-avoidance-pavlovian-conditioning-in-lymnaea-stagnalis
#17
REVIEW
Hiroshi Sunada, Satoshi Takigami, Ken Lukowiak, Manabu Sakakibara
Taste avoidance conditioning (TAC) was carried out on the pond snail, Lymnaea stagnalis. The conditional stimulus (CS) was sucrose which elicits feeding behavior; while the unconditional stimulus (US) was a tactile stimulus to the head which causes feeding to be suppressed. The neuronal circuit that drives feeding behavior in Lymnaea is well worked out. We therefore compared the physiological characteristics on 3 classes of neurons involved with feeding behavior especially in response to the CS in conditioned vs...
2014: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493505/microscopic-heat-pulse-induced-calcium-dynamics-in-single-wi-38-fibroblasts
#18
Hideki Itoh, Kotaro Oyama, Madoka Suzuki, Shin'ichi Ishiwata
Temperature-sensitive Ca(2+) dynamics occur primarily through transient receptor potential channels, but also by means of Ca(2+) channels and pumps on the endoplasmic reticulum membrane. As such, cytoplasmic Ca(2+) concentration ([Ca(2+)]cyt) is re-equilibrated by changes in ambient temperature. The present study investigated the effects of heat pulses (heating duration: 2 s or 150 s) on [Ca(2+)]cyt in single WI-38 fibroblasts, which are considered as normal cells. We found that Ca(2+) burst occurred immediately after short (2 s) heat pulse, which is similar to our previous report on HeLa cells, but with less thermosensitivity...
2014: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493504/cooperation-between-phenotypic-plasticity-and-genetic-mutations-can-account-for-the-cumulative-selection-in-evolution
#19
Ken Nishikawa, Akira R Kinjo
We propose the cooperative model of phenotype-driven evolution, in which natural selection operates on a phenotype caused by both genetic and epigenetic factors. The conventional theory of evolutionary synthesis assumes that a phenotypic value (P) is the sum of genotypic value (G) and environmental deviation (E), P=G+E, where E is the fluctuations of the phenotype among individuals in the absence of environmental changes. In contrast, the cooperative model assumes that an evolution is triggered by an environmental change and individuals respond to the change by phenotypic plasticity (epigenetic changes)...
2014: Biophysics (Nagoya-Shi, Japan)
https://www.readbyqxmd.com/read/27493503/3-d-structural-analysis-of-the-crucial-intermediate-of-skeletal-muscle-myosin-and-its-role-in-revised-actomyosin-cross-bridge-cycle
#20
REVIEW
Eisaku Katayama
Skeletal myosin S1 consists of two functional segments, a catalytic-domain and a lever-arm. Since the crystal structure of ADP/Vi-bound S1 exhibits a strong intramolecular flexure between two segments, inter-conversion between bent and extended forms; i.e. "tilting of the lever-arm" has been accepted as the established molecular mechanism of skeletal muscle contraction. We utilized quick-freeze deep-etch replica electron microscopy to directly visualize the structure of in vitro actin-sliding myosin, and found the existence of a novel oppositely-bent configuration, instead of the expected ADP/Vi-bound form...
2014: Biophysics (Nagoya-Shi, Japan)
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