Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 53, Issue 6
Issue 310
Displaying 1-21 of 21 articles from this issue
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Perspective
Overview
  • RNA Sequencing
    Katsuyuki SHIROGUCHI
    2013 Volume 53 Issue 6 Pages 290-294
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.290
    JOURNAL FREE ACCESS
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    The term “RNA sequencing (RNA-Seq)” often means the sequencing of cDNA generated from RNA as well as the direct sequencing of RNA. RNA-Seq has become well known as next generation sequencers emerge, particularly because their high throughput nature of data collection makes RNA-Seq a powerful tool for genome-wide gene expression analysis. In this review, I introduce, mainly from a technical point of view, a basic scheme of RNA sequencing, its development, and its application in several interesting studies.
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  • New Raft Hypothesis: Mechanisms for Signal Transduction via Rafts in Cell Membranes
    Kenichi G. N. SUZUKI, Akihiro KUSUMI
    2013 Volume 53 Issue 6 Pages 295-300
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.295
    JOURNAL FREE ACCESS
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    Raft domains, generated by cooperative assembly of membrane molecules through interaction with cholesterol, have been drawing extensive attention as signaling platforms. However, the old vague raft concept is haunting the signaling as well as raft research fields, inducing various misconceptions of signaling mechanisms. Here, we review historical developments of various raft concepts, and propose a new raft hypothesis for raft structure, dynamics, transformation into signaling rafts, and signaling mechanisms, based on our new findings obtained by single-molecule tracking of raft molecules.
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Review
  • Study of Interactions between Huge Membrane Proteins and Soluble Proteins
    —Application to Photosynthetic Proteins—
    Takumi UEDA, Ichio SHIMADA
    2013 Volume 53 Issue 6 Pages 301-304
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.301
    JOURNAL FREE ACCESS
    Supplementary material
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    In the photosynthetic light reactions of plants and cyanobacteria, plastocyanin plays a crucial role as an electron carrier and shuttle protein between two membrane protein complexes: cytochrome b6f and photosystem I. Using transferred cross-saturation method, we demonstrated that the hydrophobic patch residues of plastocyanin are in close proximity to PSI and cytochrome b6f, whereas the acidic patch residues of plastocyanin do not form stable salt bridges with either PSI or cyt b6f, in the electron transfer complexes. The transient characteristics of the interactions on the acidic patch facilitate the rapid association and dissociation of plastocyanin.
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  • Quantitative Analysis of Protein-Ligand Interactions by NMR
    Munehito ARAI
    2013 Volume 53 Issue 6 Pages 305-308
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.305
    JOURNAL FREE ACCESS
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    Determination of affinities and binding sites involved in protein-ligand interactions is essential for understanding molecular mechanisms in biological systems. We combined singular value decomposition and global analysis of NMR chemical shift perturbations caused by protein-protein interactions to determine the number and location of binding sites on the protein surface and to measure the binding affinities. This review focuses on the details of the quantitative analysis of NMR titration data. As an example, the study on the interactions of the intrinsically disordered AD2 subdomain of the tumor suppressor p53 with the TAZ2 domain of the transcriptional coactivator CBP is described.
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  • Comprehensive Analysis of Aggregation Propensity and Chaperone Effects for All Escherichia coli Proteins
    Tatsuya NIWA, Takuya UEDA, Hideki TAGUCHI
    2013 Volume 53 Issue 6 Pages 309-312
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.309
    JOURNAL FREE ACCESS
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    Protein folding is often hampered by protein aggregation, which can be prevented by a variety of chaperones in the cell. However, the relationship between the propensity to form aggregates and primary sequence and preferences of chaperones for substrates has not been understood. We comprehensively analyzed the aggregation propensity of all Escherichia coli proteins and the aggregation prevention effect of three major chaperones for aggregation-prone proteins by using a reconstituted chaperone-free translation system (PURE system). The resource obtained here can be used to investigate the properties of proteins of interest in terms of their solubilities and chaperone effects.
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  • Stoichiometry and Modulation of Cardiac Voltage-Gated Ion Channels
    Koichi NAKAJO, Yoshihiro KUBO
    2013 Volume 53 Issue 6 Pages 313-316
    Published: 2013
    Released on J-STAGE: November 25, 2013
    DOIhttps://doi.org/10.2142/biophys.53.313
    JOURNAL FREE ACCESS
    Supplementary material
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    KCNQ1 channel is a cardiac voltage-gated potassium channel. KCNQ1 forms an ion channel complex with auxiliary subunit KCNE proteins. KCNE proteins dramatically change KCNQ1 gating, for example, KCNE1 slows the activation kinetics of KCNQ1 channels 100-times slower. The mechanisms how KCNE1 proteins modify KCNQ1 channel gating have been central questions yet to be answered. Here we review recent findings regarding the structure-function relationships of KCNQ1/KCNE1 complex, including the stoichiometry and the functional interactions between the subunits, and discuss how KCNE1 proteins modify the gating of KCNQ1 channels.
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Topics
Salon
Activity of Regional Branch
Young Voice
Letters from Abroad
Technical term
Book Review
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