Symposium List
[Satellite Symposium]
24(Wed), November
13:30-16:00

50 years of the Protein Data Bank and the frontier of the Structural Biology in
Asia
Organizers︓Genji Kurisu（Osaka Univ.）, Toshimichi Fujiwara（Osaka Univ.）
Summary︓
In 1971, the structural biology community established the single global archive for 3D macromolecular
structure data: the Protein Data Bank (PDB). Approximately one fourth of the entire PDB data
originated from Asia. In 2000, Protein Data Bank Japan (PDBj) started on-site data processing as a
newly founded Asian hub for PDB data resource. Since 2001, PDBj has provided our newly developed
online Data-out services available freely and publicly through our own web site (https://pdbj.org),
which we have enhanced through the years. With the establishment of the worldwide PDB in 2003,
we have served as one of its regional data centers, collaborating on Data-in and Data-out activities
on a global scale. In 2021, we are celebrating the 50th anniversary of our single global archive,
especially this time in Asia, and want to discuss the frontier of the Structural Biology in Asia.

[Symposium]
25(Thu), November
9:00-11:30

Japan-US symposium on cytoskeletal motor proteins and their associatedproteins
Organizers︓Kumiko Hayashi（Tohoku Univ.）, Shinsuke Niwa（Tohoku Univ.）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Speakers in this symposium are recognized internationally as experts in the field of cytoskeletal motor
proteins such as kinesin and dynein, and their associated proteins. We are planning to prepare enoughtime to have a deep and detailed discussion among the speakers and audience on these subjects. The
symposium topics cover multidisciplinary applications of genetics, bio-engineering, bio-chemistry,
medical science, and physics, which will give us new insights into the intracellular transport and motor
proteins, as well as interesting applications of existing single-molecule techniques.

9:00-11:30

Dawn of Molecular System Engineering for Chemical AI
Organizers︓Taro Toyota（The Univ. of Tokyo）, Shogo Hamada（Tohoku Univ.）
Summary︓

C. Elegance has a brain consisting of 302 cells, which controls all the behaviors of the organism. The
neurons in its brain are classified into three levels, and they are connected by about 6000 synapses.
On what principle do these "wet" information processing systems operate? At least, such systems
must be constructed by the power of chemistry. A new methodology of "how to assemble individual
molecules and molecular devices into complex functional systems" is attracting attention as "molecularsystems engineering". In Grant-in-Aids for transformational research "Molecular Cybernetics" (20202024), we will investigate principles of the molecular systems engineering. Specifically, designed
molecules that function as sensors, processors, and actuators will be assembled in a micrometer-sizedcompartment (artificial cell) such as a liposome. The resulting artificial cells can then be further
combined with each other to construct higher-order functional systems. In this symposium, we will
discuss the design principles and practice of such artificial cells and other issues related to theconstruction of chemical artificial intelligence (AI).

9:00-11:30

Recent progressexperiments

inbiometalsciences:synergy

betweentheoryandOrganizers︓Yasuteru Shigeta（Univ. of Tsukuba）, Takehiko Tosha（RIKEN）
Summary︓
Various metallic and semi-metallic elements, which are present in very small amounts in livingorganisms (defined as biometals), are essential for all living organisms. Their functions range fromsignal transduction and electron transfer to enzymatic reactions for the production and metabolism of
substances. It is mystery that these trace amounts of biometals are programmed into life besides thecentral dogma. In this symposium, the latest researches on biological reactions and structures
involving biometals and their kinetic analysis will be presented from both theoretical and experimental
approaches.

9:00-11:30

Structural and Functional Dynamics of Biomolecules: Interplay between Single
Molecule Measurement and Molecular Simulation
Organizers︓Tadaomi Furuta（Tokyo Inst. of Tech.）, Kiyoto Kamagata（Tohoku Univ.）
Summary︓
Currently, the qualitative and quantitative developments of experimental and computational methods
have made it possible to directly observe important structural and functional dynamics of various
biomolecules. Recently, there have been many reports that lead to further understandings of biologicalphenomena by integrating information obtained from these experiments and simulations. In view ofthis situation, the theme of this symposium is at the stage where it should be promoted further.
Therefore, in this symposium, several researchers on the experimental side, simulation side, andintegrated researches will present the latest research results and general remarks, which would beclues leading to profound understandings of biological phenomena.

