Probing life at the nanoscale

Tra ns di s ci p l i nar y Researchat NanoLSI

Feb.2019 1st ed.

NanoLSIB o l d l y pi o n eer i n g t h e unch a r t ed na no rea lm o f t h e lif e s c ienc es

Kanazawa University established the Nano Life Science Institute (NanoLSI) in 2017 to fulfill its selection for the World Premier International Research Center Initiative (WPI), an effort
launched by the Ministry of Education, Culture, Sports, Science and Technology to develop research centers that have a salient presence in the global scientific community for their worldclass research environments and superlative standards of research. NanoLSI is now the staging ground of bold explorations for pioneering the uncharted nano realm of the life sciences.

Elucidating the truths of biologicalph en omen a on the na nosca leOver the centuries, humankind has developed various

NanoLSI is a community of scientists who for many years have produced world-class research

microscopes to peer into microcosms invisible to theachievements spanning four domains: Nanometrology, Life Science, Supramolecular Chemistry, andunaided eye. Those observations have taught us about all

Computational Science.

sorts of physical properties and the origins of diverse

Ta ke s h i
FukumaDi r e c t o r o f
W P I - Na n o L S I

Bringing innovation to the life sciencesth ro u g h tra n s d is c iplin a r y re s e a rch

Leveraging cutting-edge technologies in scanning probe microscopy (SPM)* and integrating/expanding

phenomena, and in so doing have helped science to evolve.

our four research domains, we strive to develop nanoendoscopic (nanoprobe) technologies that will

However, there’s a world we are still unable to observe

enable us to directly observe the relationships and action of molecules that perform critical roles insidedirectly—the nanoscale structures and dynamics of atoms

and outside cells, and thus gain the insights needed to analyze and manipulate them. By witnessing

and molecules. This is the uncharted nano realm, and webiological phenomena unseen before, we will be able to bring forth tremendous advances to the life

greatly need to develop the technologies that will allow us

sciences and establish a new domain of science, “Nanoprobe Life Science.”

to unlock its mysteries.
The surface and interior of the cells that make up our*Scanning probe microscopy (SPM): Microscopy that measures a specimen’s surface form and properties via an
ultrafine-tipped probe tracked near the specimen’s surface.

bodies are populated with countless molecules that
perform many functions in diverse ways, giving rise tobiological phenomena. For this reason, our observation of
their behavior and interactions would be a key to

A o n e - o f- a - kin d re s e a rch c e n te r

understanding and controlling the mechanisms of
biological phenomena. However, science and technology

Since the beginning, NanoLSI scientists have regularly shared insights, perspectives, and methodologies

have yet to advance to the level necessary for fully

with their colleagues in the institute’s other research domains. By engaging in such transdisciplinary

bringing that dream to reality. NanoLSI thus seeks to chart

dialogue, they have developed a deep mutual understanding that helps them to advance world-leading

the uncharted nano realm of the life sciences in order toresearch in their respective fields and to make effective use of the shared body of knowledge and research

endow humankind with a fundamental understanding ofexpertise. The result is a close-knit community of diverse scientists, and it is our goal to nurture andthe many different phenomena of life.

evolve the ideas that only such a community can produce. As a one-of-a-kind research center, we arefirmly committed to generating a steady stream of new discoveries and concepts, and translating theminto advances in science and technology, in a constant cycle of creation and evolution.

- 01 -- 02 -Sup ra m olec ula r C h em ist r y

The Tale of an Adventure to
the Secrets of Life
Life is made possible because the molecules inside and outside thecells of our bodies carry out certain duties. But, what are their shapes?
How do they work? At NanoLSI, we endeavor to unravel the secrets oflife by answering such questions.

Life Science

I can make special molecules that are able to distinguishand move molecules I’m interested in. Eventually,
I’ll become able to manipulate molecules inside cells, andthen I can help develop new types of microscopes!

Nanometrology
Wow! That means we’ll be able to directly view molecules
both inside and outside cells! Now, since we’re talking
about viewing the behavior of tiny molecules withtechnologies that haven’t been realized before, the next
step is to prove that our understanding of them is right.

Computational Science

I already know the basic functions of most molecules.
But, since I haven’t seen what actually goes on in the cell,such as the actual shape and movements of themolecules, I still don’t know their physiological functions.

I have tons of data I’ve collected, so I can use simulations
to back up our understanding of the tiny molecules’
behavior. Let’s pool together our expertise and test which
patterns are able to explain the molecular behavior!

Nanometrology
Life Science
I have cutting-edge technologies in microscopy that allow
me to make video observations of the shape and behaviorof molecules. With those technologies, I can develop evenmore amazing microscopes that can see molecules within
the world of cells. However, there are still somechallenges that need be overcome in viewing themolecules inside cells.

- 03 -

Thanks to our exploration of the world of cells, we’ve
gotten closer to uncovering the truth behind biologicalphenomena, like the mechanisms of how life starts andhow diseases develop. Our research will open the door to afuture where we can aid the development of new ways todiagnose and treat people!

