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Biophysics and Physicobiology

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BIOPHYSICS
- Vol.11(2015)
- Vol.10(2014)
- Vol.9(2013)
- Vol.8(2012)
- Vol.7(2011)
- Vol.6(2010)
- Vol.5(2009)
- Vol.4(2008)
- Vol.3(2007)
- Vol.2(2006)
- Vol.1(2005)

BIOPHYSICS Vol. 11(2015)

Regular Article

Effects of serotonin on the heartbeat of pond snails in a hunger state

Miki Yamagishi, Takayuki Watanabe, Dai Hatakeyama, Etsuro Ito

Released: January 05, 2015

p.1-5

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. An increase in 5-HT concentration in the body boosted the heartbeat rate in the food-starved snails, but did not affect the rate in the food-satiated snails. These results suggest that 5-HT application may mimic the change from a starvation to a satiation state normally achieved by direct ingestion of food.

Special Issue “TRP channels: their functional roles in medical sciences”

Preface

Preface of Special Issue “TRP channels: their functional roles in medical sciences”

Etsuro Ito

Released: February 13, 2015

p.7-8

Full Text PDF[345K]

Special Issue “TRP channels: their functional roles in medical sciences”

Regular Article

Electrophysiological characteristics of IB4-negative TRPV1-expressing muscle afferent DRG neurons

Yi-Wen Lin, Chih-Cheng Chen

Released: February 13, 2015

p.9-16

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. Here we showed that IB4-negative TRPV1-expressing muscle afferent neurons are heterogeneous in terms of cell size, resting membrane potential, AP configuration, tetrodotoxin (TTX)-resistance, and acid-induced current (I_acid), as well as capsaicin-induced current (I_cap). TRPV1-expressing neurons were all acid-sensitive and could be divided into two acidsensitive groups depending on an acid-induced sustained current (type I) or an acid-induced biphasic ASIC3-like current (type II). Type I TRPV1-expressing neurons were distinguishable from type II TRPV1-expressing neurons in AP overshoot, afterhyperpolarization duration, and all I_acidparameters, but not in AP threshold, TTX-resistance, resting membrane potential, and I_capparameters. These differential biophysical properties of TRPV1-expressing neurons might partially annotate their different roles involved in the development and maintenance of chronic muscle pain.

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

TRP channels in skin: from physiological implications to clinical significances

Ji-Chen Ho, Chih-Hung Lee

Released: February 13, 2015

p.17-24

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. TRPA1 also enhances responses in contact hypersensitivity. TRPCs in keratinocytes regulate epidermal differentiation. In human diseases with pertubered epidermal differentiation, the expression of TRPCs are altered. TRPMs, which contribute to melanin production in melanocytes, serve as significant prognosis markers in patients with metastatic melanoma. In summary, not only act in sensory processing, TRP channels also contribute to epidermal differentiation, proliferation, barrier integration, skin regeneration, and immune responses. In diseases with aberrant TRP channels, TRP channels might be good therapeutic targets.

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

Role of TRP channels in the induction of heat shock proteins (Hsps) by heating skin

Wen-Li Hsu, Tohru Yoshioka

Released: February 13, 2015

p.25-32

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.

Special Issue “TRP channels: their functional roles in medical sciences”

Note

Thermodynamic implications of high Q₁₀ of thermoTRP channels in living cells

Etsuro Ito, Yusuke Ikemoto, Tohru Yoshioka

Released: February 13, 2015

p.33-38

The activity of thermo-transient receptor potential (TRP) channels is highly dependent on temperature, and thus thermo-TRP reactions have a high temperature coefficient Q₁₀. In thermodynamics, a high value of Q₁₀ 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. These large values of enthalpy and entropy seem to be a match for the values of the unfolding process of globular proteins. We outline these thermodynamic issues in thermo-TRPs.

