HOMEResearch
Divisions

Professor

NAMBA, Keiichi, Ph.D.

TEL

+81-774-98-2543

Associate Prof.

IMADA,
Katsumi, Ph.D.

TEL

+81-774-98-2543

Assistant Prof.

YONEKURA, Koji, Ph.D.

TEL

+81-774-98-2543

FAX

+81-774-98-2575

Postal Mail Address

Protonic NanoMachine Project, ERATO,
JST 3-4 Hikaridai, Seika, Kyoto 619-0237
Japan

Protonic NanoMachine Group aims at the
ultimate understanding of the mechanisms of self-assembly and
its regulation, conformational switching, force generation,
and energy transduction by biological macromolecular
complexes. By convergence of complementary techniques, such as
X-ray diffraction and electron cryomicroscopy for
high-resolution analysis of three-dimensional structures, and
optical and electronic measurements on individual molecular
complexes for analyzing their dynamic behaviors, we try to
reveal the basic principles behind their functional
mechanisms, in the hope that they will become a basis for
artificial nanomachine design and nanotechnology.

1

Mechanism of self-assembly and its
regulation

The bacterial flagellum, a motile organelle, for
example, is a huge protein complex made of about 25 proteins, each
of which forms either a ring or rod-like structure with a range of
subunit copy numbers from a few to few tens of thousands. The whole
structure spans from the cytoplasmic face of the cell membrane to
the extra-cellular space, where the helical filament grows up to
around 15 micrometer. The assembly proceeds one part after another
from the base to the tip in an efficient and well-regulated manner.
We try to reveal the regulatory mechanisms based on the structure
and folding dynamics of individual component proteins and
sub-complexes.

2

Mechanism of conformational
switching

Quick reversal of the flagellar motor rotation and
polymorphic switching of the flagellar filament between left- and
right-handed helical forms switch the direction of cell swimming.
The universal joint function of the flagellar hook is essential in
transmitting the torque to the long helical filament that could be
oriented in various directions. All these processes involve highly
precise and cooperative switching in the subunit protein
conformation coupled with switching in the interactions with other
protein subunits. We try to visualize these conformational switching
and understand the mechanisms of mechanical signal transduction
based on the structure and dynamics.

3

Torque generation
mechanism

The flagellar motors are only 30 to 40 nm in diameter,
and yet, they rotate as fast as 20,000 to 100,000 rpm. We try to
understand the mechanism of torque generation by studying the
three-dimensional structure and dynamic behavior of its rotation at
high spatial and temporal resolution.

4

Energy transduction
mechanism

The high-speed rotation of the flagellar
motor is powered by the flow of protons or Na ions through a
membrane channel protein complex that performs the stator function
of the flagellar motor. The proton or ion flow is driven by the
proton or ion motive force across the cytoplasmic membrane, and the
current amounts only to several tens femtoampere. We try to measure
this extremely small electric current precisely to obtain clues to
the energy transduction mechanism.

5

Protein export
mechanism

The assembly of the flagellar axial
structure with tens of thousands of protein subunits always occurs
at the distal end of the growing flagellum. The component proteins
are selectively exported from the cytoplasm into the narrow central
channel of the flagellum by a protein complex attached on the
cytoplasmic face of the motor. This flagellar protein export
apparatus uses the energy of ATP hydrolysis and is highly homologous
to the type III protein secretion system of pathogenic bacteria, by
which pathogenic effecter proteins are secreted into host cells. We
try to visualize the export process by single molecule technique and
understand the mechanism of selective export based on the
structure.

6

Design principles for protein
nanomachine

Protein nanomachines have a unique and
special ability to form three-dimensional structures and large
complexes so that individual atoms take well-defined
three-dimensional positions to perform specific and yet various
functions in a highly precise manner. This ability of
self-organization is a great advantage in nanotechnology
development, because, without this feature, mass production of
nanomachines is impossible and therefore practical applications
cannot be expected no matter how useful individually made
nanomachines could be. The outcome of our studies on protein
nanomachines, which work flexibly and precisely at the same time, is
expected to produce much useful knowledge to eventually form a basis
for design principles for artificial nanomachines of practical
use.

HOMEResearch
Divisions

(C) 2002
Osaka University Graduate School of Frontier
Biosciences