9:00-11:30

New perspectives on cells provided by single cell analyses
Organizers︓Yuichi Taniguchi（Kyoto Univ.）, Shinya Kuroda（The Univ. of Tokyo）
Summary︓
Single cell biology is a growing field to quantitatively understand the nature of individual cells that
inherently have large heterogeneity. This growth is supported by progresses in a variety of single-cellapproaches such as DNA/RNA sequencing, optical imaging, mass spectroscopy, high-throughput
measurement, theory and informatics. In this symposium, we invite several single-cell biology
scientists who conduct cutting-edge research using different approaches, aiming at discussing whatsingle cell biology will bring towards understanding of life phenomena.

9:00-11:30

New concepts in GPCR research and implications for drug discovery
Organizers︓Kota Katayam（Nagoya Inst. of Tech.）, Ryoji Suno（Kansai Medical Univ.）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
The recent trend in the field of structural studies of G-protein-coupled receptors (GPCRs) using cryoelectron microscopy (Cryo-EM) and 3D reconstruction techniques supported by biophysical,
computational and advanced biochemistry have facilitated GPCRs research towards drug discovery.
These techniques contributed significantly to our understanding about GPCRs functions, ligand
recognition, pharmacological targets in biomedicine. This symposium will highlight the latest
developments in GPCR structure/function, ligand discovery and design, intracellular signalling
pathways and their impact on modern drug discovery.

16:00-18:30

India-Japan joint symposium: Various challenges on biophysical research
Organizers︓Miyuki Sakaguchi（Saitama Univ.）, Ken H. Nagai（JAIST）
Summary︓
To promote the exchange between the Indian Biophysical Society (IBS) and the Biophysical Society ofJapan (BSJ), this joint symposium focusing on energetic young scientists was planned. Four up-andcoming researchers are nominated by IBS, and they will give talks in a wide range of fields like proteinfunction during embryogenesis, super-resolution imaging with DNA, morphogenesis in an active-polargel, and the physical basis on self-reproducing catalytic RNAs. From BSJ, three leading researchers in
related fields will also give talks. In the symposium, we will share the problems at the forefront, andexchange cutting-edge technologies and knowledge.

16:00-18:30

Water dynamics and biological functions: Revisit
Organizers︓Masahiko Imashimizu（AIST）, Hiroshi Murakami（QST）[Pick up speakers from the students and post-doctoral fellows]
Summary︓

Extensive studies of hydration water dynamics show that they occur from the picosecond tonanosecond timescales. We, however, consider from recent studies that much slower dynamics ofwater may play critical roles in expressing biological functions. Such studies include findings of glasslike water in a model of cells and glassy behaviors of cytoplasm, and of nonthermal effects on slow
biomolecular dynamics and reactions by the externally applied alternating electromagnetic field withterahertz frequency. In this symposium, we will attempt to discuss new directions that connect thephysicochemical studies of hydration to biological functions through water relaxation processes in awide temporal range.

16:00-18:30

Trends in the research field of thermo-sensation
Organizers︓Kunitoshi Uchida（Univ. of Shizuoka）, Yuichiro Fujiwara（Kagawa Univ.）
Summary︓
Since TRPV1 channel, the worldʼs first mammalian thermo-receptor, was uncovered in 1997, several
thermo-receptors have been elucidated, and the biological meaning of thermo-sensation are becoming
clearer.

In this symposium, we will introduce the recent works aimed to evaluate the measurement

and manipulation techniques of temperature in living matter, and to elucidate the gating mechanismsof thermo-receptors by temperature changes and physiological roles of thermo-sensation.

We willalso discuss the biological significances and future perspectives of thermo-sensation.

16:00-18:30

Recent Advances in Origins of Life and Protocell Research
Organizers︓Tony Z. Jia（Tokyo Inst. of Tech.）, Yutetsu Kuruma（JAMSTEC）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
One of the major questions in ancient and modern science is the question of our own creation. How
did life emerge on Earth? What were the structures and functions of the first cells? Recent
technological advances in biophysics, especially in Japan, are now allowing researchers in a variety offields such as synthetic biology, evolutionary biology, and biochemistry to finally begin to answer thesequestions. This symposium highlights recent advances in Origins of Life and Protocell research bybiophysicists from Japan and around the world. We hope to inspire other biophysicists, especially
young researchers, to also consider studying these very difficult (but important) unansweredquestions.

