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Program

Timetable
*Tentative Schedule as of February, 2025

PSSJ Basic course

June 17（Tue）13:30-14:15[Session Language:TBA]
TBA

Organizers： Hidekazu Hiroaki（Nagoya Univ.）, Hiroki Shirai（RIKEN）

Speakers：TBA

TBA

Symposium

June 18（Wed）9:15-11:45 [Session Language: Japanese]
Trends in Structural Bioinformatics and Drug Discovery

Organizers： Tsuyoshi Inoue(Osaka Univ.), Takatsugu Hirokawa(Univ. of Tsukuba), Kei Yura(Waseda Univ.)

Speakers： Takashi Nagata(Kyoto Univ.), Masahito Ohue(Institute of Sicence Tokyo), Yoshitaka Moriwaki(Institute of Sicence Tokyo), Shun Sakuraba(National Inst. for Quantum Sci. and Tech.), Kazuyoshi Ikeda(RIKEN)
This symposium focuses on AI-driven innovations in bioinformatics, particularly AlphaFold’s advancements in protein structure prediction. Topics include 3D structure-function relationships, interaction mechanisms, new prediction methods, and AI-integrated drug discovery. Discussions will explore AI’s limitations, future potential, and foster collaboration among researchers to advance computational biology and biomedical applications.

Young Scientist Award Symposium

June 19（Thu）9:15-11:30 [Session Language: English]

Chairs： Mitsunori Ikeguchi（Yokohama City Univ.）, Nobuyasu Koga (Osaka Univ.)

Workshop

Day 1 June 18 (Wed)

June 18 (Wed) 9:15-11:45　[Session Language: English]
WS1 Redesign of molecular machines

Organizer：Hiroyuki Noji (The Univ. of Tokyo), Ryota Iino (Institute for Molecular Science)

Speakers：Takanori Harashima (Institute for Molecular Science),Hiroshi Ueno (The Univ. of Tokyo),Ken’ya Furuta (NICT),Keisuke Motone (Osaka Univ.),Rieko Sumiyoshi (The Univ. of Tokyo),Shunji Suetaka (The Univ. of Tokyo),Shintaroh Kubo (RIKEN)

While the structure prediction and the de novo design of proteins have entered a new era, the design of molecular machines that undergo large-scale conformational changes still remains highly challenging. Despite these difficulties, recent years have witnessed remarkable achievements in this area. This workshop will highlight groundbreaking successes in the redesign of molecular machines and provide a platform to discuss the future potential for rational design in this field.
June 18 (Wed) 9:15-11:45　[Session Language: Japanese]
WS2 Unfolded structures are key!

Organizer：Kenji Iwasaki (Univ. of Tsukuba), Hidekazu Hiroaki (Nagoya Univ.)

Speakers：Kiyoto Kamagata (Gifu Univ.),Hiroto Anbo (Maebashi Institute of Technology),Takafumi Ueno (Institute of Science Tokyo),Ayaka Asai (Nagoya Univ.),Mikuru Ebihara (Univ. of Tsukuba)

The Nobel Prize was awarded to AlphaFold, but it is the “unfolded, unstructured regions” that are important for understanding protein function. Genome-wide analyses have confirmed that nearly half of the proteins in the nucleus are such unstructured proteins, but that they are mainly responsible for cancer. We will discuss the state-of-the-art research on the analysis of these proteins in the nucleus, which even antibodies cannot reach.
June 18 (Wed) 9:15-11:45　[Session Language: Japanese]
WS3 Ensemble of Protein Science on the Phopholipid Bilayer

Organizer：Hironori Takeda (Kobe Univ.), Yasunori Watanabe (Yamagata Univ.)