Regular Article

FTIR study of CPD photolyase with substrate in single strand DNA

I M. Mahaputra Wijaya, Tatsuya Iwata, Junpei Yamamoto, Kenichi Hitomi, Shigenori Iwai, Elizabeth D. Getzoff, Hideki Kandori

Released: February 13, 2015

p.39-45

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. The difference spectra of photoactivation, the fully-reduced (FADH^–) minus semiquinone (FADH^•) spectra, are almost identical in the presence of single strand and double-stranded DNA, except for slight spectral modification in the amide-I region. On the other hand, the difference spectra of photorepair were highly substrate dependent. Strong bands of the C=O stretch (1,720–1,690 cm^–1) and phosphate vibrations (1,090–1,060 cm^–1) of double-stranded DNA may have disappeared in the case of single strand DNA. However, an isotope-labeled enzyme study revealed that spectral features upon DNA repair are similar between both substrates, and the main reason for the apparent spectral difference originates from structural flexibility of DNA after repair.

Lever arm extension of myosin VI is unnecessary for the adjacent binding state

Keigo Ikezaki, Tomotaka Komori, Yoshiyuki Arai, Toshio Yanagida

Released: February 28, 2015

p.47-53

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). To clarify this issue, we constructed a myosin VI/V chimera that replaces the myosin VI LAE with the IQ3-6 domains of the myosin V lever arm, which cannot fold, and performed single molecule imaging. Our chimera showed the same stepping patterns as myosin VI, indicating the LAE is not responsible for the adjacent binding state.

The activity of isolated snail neurons controlling locomotion is affected by glucose

Varvara Dyakonova, László Hernádi, Etsuro Ito, Taisia Dyakonova, Igor Zakharov, Dmitri Sakharov

Released: March 03, 2015

p.55-60

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. Additionally, the excitatory response of the isolated serotonergic neurons to the neuroactive microenvironment of the pedal ganglia was significantly lowered by glucose application. Because hunger has been reported to increase the activity of select neurons and their responses to the pedal ganglia microenvironment, these responses to glucose are in accordance with the hypothesis that direct glucose signaling is involved in the mediation of the hunger-related behavioral state.

Review Article

FTIR study of primate color visual pigments

Kota Katayama, Hideki Kandori

Released: March 04, 2015

p.61-66

How do we distinguish colors? Humans possess three color pigments; red-, green-, and blue-sensitive proteins, which have maximum absorbance (λ_max) 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. We thus started structural studies of primate color visual pigments using low-temperature Fourier-transform infrared (FTIR) spectroscopy, which needs only 0.3 mg protein for a single measurement. Here we report the first structural data of monkey red- (MR) and green- (MG) sensitive pigments, in which the information about the protein, retinal chromophore, and internal water molecules is contained. Molecular mechanism of color discrimination between red and green pigments will be discussed based on the structural data by FTIR spectroscopy.

In vitro directed evolution of alpha-hemolysin by liposome display

Satoshi Fujii, Tomoaki Matsuura, Tetsuya Yomo

Released: March 04, 2015

p.67-72

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. Liposomes displaying the desired membrane protein function were selected, thus accumulating the DNA molecule encoding the desired membrane protein. We have applied this method to alpha-hemolysin, a membrane protein derived from Staphylococcus aureus. Alpha-hemolysin forms a nanopore in the membrane, which allows the penetration of small molecules. We aimed to improve this nanopore activity by using the liposome display method. Consequently, alphahemolysin evolved and attained a higher specific affinity for the liposome membrane. In this review, we describe the essential characteristics of liposome display and the properties of the evolved alpha-hemolysin obtained by this method.

Experimental Methods and Protocols

A new antigenic marker specifically labels a subpopulation of the class II Kenyon cells in the brain of the European honeybee Apis mellifera

Takayuki Watanabe, Takeo Kubo

Released: March 19, 2015

p.73-77

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. In the brain of A. mellifera, a monoclonal antibody (mAb) 15C3, which was originally developed against an insect ecdysone receptor (EcR) protein, immunolabels a single layer of the vertical lobes that correspond to the most dorsal layer of the γ-lobe. The 15C3 mAb recognizes a single ~200 kDa protein expressed in the adult honeybee brain. In addition, the 15C3 mAb immunoreactivity was also observed in the lobes of the developing pupal mushroom bodies. Since γ-lobe is well known to their extensive reorganization that occurs during metamorphosis in Drosophila, the novel antigenic marker for the honeybee γ-lobe allows us to investigate morphological changes of the mushroom bodies during metamorphosis.