16:00-18:30

Toward understanding biological functions: atomic-level characterization of
structures and dynamics of biomolecules
Organizers︓Osamu Miyashita（RIKEN）, Eriko Nango（Tohoku Univ.）
Summary︓
Information on the structures and dynamics of biological molecules plays a critical role inunderstanding their functional mechanisms and possible medicinal applications. Time-resolved serialfemtosecond crystallography (TR-SFX) using X-ray free electron laser (XFEL) is a state-of-art
technique that can provide 3D structures of the molecules following the time-development of reactions.
Furthermore, integrative analyses combining TR-SFX data with other approaches could provide moredetailed information on dynamic structures and energetics. This symposium will focus on recent
updates on TR-SFX experiments and applications, as well as recent developments of otherexperimental techniques and computational approaches, aiming to advance our understanding of
biomolecular functions through integrative research.

16:00-18:30

Bridging biophysics/soft-matter physics and medical science
Organizers︓Hiroshi Fujisaki（Nippon Medical School）, Komura Shigeyuki（Tokyo Metro. Univ.）
Summary︓
Research towards tailor-made and precision medicine is accelerating, and this requires mathematicaland physical approaches in addition to empirical medical traditions. Medical physics has been
established as a field that links medicine and physics, and recently, AI has been used for pathologicalimaging diagnosis and particle therapy. On the other hand, biological phenomena have various
hierarchies, starting from the molecular level to cells, organs, individuals, and populations, and withthe advancement of computers, highly precise simulations of these phenomena are now becoming
possible. In this symposium, we will explore the possibility of medical applications, including
therapeutic methods, from the standpoint of biophysics and soft matter physics. The main purpose ofthis symposium is to have a lively discussion among medical scientists, biophysicists, and physicists
about the awareness of problems in the field of medicine and how to deal with them in theory andcalculations.

16:00-18:30

Approaches to diverse biological phenomena produced by singularity cells
Organizers︓Hiroko Bannai（Waseda Univ.）, Ken-ichi Wakabayashi（Tokyo Inst. of Tech.）
Summary︓
In multicellular systems, there are many phenomena that result in dramatic changes in morphology
and dynamics caused by a small number of cells. In this symposium, we will introduce challenging
research to find rare cells, i.e. "singularity cells", which are the driving force of dramatic changes indiverse biological phenomena such as algal behavior, stem cell differentiation, organogenesis, andneurological diseases. Elucidating the mechanism by which "singularity cells" significantly change theentire system requires new perspectives and methodologies. By sharing this approach with members,
we aim to spread a new methodology of biophysics and a new academic field "Singularity Biology".

16:00-18:30

Information biophysics of gradient sensing in organisms
Organizers︓Akihiko Ishijima（Osaka Univ.）, Yasushi Okada（RIKEN/The Univ. of Tokyo）[Pick up speakers from the students and post-doctoral fellows]
Summary︓

Biological sensory systems, such as chemotaxis, phototaxis, gradient sensing and so on, are functions
that are widely available in the biological world. For example, bacterial chemotaxis is one of the mostwell-studied areas from both theoretical and experimental perspectives. Various methods have beenused in experiments, including genetics, biochemistry, and imaging. Theories have been discussed
from various perspectives such as Ising model, information theory, and efficiency. In this symposium,
we would like to gather theoretical and experimental researches to promote mutual integration fromthe viewpoint of information biophysics.

26[Fri], November
9:00-11:30

Technical Development
Microscopes

andSharingofHigh-Resolution

Cryo-Electron

Organizers︓Haruki Nakamura（Osaka Univ.）, Masahide Kikkawa（The Univ. of Tokyo）, Takeshi
Murata（Chiba Univ.）
Summary︓
So far, high-end cryo-electron microscopes (EMs) have been installed along with the BINDS (Basis for
Supporting Innovative Drug Discovery and Life Science Research) program since 2017, and 8 morecryo-EMs are going to be introduced in 2021 at several laboratories in Japan. Recent technologicalprogresses including development of new grids and methods for on-line usage will surely provide
higher-resolution, higher-throughput structural analysis, by sharing the cryo-EM devices among
researchers in Japan. In this symposium, we will review the results of single particle analysis,
tomography, and micro-ED by cryo-EMs, and will introduce the issues to be overcome by the recent
technologies. Finally, we will discuss the future development including the scope of the next BINDS
program, which is expected to start in 2022.

9:00-11:30

Biophysical basis for understanding the protein-protein interaction involved inessential cellular process
Organizers︓Risa Mutoh（Fukuoka Univ.）, Takumi Koshiba（Fukuoka Univ.）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Protein-protein interactions are essential biological reactions occurring at inter- and intra-cellular levels.
The analysis of their mechanism is generally required in order link to understand their various cellularfunctions. Recent biophysical methodologies provide us useful tools for investigating protein-protein
interactions, especially in live cells.

