Seibutsu Butsuri
Online ISSN : 1347-4219
Print ISSN : 0582-4052
ISSN-L : 0582-4052
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Volume 52, Issue 1
Issue 299
Displaying 1-22 of 22 articles from this issue
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Perspective
Overview
  • Genetic Code Reprogramming
    Tatsuya KOJIMA, Yuuki HAYASHI, Hiroaki SUGA
    2012 Volume 52 Issue 1 Pages 004-009
    Published: 2012
    Released on J-STAGE: January 31, 2012
    DOIhttps://doi.org/10.2142/biophys.52.004
    JOURNAL FREE ACCESS
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    Genetic code reprogramming enables us to assign nonproteinogenic amino acids to codons in place of proteinogenic amino acids according to the genetic code, which allows us to express desired nonstandard peptides using an in vitro translation system. Here, we discuss FIT (Flexible In vitro Translation) system, which is a method that facilitates genetic code reprogramming by employing flexizymes. Furthermore, we also report a method called RaPID (Random non-standard Peptide Integrated Discovery) system, which is an integration of FIT system with an in-vitro mRNA display. RaPID system allows us to select peptides with high binding affinities from highly diverse nonstandard peptide libraries and is quickly becoming a valuable new tool for drug discovery.
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Review
  • One-dimensional Brownian Motion of Charged Particles along Microtubules: A Model System for Weak, Nonspecific Interactions
    Itsushi MINOURA, Etsuko MUTO
    2012 Volume 52 Issue 1 Pages 010-013
    Published: 2012
    Released on J-STAGE: January 31, 2012
    DOIhttps://doi.org/10.2142/biophys.52.010
    JOURNAL FREE ACCESS
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    To understand the mechanism underlying the one-dimensional (1D) Brownian motion of proteins, we analyzed the behaviors of counterions along microtubules using the electroorientation method and compared these with the 1D Brownian motion of charged nanoparticles. Both results demonstrated that during 1D Brownian motion, each positively charged nanoparticle behaves as a polycation constrained within the electrostatic field around the microtubules. Owing to the polyelectrolytic nature of microtubules, nanoparticles can move along microtubules with a diffusion constant independent of the charge density of the microtubules. The study highlights the possibility that 1D Brownian motion of proteins is based on a similar, nonspecific charge-dependent mechanism.
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  • New Understanding of Chemomechanical Coupling Mechanism of F1
    Rikiya WATANABE, Hiroyuki NOJI
    2012 Volume 52 Issue 1 Pages 014-017
    Published: 2012
    Released on J-STAGE: January 31, 2012
    DOIhttps://doi.org/10.2142/biophys.52.014
    JOURNAL FREE ACCESS
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    F1-ATPase (F1) is a rotary motor protein which couples ATP hydrolysis/synthesis to rotary motion in a reversible fashion. Compared to other motor proteins, F1 is unique for its high efficiency and reversibility in converting chemical energy into mechanical work. To elucidate its marvelous mechanism, we developed the novel single-molecule manipulation technique with magnetic tweezers and determined the timing of Pi release, which was the last unknown piece of the puzzle of chemomechanical coupling scheme of F1. The established fundamental chemomechanical coupling scheme gave us a clue for high reversibility between catalysis and mechanical work.
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  • Assembly and Activation Mechanism of the Flagellar Stator Revealed by the Crystal Structure of Its Periplasmic Region
    Seiji KOJIMA, Katsumi IMADA
    2012 Volume 52 Issue 1 Pages 018-021
    Published: 2012
    Released on J-STAGE: January 31, 2012
    DOIhttps://doi.org/10.2142/biophys.52.018
    JOURNAL FREE ACCESS
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    Bacterial flagellar motor is an ion-driven supramolecular nanomachine embedded in the cell envelope. Rotor-stator interaction that couples to the specific ion translocation through the stator channel is the nature of torque generation. To produce fully functional motor, multiple stator complexes must be incorporated around the rotor at appropriate places. However, such stator assembly mechanism has not been investigated by the structural point of view. Here we describe stator assembly and activation mechanism revealed from the crystal structure of a motor component located in the periplasmic space, suggesting the dynamic conformational changes in the stator during its assembly-coupled activation.
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