Speakers：Shigekazu Nagata (Osaka Univ.),Kazuhiro Abe (Hokkaido University),Shiori Akabane (Rikkyo University),Tatsuro Maruyama (Institute of Microbial Chemistry), Hironori Takeda (Kobe Univ.), Yasunori Watanabe (Yamagata Univ.)
Phospholipids self-assemble to form a higher-order structure called the “phospholipid bilayer”, which constitutes cells and organelles. The quality of the phospholipid bilayer is maintained through the regulation of phospholipid distribution by flip/scramble and transport, and the degradation of the membrane itself. In this session, we aim to present the latest findings from researchers who are actively studying proteins involved in the regulation of phospholipid distribution and membrane dynamics. We will discuss the mechanisms of various proteins that govern the phospholipid bilayer.
June 18 (Wed) 16:00-18:30　[Session Language: English]
WS4 Dynamic structure and biological function of biomolecular complexes revealed by cross-scale measurements

Organizer：Kenji Inaba (Kyushu Univ.), Yuji Sugita (RIKEN)

Speakers：Ryo Nitta (Kobe Univ.),Motomasa Tanaka (RIKEN),Kento Kasahara (Osaka Univ.),Sayaka Sekine (Tohoku Univ.),Tamar Schlick (New York Univ.),Osamu Nureki (The Univ. of Tokyo)

Quantitative cross-scale measurements from the molecular and protein levels to the organelle and cellular levels, and in particular, structure and dysnamics analyses of “meso-complexes” of around 20 to 500 nm in size within cells are important for understanding the mechanisms of action of biological phenomena and the causes of disease. The development of various measurement and analysis techniques, as well as their integration with computational science, can create a new framework for cell biology. In this session, we will discuss the latest research on various “meso-complexes” working in the cytoplasm, biomembranes, and nucleus.
June 18 (Wed) 16:00-18:30　[Session Language: Japanese]
WS5 Protein Self-Condensation in Dynamic Solution Environments: A New Paradigm Shift in Life Science through Innovative Technology

Organizer：Kenji Sugase (Kyoto Univ.), Naotaka Sekiyama (Kyoto Univ.)

Speakers：Kenji Sugase (Kyoto Univ.),Naotaka Sekiyama (Kyoto Univ.),Norio Yoshida (Nagoya Univ.),Tomoko Inose (Kyoto Univ.),Yusuke Nakasone (Kyoto Univ.),Moeto Nagai (Toyohashi Univ. Tech.)

Fluctuations in solution environments, fundamental to biological activity, have been identified as key drivers of processes like protein phase separation and amyloid fibrillation, which are implicated in neurodegenerative diseases. This workshop will highlight innovative methods, from atomic to cellular levels, to analyze these dynamic solution behaviors and explore their implications, fostering a paradigm shift in life sciences.
June 18 (Wed) 16:00-18:30　[Session Language: English]
WS6 Understanding and expanding protein functions to enable their generative design

Organizer：Takuya Terai (The Univ. of Tokyo), Misao Mizuno (Kyoto Univ.)

Speakers：Misao Mizuno (Kyoto Univ.),Akio Kitao (Institute of Science Tokyo),Masahiro Fukuda (The Univ. of Tokyo),Hidetsugu Asada (Kyoto Univ.),Koji Oohora (Osaka Univ.),Yuta Suzuki (Kyoto Univ.)

Dynamic structural analysis using state-of-the-art computational and experimental techniques is now enabling us to predict and observe the transient active states of proteins, which is key to understanding their functions. These insights will lead to the generative design of proteins with novel functions. In this workshop, we will discuss protein functions in terms of both understanding and expansion.
June 18 (Wed) 16:00-18:30　[Session Language: Japanese]
WS7 Latest researches into protein behavior reveal new functions

Organizer：Tomohide Saio (Tokushima Univ.), Masaki Okumura (Tohoku Univ.)

Speakers：Eiichiro Mori (Nara Medical Univ.),Tomohide Saio (Tokushima Univ.),Lee Young-Ho (Korea Basic Science Institute),Takahiro Muraoka (Tokyo Univ. of Agriculture and Technology),Hideki Nakamura (Kyoto Univ.),Mai Watabe (Tohoku Univ.)

The structural behavior of proteins is fascinating because they function not only in folded states but also in intrinsically disordered and condensed states. This workshop will feature the latest findings on protein behavior, namely folding, aggregation, and condensation from the aspects of molecules, proteins, organelles, and cellular dynamics.
June 18 (Wed) 16:00-18:30　[Session Language: English]
WS8 Frontier of Biomolecular Functional Analysis innovated by Data Assimilation and Multi-scale Simulation

Organizer：Shingo Ito (R-CCS), Mao Oide (Osaka niv.)

Speakers：Yoshifumi Nishimura (Waseda Univ.),Giovanni Brandani (Kyoto Univ.),Atsuko Yamashita (Osaka Univ.),Eiji Yamamoto (Keio Univ.)