- 04 -

Nanometrology

Life Science

Developing nanoprobe technologies

Elucidating t he basic principles offun d a men t a l cellula r fu n ct io n s

The Nanometrology group brings together many

By examining molecular dynamics through comparison

scientists who have pursued world-leading researchof normal cells and cancer cells, we can learn theutilizing two forms of SPM: atomic force microscopy

molecules’ physiological functions and gain(AFM), which offers high-speed, high-resolution, andunderstanding of the mechanisms by which theirthree-dimensional observation, thanks to theabnormalities lead to cancer. Using newly developed

application of unique developmental technologies, andnanoprobe technologies such as SPM and molecularscanning ion-conductance microscopy (SICM), which

sensors that react only to specific molecules, the Life

enables observation of the soft surfaces of cells because

Science group observes “as is” the molecules essential tothe probe does not come into contact with thebiological phenomena, with the aim of elucidating thespecimen’s surface. While continuing to evolve both AFM

basic principles of fundamental cellular functions,and SICM, this group seeks to establish nanoprobe

including cell proliferation, differentiation, death,technologies that, through fusion with supramolecular

movement, and so on. In the future, this group will

chemistry, realize direct observation, analysis, andutilize its discoveries to develop new methods ofmanipulation of biomolecular dynamics.

diagnosing and treating cancer and many other diseases.

A fusion of four sciences

Nanoprobe Life Science

Supramolecular Chemistry

Computational Science

M an i p u l at i n g m o l ec u l e
w i t h s u p ram o l ec u l a r fo rc es

Bridging t he gap between
ima gin g a n d rea lit yThis group freely designs molecules through the ingenious

It is not easy to identify new principles of dynamics only

use of diverse molecular structures. It seeks to develop

through observation with novel measurement

supramolecules as sensors that bind only to a specifictechnologies, notably SPM, which visualizes themetabolite or protein through molecular recognition—nano-level structure and properties of the target

whereby the size and shape of a molecule are identified

molecule through its interactions with the probe.

based on its interactions with other molecules—and thus

Sophisticated simulation technologies are also necessary.

can be used to reveal the intracellular distribution of the

The Computational Science group endeavors to

metabolite or protein. In addition, the group plans use

understand the reality of biological phenomena bymolecular machines—whose structures change inelucidating the principles of dynamics. To do this, they

response to external stimuli such as light and ions—toreproduce the patterns of molecular dynamics inferred

realize endoscopic manipulation techniques forfrom the images obtained from imaging techniques andmanipulating the shape and position of specific molecules

integrate the knowledge and experiences of various

in a cell during observation with a nanoprobe microscope.

disciplines.
- 05 -

NanoLSI

Wo rking toward the creation of a new discipline: Nanoprobe Life Science

Scientists in NanoLSI’s four research groups—Nanometrology, Life Science, Supramolecular Chemistry, and Computational Science—are pursuing diverse transdisciplinary research projects driven by nanometrology.

New insights from the merger of original AFM
technology and sophisticated simulation＞ Sh e ddi n g l ight on t he unknow norigins and principles of naturalp h e n o me n a

Nuclear pore complexes: Exploring
molecular nanogates at the nano leve l＞ Uncovering the action of NPCs,
molecular nanogates

Takeshi Fukuma

Richard Wong
Li fe S c i e n c e

N anometrology

Nuclear pore complexes, NPCs, are the sole passageway
Prof. Takeshi Fukuma has developed technologies for&frequency modulation atomic force microscopy (FM-AFM),&

for the transport of materials between a cell’s nucleus
and cytoplasm. They are protein complexes that monitor

which enables high-speed, high-resolution observation at thethe vast quantity of information used in biological

Adam S.Foster

atomic level, and three-dimensional AFM (3D-AFM), which
can be used to observe the three-dimensional spatial

genetic information. They are indispensable to biologicalComputational
S c ie nc e

distribution of water molecules and molecular chains, among

Toshio Ando

phenomena and selectively control the exchange of

N anometrology

phenomena, as attested by their control of theothers. Seeking to uncover new insights in well-known
phenomena, he has turned his attention to calcite, a mineralthat, as the world’s largest carbon pool, poses a critical

1][42

0.5 nmproliferation- and metastasis-related signaling in cancer
0][01

impact on the global carbon cycle. Using high-speed FM-

the atomic level by combining his technique with Prof. Adam
Foster’s high-precision simulation analyses.

20 s

3 nm

0 nm

10 s
[441]

atomic-resolution observation of the calcite dissolution
process, and he has elucidated the dissolution mechanism atmembranes of human colorectal cancer cells andHigh-speed AFM cantileverobserved them using the high-speed AFM system
0s

AFM, he became the first in the world to succeed incells. Prof. Richard Wong has isolated the nuclear

CaCO3

Ca(OH)2

Nuclear pore complexes,
NPCs

developed by Prof. Toshio Ando. Through this research,he has shed light on NPC structure and dynamics, and[461]

The dissolution process of calcite surface as observedwith high-speed FM-AFM (top) and a simulation model
demonstrating the molecular-level changes (bottom).

uncovered the characteristic deformation of NPCs when
the cancer cells die from the administration of cancer
drugs.

