Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 43, Issue 2
Issue 246
Displaying 1-10 of 10 articles from this issue
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Perspective
Overview
  • Analysis of Intermediate Structures of Photoactive Yellow Protein by Raman Spectroscopy and Quantum Chemical Calculations
    Masashi UNNO, Seigo YAMAUCHI
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 58-63
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.58
    JOURNAL FREE ACCESS
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    Recent advances in computational chemistry have significantly enhanced the capability of vibrational spectroscopy such as a Raman technique. It is now possible to simulate the Raman spectrum for large molecules such as proteins on the basis of ab initio quantum chemistry. Using both resonance Raman spectroscopy and quantum chemical calculations, we have determined the chromophore structures in the intermediate states of photoactive yellow protein(PYP). We have successfully extracted key information on the chromophore-protein interactions. The results permit us to propose structural models of the intermediates, which reveal the photocycle mechanism of PYP under physiological conditions.
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  • Protein Conformational Analysis by Multicanonical Molecular Dynamics Simulation
    Kazuyoshi IKEDA, Junichi HIGO
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 64-69
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.64
    JOURNAL FREE ACCESS
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    Energy landscapes of three peptides were studied with multicanonical molecular dynamics. The landscapes were different depending on the amino-acid sequence of the peptides. The landscapes, which consisted of conformational clusters, showed the existence of free-energy barriers among the clusters, and provided pathways of conformational changes. Folding mechanism of proteins was discussed from the current results. Some problems, which should be overcome to treat a protein system, are pointed out.
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  • Various Biological Activities of a Vitamin E Ester
    Kentaro KOGURE
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 70-74
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.70
    JOURNAL FREE ACCESS
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    Various effects of the most commonly used Vitamin E have been thought to be due to its antioxidative effect. Recently, α-tocopheryl succinate(Toco-S), an ester of Vitamin E, which lacks antioxidative ability, has been gaining considerable attention, because Toco-S has various biological activities such as induction of apoptosis and activation of protein kinase C. All of these effects of Toco-S are completely different from those of vitamin E. In this article, different effects of Vitamin E and Toco-S are described mainly based on their physical properties.
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Review
  • Molecular Diversities and Functions of Ribonucleases H
    Shigenori KANAYA
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 75-80
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.75
    JOURNAL FREE ACCESS
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    Ribonuclease H specifically cleaves the RNA strand of RNA/DNA hybrids. Based on the difference in the amino acid sequences, RNases H are classified into two major families, Type 1 and Type 2 RNases H. Type 1 and Type 2 RNases H share a common three-dimensional structure despite their poor amino acid sequence similarity. Whether their in vivo functions are cooperative or independent is of great interest. In addition, the enzymes, especially E. coli RNase HI, have been shown to be an excellent model not only for analyzing protein stability and protein folding, but also for protein engineering. I would like to summarize a recent progress in the RNase H studies.
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  • Simple Information Operation Depends on Geometry
    Ikuko MOTOIKE N.
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 81-86
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.81
    JOURNAL FREE ACCESS
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    In living organisms, signals propagate through various kinds of geometrical or boundary paths. It is well established that a traveling wave can be generated on an excitable field; this generation is described by reaction-diffusion equations for an activator and inhibitor. I use a numerical simulation to show that the signaling pulse can be transmitted from an excitable field to an opposing excitable field via an intervening passive diffusion field in a characteristic manner that depends upon the spatial geometry of the excitable fields. Using such characteristics, it is possible to design various kinds of simple information operations.
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  • Influence of Inter-Residue Interactions in Protein Structures
    Gromiha M. Michael
    Article type: scientific monograph
    Subject area: Infomation Science
    2003 Volume 43 Issue 2 Pages 87-92
    Published: 2003
    Released on J-STAGE: March 25, 2003
    DOIhttps://doi.org/10.2142/biophys.43.87
    JOURNAL FREE ACCESS
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    During the process of protein folding, the amino acid residues along the polypeptide chain interact with each other in a cooperative manner to form the stable native structure. The knowledge about interactions between amino acid residues in protein structures is very helpful to understand the mechanism of protein folding and stability. In this review, I classify the inter-residue interactions into short, medium and long range based on a simple geometric approach. The features of these interactions in different structural classes and folding types of globular proteins have been delineated. Further, the development of a new parameter, long-range order, based on inter-residue interactions and its application for predicting the protein folding rates are highlighted. The information gained from the studies on inter-residue interactions provides valuable insights for understanding protein folding and de novo protein design.
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Topics
Experimental techniques
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