In this symposium, we invite domestic young investigators anddiscuss on new techniques (e.g. IP-MS, lipid mixing assay, bioluminescence) that explore a new studyof protein-protein interaction and membrane protein complexes involved in essential cellular processes.

9:00-11:30

A variety of photoreceptors and the frontiers of optogenetics.
Organizers︓Satoru Tokutomi（Osaka Prefect. Univ.）, Satoshi P Tsunoda（Nagoya Inst. Tech.）
Summary︓
Lives have acquired a variety of photoreceptors which absorb light in the UV to far red region during
the evolution, such as many different types of rhodopsin, blue-light receptors, cryptochrome andphototropin, and red-far red-light reversible phytochromes. Researchers have adapted and utilized
them for photobiological studies including optogenetics. The present Symposium introduces someleading results which includes channel rhodopsin in the trendy neuroscience, a novel function of mouse
cryptochrome in circadian rhythm, use of a light-inactivated rhodopsin, peropsin, for vision restoration,
photoregulation of protein kinase by phototropin, application of phytochrome-PIF and cryptochromeCIB for optogenetics, and color tuning of cyanobacteriochrome.

9:00-11:30

Biophysics on Genome DNA - Toward Understanding of Genome Modality Organizers︓Masahiro Takinoue（Tokyo Inst. of Tech.）, Shoji Takada（Kyoto Univ.）,
Kazuhiro Maeshima（NIG）
Summary︓
The current trends in genome research, from genome sequencing to enome editing, have revolved
based on the understanding of the informational aspects of genome, such as the replication andrecombination of base sequences, and epigenetic regulation by histone modifications. However, thephysical properties of genomic DNA as a polymer have not been fully elucidated yet, although it is an
important property underlying all the phenomena caused on the genome. In this symposium, we will
introduce a research area “Genome Modalities”, which aims to reveal the true nature of genomes
through understanding the physical properties of DNA, and discuss this issue with researchers insideand outside this area.

9:00-11:30

An Integrated Multi-scale Approach for Studying Cyanobacterial Circadian
Clock System
Organizers︓Shuji Akiyama（CIMoS）, Hironari Kamikubo（NAIST）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Circadian rhythms are self-sustained oscillations with a period of approximately 24 h, enablingorganisms to adapt to daily alterations in the environment. So far, many studies have investigated thetime-measuring mechanism in the circadian clocks from bacteria to mammals. However, it remains
unknown how the period is implemented in clock oscillators and kept unaffected against temperaturechanges (temperature compensation). In this symposium, we will focus especially on cyanobacterial
circadian clock as a model system and address these questions using a multidisciplinary approach
including, biophysics, structural biology, chronobiology, molecular biology, and protein engineering.

9:00-11:30

Advances in enhanced sampling methods for molecular simulations of protein
systems
Organizers︓Ayori Mitsutake（Meiji Univ.）, Hisashi Okumura（ExCELLS）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
In recent years, it has become possible to perform molecular simulations on time scales of the orderof milliseconds using special-purpose system and massive parallel computers. However, sampling
methods that is about 10 to 100 times more efficient than ordinary molecular simulations are still
important to investigate binding simulations and longer simulations. Since about 25 years ago, various
sampling methods have been energetically introduced and developed into protein systems in Japan.
Currently, many enhanced sampling methods are widely introduced in protein softwares such as
AMBER, CHARMM, GENESIS, GEMB, GROMACS, NAMD, and myPresto. In this symposium, researchers
who have originally developed sampling methods and applied to protein systems will give their talks.

9:00-11:30

New artificial approaches and biophysical communications to control functionof biological membranes
Organizers︓Ikuhiko Nakase（Osaka Prefect. Univ.）, Yoshiaki Yano（Kyoto Univ.）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Biological membranes have a complex supermolecular bilayer structure composed of diverse
biomolecules such as lipids, proteins, and sugars.

It is well known that biomembranes containreceptor proteins to detect changes in external environments, and their ligand molecules are available
for controlling cell functions.

Moreover, alternative approaches are possible to artificially perturb

function of biomembranes by e.g., changing their shape, permeability, and domain structures following
molecular interactions with lipids.

