Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 46, Issue 6
Issue 268
Displaying 1-12 of 12 articles from this issue
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Perspective
Overview
Review
  • Multiple Sequence Alignments: The Next Generation
    Kazutaka KATOH, Kazuharu MISAWA
    2006 Volume 46 Issue 6 Pages 312-317
    Published: 2006
    Released on J-STAGE: December 07, 2006
    DOIhttps://doi.org/10.2142/biophys.46.312
    JOURNAL FREE ACCESS
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    Multiple sequence alignment is an important tool for computational analysis of nucleotide or amino acid sequences. It is also a challenging combinatorial optimization problem in computer science. As a large amount of sequence data is becoming available from genome and other large-scale sequencing projects, efficiency, as well as accuracy, is currently required for a multiple sequence alignment program. Several new programs are being developed aiming at improving both efficiency and accuracy. We overview the algorithms and performances of new programs including that by ourselves.
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  • Structure and Physiological Action of Novel Multiple Family Peptides of Aplysia
    Yasuo FURUKAWA, Kosei SASAKI, Fumihiro MORISHITA, Osamu MATSUSHIMA
    2006 Volume 46 Issue 6 Pages 318-323
    Published: 2006
    Released on J-STAGE: December 07, 2006
    DOIhttps://doi.org/10.2142/biophys.46.318
    JOURNAL FREE ACCESS
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    Neuropeptides are perhaps the most diverse intercellular signaling molecules in the animal kingdom. Owing to the high-throughput methodologies using the high-performance liquid chromatography as well as the mass spectrometry, the number of peptides identified from both vertebrates and invertebrates are increasing. In many cases, the multiple structurally related peptides which are unequivocally considered to be members of the same peptide family are found in the nervous system. We call such peptides the multiple family peptides. Here, we show the structure, distribution, and action of two kinds of multiple family peptides recently identified in a marine mollusc, Aplysia.
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  • Variety of Photoreceptor in Plants and the Photoreception Mechanism
    Daisuke MATSUOKA, Shizue YOSHIHARA, Satoru TOKUTOMI
    2006 Volume 46 Issue 6 Pages 324-329
    Published: 2006
    Released on J-STAGE: December 07, 2006
    DOIhttps://doi.org/10.2142/biophys.46.324
    JOURNAL FREE ACCESS
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    Plants photoreceptors are divided into two groups, well-known phytochromes and blue-light receptors, such as cryptochromes and phototropins. Regarding one of the later, we proved the role of the LOV domains in the kinase photoactivation. In addition to the plant phytochromes, many bacteriophytochromes have been found in both photosynthetic and nonphotosynthetic prokaryotic microorganisms. One of them has been found to undergo not red/far-red but blue/green photoreversible transformaion. Furthermore, new members of blue-light receptors, FKF1 families and BULF photoreceptors, have been found. Their structures and functions are reviewed.
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  • Towards Converting a Light-Driven Proton Pump into a Photosensory Receptor
    Yuki SUDO
    2006 Volume 46 Issue 6 Pages 330-335
    Published: 2006
    Released on J-STAGE: December 07, 2006
    DOIhttps://doi.org/10.2142/biophys.46.330
    JOURNAL FREE ACCESS
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    Light is one of the most important signals providing critical information to biological systems. Four rhodopsins, bacteriorhodopsin (BR), halorhodopsin (hR), sensory rhodopsin (sR) and phoborhodopsin (pR) exist in archaeal membranes. bR and hR work as a light-driven ion pump. sR and pR work as a photo-sensor of phototaxis, and form signaling complexes in membranes with their respective cognate transducer proteins HtrI (with sR) and HtrII (with pR), through which light signals are transmitted to cytoplasm. In this review, we describe our results on the protein-protein interaction of archaeal rhodopsins/HtrII and the signal transfer reaction by the complexes.
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Theoretical and experimental techniques
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