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1 0 0 0 OA Regulatory mechanisms of mitochondrial calcium uptake by the calcium uniporter complex

著者: Akiko Yamada Akira Watanabe Takenori Yamamoto
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.20, no.1, pp.e200004, 2023 (Released:2023-02-04)
参考文献数: 27
被引用文献数: 1

Mitochondria play an important role in energy conversion as well as in intracellular calcium (Ca2+) storage. Ca2+ uptake from the cytosol to the mitochondria is mediated by the calcium uniporter, which functions as a Ca2+ ion channel. However, the molecular composition of this uniporter has remained unclear until recently. The Ca2+ ion channel consists of seven subunits. The yeast reconstitution technique revealed that the mitochondrial calcium uniporter (MCU) and essential MCU regulatory element (EMRE) are the core subunits of the complex. Furthermore, detailed structure-function analyses of the core subunits (MCU and EMRE) were performed. In this review, the regulatory mechanism of mitochondrial Ca2+ uptake is discussed.

2023-05-29 09:16:58
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1 0 0 0 OA Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins

著者: Tatsushi Nishimoto Yuta Takahashi Shohei Miyama Tadaomi Furuta Minoru Sakurai
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.16, pp.196-204, 2019 (Released:2019-11-29)
参考文献数: 41
被引用文献数: 3 2

Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant.

2023-03-15 19:09:38
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1 0 0 0 OA Solid-state NMR for the characterization of retinal chromophore and Schiff base in TAT rhodopsin embedded in membranes under weakly acidic conditions

著者: Sui Arikawa Teppei Sugimoto Takashi Okitsu Akimori Wada Kota Katayama Hideki Kandori Izuru Kawamura
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: pp.e201017, (Released:2023-03-02)

TAT rhodopsin extracted from the marine bacterium SAR11 HIMB114 has a characteristic Thr-Ala-Thr motif and contains both protonated and deprotonated states of Schiff base at physiological pH conditions due to the low pKa. Here, using solid-state NMR spectroscopy, we investigated the 13C and 15N NMR signals of retinal in only the protonated state of TAT in the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho (1′-rac-glycerol) (POPE/POPG) membrane at weakly acidic conditions. In the 13C NMR spectrum of 13C retinal-labeled TAT rhodopsin, the isolated 14-13C signals of 13-trans/15-anti and 13-cis/15-syn isomers were observed at a ratio of 7:3. 15N retinal protonated Schiff base (RPSB) had a significantly higher magnetic field resonance at 160 ppm. In 15N RPSB/λmax analysis, the plot of TAT largely deviated from the trend based on the retinylidene-halide model compounds and microbial rhodopsins. Our findings indicate that the RPSB of TAT forms a very weak interaction with the counterion.

2023-03-04 00:41:37
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1 0 0 0 OA Three-dimensional vertex model for simulating multicellular morphogenesis

著者: Satoru Okuda Yasuhiro Inoue Taiji Adachi
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.12, pp.13-20, 2015 (Released:2015-08-18)
参考文献数: 24
被引用文献数: 32 47

During morphogenesis, various cellular activities are spatiotemporally coordinated on the protein regulatory background to construct the complicated, three-dimensional (3D) structures of organs. Computational simulations using 3D vertex models have been the focus of efforts to approach the mechanisms underlying 3D multicellular constructions, such as dynamics of the 3D monolayer or multilayer cell sheet like epithelia as well as the 3D compacted cell aggregate, including dynamic changes in layer structures. 3D vertex models enable the quantitative simulation of multicellular morphogenesis on the basis of single-cell mechanics, with complete control of various cellular activities such as cell contraction, growth, rearrangement, division, and death. This review describes the general use of the 3D vertex model, along with its applications to several simplified problems of developmental phenomena.

2023-02-21 23:26:10
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1 0 0 0 OA Physico- and chemical biology using nanomanipulation and micromanipulation technologies

著者: Akira Kitamura Ryo Iizuka
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: pp.e190044, (Released:2022-11-16)

2022-11-28 17:15:10
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1 0 0 0 OA Participation in 44th Indian Biophysical Society Meeting

著者: Kayo Hibino
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.19, pp.e190033, 2022 (Released:2022-09-14)
参考文献数: 4

2022-10-11 11:51:58
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1 0 0 0 OA Multistep growth of amyloid intermediates and its inhibition toward exploring therapeutic way: A case study using insulin B chain and fibrinogen

著者: Naoki Yamamoto Eri Chatani
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.19, pp.e190017, 2022 (Released:2022-06-01)
参考文献数: 34
被引用文献数: 1

It is crucial to understand the mechanism of amyloid fibril formation for the development of the therapeutic ways against amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge prior to the fibril formation, seem to play a key role to the occurrence of nuclei of amyloid fibrils. We have focused on an insulin-derived peptide, B chain, to precisely clarify the mechanism of the fibril formation via prefibrillar intermediates. Various kinds of methods such as circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering, and atomic force microscopy were employed to track the structural changes in prefibrillar intermediates. The prefibrillar intermediates possessing rod-shaped structures elongated as a function of time, which led to fibril formation. We have also found that a blood clotting protein, fibrinogen, inhibits the amyloid fibril formation of B chain. This was caused by the stabilization of prefibrillar intermediates and thus the suppression of their elongation by fibrinogen. These findings have not only shed light on detailed mechanisms about how prefibrillar intermediates convert to the amyloid fibril, but also demonstrated that inhibiting the structural development of prefibrillar intermediates is an effective strategy to develop therapeutic ways against amyloid-related diseases. This review article is an extended version of the Japanese article, Observing Development of Amyloid Prefibrillar Intermediates and their Interaction with Chaperones for Inhibiting the Fibril Formation, published in SEIBUTSU BUTSURI Vol. 61, p. 236–239 (2021).

