Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 48, Issue 4
Issue 278
Displaying 1-17 of 17 articles from this issue
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Perspective
Review
  • Enzymatic Reaction Mechanisms of RNA Enzyme (Ribozyme) Revealed by First Principles Molecular Dynamics Simulations
    Masaru TATENO, Mauro BOERO
    2008 Volume 48 Issue 4 Pages 216-220
    Published: 2008
    Released on J-STAGE: July 25, 2008
    DOIhttps://doi.org/10.2142/biophys.48.216
    JOURNAL FREE ACCESS
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    Reaction mechanisms of ribozymes (“RNA enzymes”) revealed by the first-principles molecular dynamics simulations are discussed. The calculations are performed on an RNA fragment as a model structure of the catalytic site of ribozymes, in the absence/presence of explicit solvent water molecules, leading us to understanding the detailed mechanisms and the catalytic roles of divalent cations and solvent in in vitro reaction. Two cations, which are bound to the O2’/O5’ atoms of the catalytic nucleotide, and a hydroxide ion involved in a solvation shell of the cation bonding to the O2’ atom are indicated to concertedly decrease the activation barrier. The entire structure of a ribozyme molecule is now being investigated by using QM/MM hybrid molecular dynamics simulation. The computational methodology mentioned here is applicable also to other biological macromolecular systems.
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  • Mathematical Understanding for the Molecular Mechanism of Cyanobacterial Circadian Rhythms
    Hisako TAKIGAWA-IMAMURA, Atsushi MOCHIZUKI
    2008 Volume 48 Issue 4 Pages 221-227
    Published: 2008
    Released on J-STAGE: July 25, 2008
    DOIhttps://doi.org/10.2142/biophys.48.221
    JOURNAL FREE ACCESS
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    A cyanobacterial clock protein KaiC shows circadian cycling of the phosphorylation level in vitro. We first developed an observation-based model. The KaiC-KaiA complex formation consequently reduces free KaiA molecules, thereby may exert a negative feedback effect toward KaiC phosphorylation. However, this model was shown not to be adequate to generate the KaiC phosphorylation cycle. Then, we analyzed generalized models and determined necessary conditions to generate the cycle. Based on the result, we realized the observed pattern of the KaiC phosphorylation cycle and predicted an unknown state that lies between KaiC phosphorylation and the formation of the KaiC/KaiA complex.
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  • Biophysical Approaches for Understanding Lifespan and Aging
    Hitoshi SUDA
    2008 Volume 48 Issue 4 Pages 230-234
    Published: 2008
    Released on J-STAGE: July 25, 2008
    DOIhttps://doi.org/10.2142/biophys.48.230
    JOURNAL FREE ACCESS
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    To understand aging and lifespan at the gene level, the era is just coming. Which is lifespan due to the programming or circumstance’s factors? The outline of lifespan, in this review, will be given from the deterministic and stochastic views. In the near future, the biophysical approach such as structural biology and mathematical framework is needed to develop the study of aging and lifespan.
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Topics
Theoretical and experimental techniques
Activity of Regional Branch
Young Voice
Letters from Abroad
Promenade along Protein 3D Structures
Technical term
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