A protocol for preparing nucleotide-free KaiC monomer

Atsushi Mukaiyama, Masato Osako, Takaaki Hikima, Takao Kondo, Shuji Akiyama

Released: March 21, 2015

p.79-84

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 nucleotidefree 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. In addition, we found that reassembled KaiC hexamer was functionally active as the intact hexamer. This protocol provides a methodological basis for further analyses of first-turnover events of the ATPase/autokinase/autophosphatase activities of the KaiC hexamer.

Review Article

Experimental and theoretical bases for mechanisms of antigen discrimination by T cells

Masashi K. Kajita, Ryo Yokota, Kazuyuki Aihara, Tetsuya J. Kobayashi

Released: March 26, 2015

p.85-92

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. In this work, we review experimental and theoretical works on the antigen discrimination by focusing on these four properties and show future directions towards understanding of the fundamental principle for molecular discrimination.

How do chaperonins fold protein?

Fumihiro Motojima

Released: April 01, 2015

p.93-102

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. In contrast to the assumption, we recently found that denatured protein interacts with hydrophobic residues at the subunit interfaces of the chaperonin, and partially protrude out of the cage. In this review, we will explain our recent results and introduce our model for the mechanism by which chaperonins accelerate protein folding, in view of recent findings.

Revealing the peptide presenting process of human leukocyte antigen through the analysis of fluctuation

Saeko Yanaka, Takamasa Ueno, Kouhei Tsumoto, Kenji Sugase

Released: April 18, 2015

p.103-106

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.

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Volume And Issue List
BIOPHYSICS

BIOPHYSICS Vol. 11(2015)

Regular Article

Effects of serotonin on the heartbeat of pond snails in a hunger state

Special Issue “TRP channels: their functional roles in medical sciences”

Preface

Preface of Special Issue “TRP channels: their functional roles in medical sciences”

Special Issue “TRP channels: their functional roles in medical sciences”

Regular Article

Electrophysiological characteristics of IB4-negative TRPV1-expressing muscle afferent DRG neurons

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

TRP channels in skin: from physiological implications to clinical significances

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

Role of TRP channels in the induction of heat shock proteins (Hsps) by heating skin

Special Issue “TRP channels: their functional roles in medical sciences”

Note

Thermodynamic implications of high Q₁₀ of thermoTRP channels in living cells

Regular Article

FTIR study of CPD photolyase with substrate in single strand DNA

Lever arm extension of myosin VI is unnecessary for the adjacent binding state

The activity of isolated snail neurons controlling locomotion is affected by glucose

Review Article

FTIR study of primate color visual pigments

In vitro directed evolution of alpha-hemolysin by liposome display

Experimental Methods and Protocols

A new antigenic marker specifically labels a subpopulation of the class II Kenyon cells in the brain of the European honeybee Apis mellifera

A protocol for preparing nucleotide-free KaiC monomer

Review Article

Experimental and theoretical bases for mechanisms of antigen discrimination by T cells

How do chaperonins fold protein?

Revealing the peptide presenting process of human leukocyte antigen through the analysis of fluctuation

System Maintenance

Announcement From J-STAGE

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Volume And Issue List BIOPHYSICS

BIOPHYSICS Vol. 11(2015)

Regular Article

Special Issue “TRP channels: their functional roles in medical sciences”

Preface

Special Issue “TRP channels: their functional roles in medical sciences”

Regular Article

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

Special Issue “TRP channels: their functional roles in medical sciences”

Review Article

Special Issue “TRP channels: their functional roles in medical sciences”

Note

Regular Article

Review Article

Experimental Methods and Protocols

Review Article

System Maintenance

Announcement From J-STAGE

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BIOPHYSICS