2022-09-09 14:35:24
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1 0 0 0 OA Structural overview of the translocase of the mitochondrial outer membrane complex

著者: Yuhei Araiso Toshiya Endo
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: pp.e190022, (Released:2022-06-07)
被引用文献数: 5

Most mitochondrial proteins are synthesized as precursor proteins (preproteins) in the cytosol and imported into mitochondria. The translocator of the outer membrane (TOM) complex functions as a main entry gate for the import of mitochondrial proteins. The TOM complex is a multi-subunit membrane protein complex composed of a β-barrel channel Tom40 and six single-pass membrane proteins. Recent cryo-EM studies have revealed high-resolution structures of the yeast and human TOM complexes, which enabled us to discuss the mechanism of protein import at an amino-acid residue level. The cryo-EM structures show that two Tom40 β-barrels are surrounded by two sets of small Tom subunits to form a dimeric structure. The intermembrane space (IMS) domains of Tom40, Tom22, and Tom7 form a binding site for presequence-containing preproteins in the middle of the dimer to achieve their efficient transfer of to the downstream translocase, the TIM23 complex. The N-terminal segment of Tom40 spans the channel from the cytosol to the IMS to interact with Tom5 at the periphery of the dimer, where downstream components of presequence-lacking preproteins are recruited. Structure-based biochemical analyses together with crosslinking experiments revealed that each Tom40 channel possesses two distinct paths and exit sites for protein translocation of different sets of mitochondrial preproteins. Here we summarize the current knowledge on the structural features, protein translocation mechanisms, and remaining questions for the TOM complexes, with particular emphasis on their determined cryo-EM structures. This article is an extended version of the Japanese article, Structural basis for protein translocation by the translocase of the outer mitochondrial membrane, published in SEIBUTSU BUTSURI Vol. 60, p.280-283 (2020).

2022-06-07 21:48:05
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1 0 0 0 OA Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis

著者: Toru Kondo Yutaka Shibata
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: pp.e190013, (Released:2022-04-08)
被引用文献数: 2

2022-04-12 11:52:58
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1 0 0 0 OA Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators

著者: Bang-Chieh Huang Lee-Wei Yang
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.16, pp.473-484, 2019 (Released:2019-11-29)
参考文献数: 59
被引用文献数: 1 3

In this study, we provide a time-dependent mechanical model, taking advantage of molecular dynamics simulations, quasiharmonic analysis of molecular dynamics trajectories, and time-dependent linear response theories to describe vibrational energy redistribution within the protein matrix. The theoretical description explained the observed biphasic responses of specific residues in myoglobin to CO-photolysis and photoexcitation on heme. The fast responses were found to be triggered by impulsive forces and propagated mainly by principal modes <40 cm−1. The predicted fast responses for individual atoms were then used to study signal propagation within the protein matrix and signals were found to propagate ~8 times faster across helices (4076 m/s) than within the helices, suggesting the importance of tertiary packing in the sensitivity of proteins to external perturbations. We further developed a method to integrate multiple intramolecular signal pathways and discover frequent “communicators”. These communicators were found to be evolutionarily conserved including those distant from the heme.

2022-04-02 05:48:03
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1 0 0 0 OA Second harmonic generation polarization microscopy as a tool for protein structure analysis

著者: Junichi Kaneshiro Yasushi Okada Tomohiro Shima Mika Tsujii Katsumi Imada Taro Ichimura Tomonobu M. Watanabe
出版者: The Biophysical Society of Japan
雑誌: Biophysics and Physicobiology (ISSN:21894779)
巻号頁・発行日: vol.16, pp.147-157, 2019 (Released:2019-09-20)
参考文献数: 41
被引用文献数: 2 5

Cryo-electron microscopy and X-ray crystallography have been the major tools of protein structure analysis for decades and will certainly continue to be essential in the future. Moreover, nuclear magnetic resonance or Förster resonance energy transfer can measure structural dynamics. Here, we propose to add optical second-harmonic generation (SHG), which is a nonlinear optical scattering process sensitive to molecular structures in illuminated materials, to the tool-kit of structural analysis methodologies. SHG can be expected to probe the structural changes of proteins in the physiological condition, and thus link protein structure and biological function. We demonstrate that a conformational change as well as its dynamics in protein macromolecular assemblies can be detected by means of SHG polarization measurement. To prove the capability of SHG polarization measurement with regard to protein structure analysis, we developed an SHG polarization microscope to analyze microtubules in solution. The difference in conformation between microtubules with different binding molecules was successfully observed as polarization dependence of SHG intensity. We also succeeded in capturing the temporal variation of structure in a photo-switchable protein crystal in both activation and inactivation processes. These results illustrate the potential of this method for protein structure analysis in physiological solutions at room temperature without any labeling.