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JAPAN NANONET BULLETIN
-- 11th Issue -- February 5, 2004
Nanotechnology Researchers Network Center of Japan
Ministry of Education, Culture, Sports, Science and Technology (MEXT)

IN THIS ISSUE

Nanonet Interview:
Keiichi NAMBA, Professor, Graduate School of Frontier Biosciences,
Osaka University

Young Researchers' Introduction:
Hisao YANAGI, Research Associate, Department of Chemical Science and
Engineering, Faculty of Engineering, Kobe University

What's in the next issue?

-- NANO CALENDAR --
For information on nanotechnology related symposiums and conferences
held in the world,
http://www.nanonet.go.jp/english/calendar/

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NANONET INTERVIEW

Revealing the mystery of the bacterial flagellum
--A self-assembling nanomachine with fine switching capability--
(Issued in Japanese: March 25, 2003)

Osaka University

Nature created a rotary motor with a diameter of 30 nm. Motility of
bacteria, such as "Salmonella" and "E. coli" with a body size of 1 - 2
micron, is driven by rapid rotation of a helical propeller by such a
tiny little motor at its base. This organelle is called the flagellum,
made of a rotary motor and a thin helical filament that grows up to
about 15 micron. It rotates at around 20,000 rpm, at energy
consumption of only around 10^-16 W and with energy conversion
efficiency close to 100%. Prof. Namba's research group is going to
reveal the mechanism of this highly efficient flagellar motor that is
far beyond the capabilities of artificial motors.

The flagellum is made by self-assembly of about 25 different proteins.
The rotor ring made of protein FliF is the first to assemble in the
cytoplasmic membrane. Then, other protein molecules attach to the ring
one after another from the base to the tip to construct the motor
structure. After the motor has been formed, the flagellar filament,
which functions as a helical propeller, is assembled. Precise
recognition of the template structure by component proteins allows
this highly ordered self-assembly process to proceed without error.
The flagellar filament is made of 20,000 to 30,000 copies of flagellin
polymerized into a helical tube structure. Flagellin molecules are
transported through a long narrow central channel of the flagellum
from the cell interior to the distal end of the flagellum, where they
self-assemble in a helical manner by the help of a cap complex. The
cap is pentameric complex made of HAP2 and has a pentagonal plate and
five leg domains, whose flexible stepping movements accompanied by
rotation of the whole cap is the key mechanism to promote the
efficient self-assembly of flagellin molecules by preparing just one
binding site of flagellin at a time and guiding the binding.

Even though the filament is a polymer of chemically identical
molecules, it conforms a supercoiled structure. By using electron
cryomicroscopy and X-ray fiber diffraction, Prof. Namba's group has
discovered that the flagellar filament consists of 11 strands of
protofilaments with two slightly different conformations, named L and
R types. The repeat distance observed in the structure of the L-type
protofilament is 5.27 nm, while it is 5.19 nm in the R-type, the
difference being only 0.08 nm. The mixture of protofilaments with the
different lengths produces the helical tube structure of the filament.

Bacterial cells swim actively by rotating a bundle of flagella. The
motor switches its direction every few seconds to change the swimming
direction of the cells for bacteria to seek better environments.
Reversal of the motor rotation causes a structural change of the
flagellar filament from the left-handed to the right-handed helical
form. This makes the flagellar bundle fall apart, propelling force
imbalanced, leading to changes of the swimming direction. The switch
that triggers this change in the helical form of the filament has been
found in the atomic structure of flagellin obtained by X-ray
crystallographic analysis. When the twisting force produced by quick
reversal of the motor rotation is transmitted to the protofilaments,
part of flagellin undergoes a slight change in its conformation,
thereby making a few of the 11 protofilament strands transform from
the L-type into the R-type. As a result, normally left-handed
flagellar filament turns into right-handed helical forms. Prof.
Namba's group tried to understand the switching mechanism responsible
for these structural changes. To analyze the structure in atomic
detail by X-ray crystallography, flagellin had to be crystallized.
However, its strong tendency of polymerization made the
crystallization difficult. It took ten years for them to finally
crystallize flagellin and analyze the structure to find out the switch
mechanism, for which a super brilliant X-ray beam from SPring-8
beamlines was essential.