Conceptual image ofintracellular observationand visualization using new
SPM system that might be
developed in the futurecellnucleuscell＞ Future development of ar tificial NPCs could pave way for nanotherapies＞ The next challenge: Elucidating mechanisms of biological phenomena

In its current state, the technology used by Prof. Wong can observe NPCs only in isolated nuclear membranes.

The structure of chromatin—largely made up of DNA, the carrier of genetic information—plays a major role in gene

However, if an SPM system capable of observing the NPCs inside living cells were to be innovated, it may be

expression and control, which provide the foundation for life activities. With the aim of elucidating the genetic

possible to reveal NPC functions and dynamics in molecular interactions inside and outside the cell. By merging

abnormalities behind various diseases through investigation of the three-dimensional structure and dynamics ofcellular biology’s insights on biological functions, high-speed AFM’s revelations of structures, and clinicalchromatin, the two professors are working to improve the AFM and simulation technologies necessary forunderstanding of pathology, scientists may find ways to create therapeutic technologies for nano-level control ofanalyzing the three-dimensional structure of biomolecules.

abnormalities in various biological phenomena, such as by developing artificial NPCs.

- 06 -- 07 -

Dynamic structural biology for activating andc on t rollin g s ign alin g m olecule H GF
＞ An ef for t to unravel the truem e ch an ism b e hind HG F -ME T
receptor activation

Kunio Matsumoto

Designing an original probe for 3D spatial
distribution imaging of target molecules＞ Developing technologies for 3D spatial
distribution imaging of target molecules

Hitoshi Asakawa

L ife S cie nc e

N anometrology

3D-AFM, which was developed by Assoc. Prof. Hitoshi Asakawa
Hepatocyte growth factor (HGF) is a protein that&

promotes cell proliferation and survival when it binds

molecular structures, based on the interactions between thewith its receptor, MET. Since HGF plays a key role in tissue
regeneration/repair and is involved in cancer metastasis
as well, it is used in regenerative medicine and cancer

probe and the atoms/molecules. Meanwhile, pillararenes,

Mikihiro Shibata

molecules first discovered by Prof. Tomoki Ogoshi, are simple
rings of symmetric pillar-shaped structures. By designing a

N anometrology

diagnosis/treatment. Prof. Kunio Matsumoto, in a quest

pillararene with a suitable ring size or recognition sites, theto find the true mechanism of how HGF activates MET

pillararene can selectively incorporate into its ring a target

receptors, has teamed up with Assoc. Prof. Mikihiro

molecule with subtle differences in size or shape, like a key and
HS-AFM tip

Shibata, who has used high-speed AFM to capture the

keyhole relationship. This project is exploring the possibilities

actual behavior of biomolecules. To date, Shibata and his

for attaching molecule-recognizing pillararenes on probes to 
Conceptual image ofhigh-speed AFM
observation of themechanism behind
HGF activation of
MET receptors

the blueprint of life. In this research project, they havestarted to shed light on the unknown realm of the
dynamic structure of MET activation.

S u p ra mo l e c u l a r
ChemistryThree-dimensional
observation by 3D-AFM

Molecular recognition
with pillararenes

Probedetect the distinctive forces acting between the pillararenes
and the target molecule in three-dimensional space, and thus
enable visualization of the spatial distribution of tiny target
molecules in real space.

MET(receptor)

MET(receptor)＞ Innovative discoveries may open door to new drugs and other therapies＞ S triving toward fusion withcomputational science and life science

Elucidation of the dynamics of the interactions that take place between the miniscule proteins in the body would

Going forward, scientists will not only need to use simulations to develop

not only provide substantive understanding of functions and structural changes, but also open the door to thebetter understanding of measurement data, but also design supramolecules

creation of new drugs and other forms of therapy. The ability to use high-speed AFM for direct video observation inthat can recognize specific proteins or metabolites essential to functionala near-in vivo environment offers the potential for new discoveries that shatter established thinking and thus

analysis for understanding biological phenomena. NanoLSI is stepping up

contribute to the advancement of the life sciences. As a potential precedent for such evolution, this project will

research for developing technologies in both areas, aiming to bring about acontinue to engage in transdisciplinary research founded on the elucidation of HGF-MET dynamics.

fusion of both areas with computational science and life science.

- 08 -

Tomoki Ogoshi

Scanning trajectorycolleagues have visualized the behavior of DNA/RNA andproteins related to the editing of genomic information,&and colleagues, enables three-dimensional spatial imaging of- 09 -

Acquiring 3D data by
moving the probe in
both horizontal andvertical directions

Molecules with evenjust small differences insize or shape are notincorporated

Visualization of a target molecule’s distribution byusing an originally designed probe that reacts only tomolecules taken in by pillararenes