| POLYMERS Vol.72 No.8 |
| >> Japanese | >> English |
COVER STORY
Visualization of Structures and Dynamics of Proteins |
| COVER STORY: Highlight Reviews |
| Liquid-Liquid Phase Separation Based on Protein Phase Transition and Solution Mutual Solubility | Akira NOMOTO, Kentaro SHIRAKI |
| <Abstract> Liquid-liquid phase separation (LLPS) of proteins has attracted much attention as a mechanism for regulating biological reactions in cells. In this paper, we summarize the characteristics of proteins that perform LLPS and then discuss the intrinsic phase transition of proteins from the thermodynamic viewpoint. Finally, we explain the LLPS of proteins from the solution theory, such as solution mutual solubility. Keywords: Liquid-Liquid Phase Separation / Protein / Amino Acid / Phase Transition / Melting Point / Mutual Solubility / Solubility Parameter / Protein Solution |
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| Molecular Features of Calcium Pumps Revealed by Cryo-EM Analysis | Kenji INABA |
| <Abstract> Using cryo-EM single particle analysis, we are, at present, able to determine protein structures at high resolutions without considerable difficulty. This technology also provides information on multiple substate conformations and structure dynamics of proteins in solution. This review article describes structures and mechanisms of operation of human ER-resident calcium pump SERCA2b and Golgi-resident calcium pump SPCA1a, based on their recent cryo-EM analyses. Keywords: Cryo-EM / SERCA2b / SPCA1a / Ca2+ / Mn2+ / P-Type ATPase / ER / Golgi |
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| Recent Progress in Protein Labeling Techniques for Live-Cell Imaging | Takuya KAMIKAWA, Yuichiro HORI |
| <Abstract> In recent years, protein labeling techniques using a protein tag and its specific fluorescent probes have been widely used as powerful tools for live-cell imaging of proteins. This technique utilizes a pair of a protein tag and its specific ligands connected to synthetic fluorescent dye, allowing superresolution imaging, pulse-chase labeling and so on. In this review, we introduce the recent progress and prospects of the development of these technologies. In addition, we introduce OFF-ON-OFF fluorescence probe for real-time visualization of the degradation of short-lived proteins in cellular system using the authors’ original labeling techniques which is called PYP-tag system. Keywords: Fluorescence Probe / Protein Tag / Halo Tag / PYP-Tag / OFF-ON-OFF Fluorescence Probe |
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| COVER STORY: Topics and Products |
| Conformational Study of Multi-Domain Proteins Using Paramagnetic Lanthanide Ions | Tomohide SAIO |
| <Abstract> Despite the functional importance of drastic conformational changes of multidomain proteins, the scarcity of efficient methods obscured mechanistic insights. Recent developments in the structural biology field exploiting paramagnetic lanthanide ions shed light on novel aspects of multidomain proteins in solution. Here I briefly introduce examples of structural studies on a multidomain protein by the use of paramagnetic lanthanide ions. Keywords: Solution Protein Structure / Paramagnetic Lanthanide Ions / Multi-Domain Protein / Conformational Change / Conformational Ensemble |
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| Analysis of Binding Dynamics between Ion Channel and Ligand by High-Speed Atomic Force Microscopy | Ayumi SUMINO |
| <Abstract> Atomic force microscopy (AFM) can observe the surface structure of a sample by detecting the interaction force between the sample and the AFM probe. High-speed AFM (HS-AFM) is a fast scanning version of the AFM. Thanks to high spatiotemporal resolution of the HS-AFM (horizontal: 1nm, vertical: 0.1 nm, 0.1 sec/frame), the HS-AFM has been applied to single-molecule imaging of a wide variety of biomolecules including membrane proteins. This article describes a method to reconstitute ion channels suitable for HS-AFM observation and presents an example of applying this method to observe the binding dynamics of K+ channel KcsA and scorpion venom peptide AgTx2. The research examples presented here can be applied to other membrane proteins, and we expect to be able to elucidate the functional dynamics of various membrane proteins and membrane-bound molecules in the future. Keywords: High-Speed AFM / K+ Channel / Scorpion Toxin / Binding Kinetics / Induced Fit |