Prof. Namba first saw an electron micrograph of the bacterial
flagellum and its motor when he was a graduate student. He was
surprised to see such complex and sophisticated structure exist in
living organisms. It impressed him deep enough to switch his research
from muscle to flagella after a while. "Looking at the shape of the
flagellar basal body, it is obviously designed to rotate. Looking at a
picture of the flagellar motor on the wall every day, I feel up
towards revealing the mystery by any means." The design concepts of
protein molecules to realize various functional mechanisms by their
three-dimensional architecture are quite different from those we
design by our engineering technique with bulk materials. Folding of
single polymer chain into some three-dimensional structures gives a
huge amount of freedom and flexibility in both function and structure.
Individual atoms are used as functional parts, and this is the
essential feature that makes biological macromolecules distinct from
artificial machines at present. The design concepts have to be well
understood and learned for future nanotechnology applications. So far,
for the flagellar motor, the deeper our insights get into the
mechanism, the deeper the mystery becomes. Now the mystery of
conformational switching of the filament has been solved, and in terms
of the number of protein molecules, the filament makes up 99% of the
entire flagellum, it does not mean 99% of the mystery is solved. It is
the motor mechanism that is even more difficult to understand.

When Prof. Namba's group attached a 40 nm fluorescence bead to the
flagellar motor and observed the motor rotation, the group was
surprised to see large and rapid fluctuations of the rotation speed.
The key to revealing the mystery of the motor must be hidden behind
the thermal fluctuation of the protein structure, which is still so
far from understanding. "The atoms constituting proteins do fluctuate
but the average positions of individual atoms are very precisely
determined with an accuracy of sub-angstrom level. That is why
individual proteins can properly identify partner molecules to bind
and get assembled into the higher order structures of living organisms.
The fluctuations of protein structure, that's what makes living
organisms function in such sophisticated and well regulated ways. I am
willing to dedicate my entire life to the hard work unveiling the
mysterious world of protein structure and function."

(Interviewer: Kuniko Ishiguro, Cosmopia Inc.)

For more information,
http://www.nanonet.go.jp/english/mailmag/2004/011a.html

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YOUNG RESEARCHERS' INTRODUCTION

Molecular nanoelectronics and photonics - Research on organic
semiconductor laser and single-molecular switching device -
(Issued in Japanese: March 25, 2003)

Hisao YANAGI, Research Associate, Department of Chemical Science and
Engineering, Faculty of Engineering, Kobe University and Researcher,
Precursory Research for Embryonic Science and Technology (PRESTO),
Japan Science and Technology Agency (JST)

Electronic band structures play an important role in covalently bound
crystals of inorganic semiconductor materials. A variety of
optoelectronic devices have been developed based on their quantum
effects using bulk downsizing technology. On the other hand, a bottom-
up molecular organization is important for organic materials, in which
molecules interact by weak van der Waals force, since their solid-
state properties are basically ascribed to individual molecular
characteristics.

Moreover, molecular orientation in the solid-state strongly affects
their properties due to a low-dimensional anisotropy of chainlike and
planar molecules. This study aims at developing novel molecular
electronic/photonic materials by low-dimensional ordered structuring
of functional molecules across single-molecule, nanoscale and
microscale ranges.

To date, we have observed lasing actions from self-organized zero-
dimensional microdots and one-dimensional nanoneedles of fluorescent p
-conjugating oligomers based on the microcavity and self-wave guiding
effects of light confined in these low-dimensional structures.
Furthermore, a reversible flip-flop single-molecular switching
phenomenon induced by scanning tunneling microscopy has been observed
for two-dimensional monolayer arrays of ansymmetric, and polar
subphthalocyanine molecules adsorbed on a metal surface in ultrahigh
vacuum.

We are now investigating their detailed mechanisms for the practical
development of organic semiconductor lasers and high-density molecular
information storage devices.

For more information,
http://www.nanonet.go.jp/english/mailmag/2004/011b.html

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WHAT’S IN THE NEXT ISSUE?

Nanonet Interview:
Toshio KIMURA, Fellow and General Manager, Central Research
Institute, Mitsubishi Materials Corporation

Young Researchers' Introduction:
Hidekazu TANAKA, Associate Professor, Atom Scale Science Division,
The Institute of Scientific and Industrial Research, Osaka University,
and Researcher, Precursory Research for Embryonic Science and
Technology (PRESTO), Japan Science and Technology Agency (JST)

The next issue of JAPAN NANONET BULLETIN will be delivered on February
19, 2004.

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Nanotechnology Researchers Network Center of Japan distributes
this e-mail newsletter, "JAPAN NANONET BULLETIN", every other Thursday
with the aim of promoting information exchange and cooperation among
researchers in nanotechnology and related fields.

JAPAN NANONET BULLETIN contains articles, "Nanonet Interview", in
which we interview a leading researcher about current issues and/or
research strategies for the future and "Young Researchers'
Introduction", in which a young researcher in the nanotechnology field
introduces his/her own recent research.

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Nanotechnology Researchers Network Center of Japan
Ministry of Education, Culture, Sports, Science and Technology (MEXT)
Our website: http://www.nanonet.go.jp/english/
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