Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 46, Issue 2
Issue 264
Displaying 1-11 of 11 articles from this issue
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Perspective
Overview
Review
  • Chemical Reactions in Biological Systems Studied by Hybrid QM/MM Simulations
    Shigehiko HAYASHI
    2006 Volume 46 Issue 2 Pages 76-81
    Published: 2006
    Released on J-STAGE: March 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.76
    JOURNAL FREE ACCESS
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    Chemical reactions play important roles in biological functions. In order to elucidate molecular mechanism of the chemical reactions in biosystems, so-called hybrid quantum mechanical/molecular mechanical (QM/MM) methods have been developed and applied to many biochemical reactions recently. The methods permit one to calculate electronic states of reaction substrate molecules in protein binding pockets by taking into account molecular interactions with the surrounding protein environment. In this review, we survey our QM/MM studies for chemical reactions in rhodopsin photoreceptor proteins and F1-ATP synthase along with a brief introduction of the methodology.
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  • Transglutaminase-Catalyzed Cross-Linking and Its Modification of Protein Aggregation
    Takashi KONNO, Takashi MORII, Koji IKURA
    2006 Volume 46 Issue 2 Pages 82-86
    Published: 2006
    Released on J-STAGE: March 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.82
    JOURNAL FREE ACCESS
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    Tissue-type transglutaminase, which modifies protein assembly in the living body by the cross-linking reaction, is known to be involved in a variety of physiological and pathological processes. For understanding the phenomena related to the functions, not only the biological studies but also the physico-chemical analyses of the cross-linked products are highly required.
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  • Regulating the Activity of the Herpesviral Protease and Its Viable Target for Inhibition
    Nobuhisa SHIMBA
    2006 Volume 46 Issue 2 Pages 87-92
    Published: 2006
    Released on J-STAGE: March 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.87
    JOURNAL FREE ACCESS
    Supplementary material
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    Kaposi’s sarcoma-associated herpesvirus (KSHV), like all herpesviruses, encodes a protease (KSHV Pr), which is necessary for the viral lytic cycle. Herpesviral proteases function as obligate dimers, however, each monomer has an active site, which is spatially separate from the dimer interface. To address the potential of targeting the dimer interface, a 30 amino acid helical peptide was synthesized by protein grafting of an interfacial KSHV Pr a helix with a small stable protein, avian pancreatic polypeptide (aPP) to disrupt the dimerization of KSHV Pr. Biochemical analysis revealed that the rationally designed helical peptide inhibited KSHV Pr dimerization and activity. These results indicate that the dimer interface, as well as the active sites, of herpesvirus proteases is a viable target for inhibiting enzyme activity.
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  • Ligand-Receptor Interactions of the Ionotropic Glutamate Receptor
    Minoru KUBO
    2006 Volume 46 Issue 2 Pages 93-97
    Published: 2006
    Released on J-STAGE: March 25, 2006
    DOIhttps://doi.org/10.2142/biophys.46.93
    JOURNAL FREE ACCESS
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    Ionotropic glutamate receptors are ligand-gated ion channels involved in neurotransmission. In 1998, a crystal structure was first solved for the soluble mini-receptor that only included the S1S2 ligand-binding domain of the rat GluR2 subunit. Since then, a lot of crystal structures of the S1S2 construct both in the apo and in various liganded states have been reported. More recently, biophysical studies revealed the structural flexibility of the S1S2 construct. Here, I summarize the ligand-receptor interactions based on the recent progress in characterizing the dynamic structures of the S1S2 construct and the glutamate ligand.
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