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| Dynamics of Proteins in Solution as Seen by Neutron Scattering | Rintaro INOUE |
| <Abstract> Various biomacromolecules including proteins exhibit various biological functions in the solution state. Hence, elucidation of both structure and dynamics of biomacromolecules in solution are indispensable for clarifying the functions. There are mainly two notable points associated with neutron scattering. One is a discernment of hydrogen from its isotope, deuterium due to the difference of their neutron scattering length. Since the energy of thermal fluctuation of biomacromolecules is comparable to that of a cold neutron, another point is a direct detection of dynamics of biomacromolecules. In this manuscript, I present two main topics focused on the detection and analysis of protein dynamics in solution. First is a detection of slow dynamics, subunit exchange of protein complex through the combination of small-angle neutron scattering and deuteration technique. Second is a detection of internal dynamics of proteins in solution through quasielastic neutron scattering. These studies reveal that neutron scattering is a quite fitting method for studying the dynamics of proteins in solution. Keywords: Neutron Scattering / Deuteration / Protein Complex / Internal Dynamics |
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| Observing Macromolecular Assemblies by Cryo-Electron Microscopy | Takeshi YOKOYAMA |
| <Abstract> Cryo-electron microscopy (cryo-EM) is a powerful technique to directly observe macromolecular assemblies of proteins and nucleic acids embedded in amorphous ice using the transmission electron microscope. Recent advancement in this technique allows us to obtain high-resolution structures of macromolecules more efficiently than before. Single particle analysis (SPA) collects macromolecule images as particles and classifies them based on their structural differences. Therefore, comparing three-dimensional structures from the dataset facilitates us in understanding the dynamics of the molecule. Here, I present the overview of cryo-electron microscopy for analyzing macromolecular assemblies. Keywords: Cryo-Electron Microscopy / Macromolular Assembly / Ribosome |
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| Polymer Science and I: A Personal Account |
| My Steps from NANO to POLY | Asae ITO |
| <Abstract> This article describes my journey to encounter polymers. Polymers brought an impact on me that it has a high-resistance to some contaminations, as I had been dealing with nanomaterials. I would be happy if I can tell the readers how polymers are wonderful materials and interesting research subjects. |
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| Front-Line Polymer Science |
| π-Stacked Cyclic Oligomers and Macrocycles | Yasuhiro MORISAKI |
| <Abstract> This short review focuses on optically active π-stacked oligomers and cyclic molecules based on planar chiral [2.2]paracyclophane scaffolds. [2.2]Paracyclophane is also a cyclic molecule consisting of face-to-face phenylenes stacked in proximity (approximately 3 Å between phenylenes). [2.2]Paracyclophanes with substituent(s) are planar chiral compounds without chiral centers because of the suppressed rotational motion of the stacked benzene rings. Recently, practical optical resolutions of [2.2]paracyclophanes by a diastereomer method have been reported, and enantiopure [2.2]paracyclophanes have been used as chiral building blocks for optically active π-stacked molecules. In addition, [2.2]paracyclophane-containing chiral cyclic oligomers have also been prepared from the corresponding racemate and separated by liquid chromatography using chiral columns. Many planar chiral [2.2]paracyclophanes consisting of chiral cyclic oligomers and macrocycles emit circulaly polarized luminescence (CPL) with good anisotropy factors. The structures of such chiral π-stacked cyclic oligomers and macrocycles and their excellent CPL profiles are introduced. Keywords: [2.2]Paracyclophane / Planar Chirality / Circularly Polarized Luminescence / Photoluminescence / π-Conjugation / π-Stacked Molecule / Macrocycle |
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