New approaches using hybrid/designed molecules, model

membranes, ultrafast spectroscopy, and chemistry on/in cells, will be introduced to discuss complex
membrane functions with biophysical communications and their usefulness for molecular sensing andcontrolling cell functions

27[Sat], November
9:00-11:30
ASB-BSJ Joint Symposium
Organizers︓Kota Katayam（Nagoya Inst. of Tech.）, Matthew AB Baker（Univ. of New South
Wales）
Summary︓
This symposium aims at highlighting the current main stream topics in protein science and biophysics
and also searching for the collaboration and development in research filed of biophysics in the Japan-

Australia region. The symposium includes three up-and-coming young researchers related tobiophysics from the ASB and BSJ sides. With the rapid progress of science and technology in recent
years, through this constructive discussion, we wish to keep the scientific activity, and to give a large
impact to the community.

9:00-11:30

Parametric biology based on translation rate regulatory mechanism
Organizers︓Kohki Okabe（The Univ. of Tokyo）, Yoshie Harada（Osaka Univ.）
Summary︓
Translation is not just a linear bridge between mRNA and protein, but is highly variable andcharacterized by a wide dynamic range (1,000 times that of transcription), local control within the cell,and reactions that consume up to 50% of the energy in the cell. This raises the possibility thattranslation is not controlled by 0 or 1 on/off control, but is subtly controlled by "rate variation" withina continuous reaction. Currently, we are beginning to create a translation parametric biology that
focuses on the concept of "variable translation rate. This will elucidate its role in the flexible functional
control of life.

9:00-11:30

Protein hydration and its freezing phenomena -toward the application for cellfreezing and food frozen storageOrganizers︓Naoki Yamamoto（Jichi Medical Univ.）, Hiroshi Nakagawa（J-PARC）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Protein hydration water is crucial for the activation of the dynamics related to the protein functional
expression. We introduce recent progress on the understanding of the interplay between hydrationwater and protein in terms of the freezing of hydration water. Recent experimental results obtainedby broadband dielectric spectroscopy and neutron scattering on proteins and tissues will be reported.
Furthermore, present recent progress in the understanding the cell-freezing and food frozen storage
will be represented. Especially, polymeric cryoprotectants, which have low toxicity and high protection
capability, have been paid attention for those purposes, will be introduced and it physicochemical
property will be discussed.

9:00-11:30

Probing large-scale dynamics in protein through integrative approaches
Organizers︓Tomohide Saio（Tokushima Univ.）, Rintaro Inoue（Kyoto Univ.）
Summary︓
Large scale dynamics” (LS-dynamics) such as domain-domain correlation motion, often drives protein
activity, but the scarcity of the information regarding them impedes the understanding of themechanism. In other words, the LS-dynamics of protein is still a frontier in protein science. Everyone
recognizes that, although state-of-the-art techniques provide the knowledge of various aspects of LSdynamics, only a single method could not adequately cover the ranges of length and time scalesrequired for the LS-dynamics. Hence, agenda are how to integrate their results and build the full
picture of LS-dynamics. In this symposium, young scientists from variety of scientific fields, solution
scattering, NMR, cryo-EM, and computation, will lead to discuss about the integration of their methods
aiming to unveil the biologically significant LS-dynamics.

9:00-11:30
Peptide-Membrane

Biophysics:

Current

BiophysicalStudiesofMembrane-boundAntimicrobial Peptides and Amyloid Peptides
Organizers︓Izuru Kawamura（Yokohama Natl. Univ.）, Tomoyasu Aizawa（Hokkaido Univ.）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
In the biophysical research field, the structure and dynamics of peptide and lipid molecules withincomplex biomolecular assemblies have been investigated for many years with a special focus on
membrane-interaction of antimicrobial peptides (AMPs) and kinetics of amyloid fibril formation. In this
symposium, current research topics on "peptide-membrane biophysics" by imaging, NMR, andcomputational methods will be presented. Additionally, advanced over-expression technology anddeep learning for molecular design of AMPs will be presented.

9:00-11:30

New Trends in Functional Omics Analysis Integrated with Live Cell Imaging
Organizers︓Yoshitaka Shirasaki（The Univ. of Tokyo）, Katsuyuki Shiroguchi（RIKEN）[Pick up speakers from the students and post-doctoral fellows]
Summary︓
Cells change their function from time to time based on the alteration of their gene expression.
Live cell imaging is an excellent technique for tracking the cellular functions, though it has limited
targets. On the other hand, omics analyses such as high-throughput sequencing and mass
spectrometry have advantages for comprehensiveness on gene expression analysis, although theycannot obtain time-series information due to disruptive manipulations. In this symposium, we will
focus on advanced single-cell technologies that bridge the gap between time-series andcomprehensive information on dynamic cellular functions, and will discuss the future prospects of thisfield.