Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 46, Issue 3
Issue 265
Displaying 1-10 of 10 articles from this issue
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Perspective
Overview
Review
  • Molecular Mechanism of Chaperonin GroEL: The Role of ATP and the Substrate Protein
    Hideki TAGUCHI
    2006 Volume 46 Issue 3 Pages 130-136
    Published: 2006
    Released on J-STAGE: May 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.130
    JOURNAL FREE ACCESS
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    The chaperonin GroEL is an essential molecular chaperone that assists protein folding in the cell. ATP-dependent conformational change of GroEL leads to the stable binding of cochaperonin GroES, forming a cage-shaped complex that accommodates a substrate protein to complete the folding. After the elucidation of the outline of the molecular mechanism over the last decade, now we are ready to answer the important questions; how GroEL encapsulate the substrate protein? How the substrate protein influences the functional cycle of GroEL? What is the role of ATP hydrolysis in the GroEL-assisted folding? Is the folding in the GroEL-ES cavity is same as that in the bulk solution? Here I review the recent progress on the GroEL study and discuss the essential role of chaperonin GroEL.
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  • An Interpretation of Evolutionary Dynamics in in vitro Molecular Evolution from Thermodynamical and Informational View Point
    Takuyo AITA, Yuzuru HUSIMI
    2006 Volume 46 Issue 3 Pages 137-143
    Published: 2006
    Released on J-STAGE: May 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.137
    JOURNAL FREE ACCESS
    Supplementary material
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    In vitro protein evolution is comprehended as a hill-climbing process on a fitness landscape in sequence space, just like the protein folding is comprehended as a valley-descending process on an energy landscape in comformation space. In this review, based on a mathematical model for in vitro molecular evolution, we demonstrated an analogy between evolutionary dynamics and thermodynamics and then many concepts in evolutionary dynamics became comprehensible. By introducing thermodynamics-like concepts such as “free fitness”, it is interpreted that evolution is driven in the direction in which free fitness increases. In this process, the evolving population climbs the fitness landscape by absorbing “fitness information” as the negative entropy from the surroundings as an experimental set-up.
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  • Statistical Analysis of the Relationship between the Folding Rate and Structure-Based Parameters of Globular Proteins
    Kiyoto KAMAGATA, Kunihiro KUWAJIMA
    2006 Volume 46 Issue 3 Pages 144-149
    Published: 2006
    Released on J-STAGE: May 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.144
    JOURNAL FREE ACCESS
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    Folding rates of many globular proteins which exhibit two-state and non-two-state folding have been determined experimentally. Previous studies have focused on the two-state folding, and clarified that the folding rate of two-state proteins depends on the native backbone structure. Here, we performed a statistical analysis of the relationship between the folding rate and structure-based parameters of non-two-state proteins. As a result, we found that the formation rates of both the intermediate and the native state of non-two-state folding similarly depend on the native backbone structure. The comparison of non-two-state and two-state folding suggests that non-two-state folding is more general than two-state folding.
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  • Phototriggered DNA Manipulation via Artificial Oligodeoxynucleotide
    Kenzo FUJIMOTO
    2006 Volume 46 Issue 3 Pages 150-153
    Published: 2006
    Released on J-STAGE: May 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.150
    JOURNAL FREE ACCESS
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    While many methods for enzymatic and chemical ligation of DNA fragment via a native phosphodiester bond or non-native linkages have been demonstrated, there are only a few methods for photoinduced non-enzymatic chemical ligation. The merit of the photochemical ligation avoiding the need for additional reagent is obvious. Furthermore, their actions are controllable within space and time by the choice of proper irradiation methods. The photoligation methods can be used as a tool for DNA engineering and nanotechnology, and as photoregulated diagnostic and therapeutic agents. Therefore, the target in my research program is the development about phototriggered DNA manipulation via intelligent nucleic acids toward for the next generation DNA manipulation.
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Topics
Theoretical and experimental techniques
Technical term
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