Multi-scale molecular dynamics (MD) simulation with integration of experimental data through Bayesian optimization has become a powerful technique to understand the actual biological functional events based on simulated microscopic molecular dynamics. In this workshop, we will introduce the latest research using not only data assimilation and multi-scale MD simulation, but also machine learning to help understanding the frontier of simulation-based biomolecular functional analysis.
June 18 (Wed) 16:00-18:30　[Session Language: Japanese]
WS9 PSSJ Archives WS: Frontiers of Protein Production Technologies for Life Science Research

Organizer：Takao Arimori (Osaka Univ.), Maho Yagi-Utsumi (Nagoya City Univ.)

Speakers：Hironobu Hojo (Osaka Univ.),Teruyo Kato (Nagoya Univ.),Ryo Matsunaga (The Univ. of Tokyo),Hiroyuki Takeda (PROS, Ehime Univ.),Takao Arimori (Osaka Univ.)

Sample preparation of target proteins is an essential process in life science research. In this workshop, five speakers with expertise in chemical synthesis, cell-free expression systems, and expression systems using E. coli, Brevibacillus, and mammalian cells will introduce the characteristics of each system, as well as various technologies related to protein production and purification.

Day 2 June 19 (Thu)

June 19 (Thu) 16:00-18:30　[Session Language: Japanese]
WS10 Frontiers of Functional Prediction, Characterization, and Alteration of Natural Product Biosynthetic Enzymes

Organizer：Tohru Terada (The Univ. of Tokyo), Munehito Arai (The Univ. of Tokyo)

Speakers：Munehito Arai (The Univ. of Tokyo),Osami Shoji (Nagoya University),Tohru Terada (The Univ. of Tokyo),Eriko Nango (Tohoku Univ.),Toshiyuki Wakimoto (Hokkaido Univ.),Kenji Watanabe (Univ. of Shizuoka)

Natural products are synthesized through multistep reactions by a set of biosynthetic enzymes. Because their functions remain unclarified in many cases, we have established a Transformative Research Area, “Forecasting Biosynthesis,” to accumulate genomic information of biosynthetic enzymes, to predict their functions, and to alter them for producing valuable compounds. Here, we present our studies in this Area conducted using state-of-the-art experimental techniques, computational chemistry, and artificial intelligence.
June 19 (Thu) 16:00-18:30　[Session Language: Japanese]
WS11 Protein Science in Hemophilia, Treatment by Antibody Drugs and Gene Therapy

Organizer：Susumu Uchiyama (Osaka Univ.), Saeko Yanaka (Science Toikyo)

Speakers：Tsukasa Ohmori (Jichi Medical Univ.),Keiji Nogami (Nara Medical Univ.),Kio Horinaka (The Univ. of Tokyo),Mina Ichiki (Chugai Pharmaceutical),Koichi Kato (National Institutes of Natural Sciences),Susumu Uchiyama (Osaka Univ.),Tomoko Yamaguchi (Tokyo Medical Univ.)

Haemophilia is a well-known disease related to blood proteins, whereas research into pathogenesis and treatment is still evolving, with treatment with bispecific antibodies that show remarkable efficacy, and gene therapy drugs being approved very recently. In this workshop, the basics and treatment of haemophilia will be introduced, followed by an overview of haemophilia from the perspective of protein science and a discussion on the protein engineering required for treatment.
June 19 (Thu) 16:00-18:30　[Session Language: Japanese]
WS12 Research advances in translation ~Focuses on fidelity and accuracy in genetic code decoding~

Organizer：Takehito Tanzawa (Osaka Univ.), Takashi Kanamori (GeneFrontier Corp.)

Speakers：Yoshihiro Shimizu (RIKEN),Asuteka Nagao (The Univ. of Tokyo),Yuhei Chadani (Okayama Univ.),Yumi Nakai (Osaka Med.&Pham.Univ.),Takuya Usui (Hokkaido Univ.),Takehito Tanzawa (Osaka Univ.)

Proteins are synthesized on ribosomes by translating mRNA-encoded genetic information into amino acid sequences. Translation factors employ multiple proofreading mechanisms to ensure accuracy and maintain quality control. This workshop focuses on fidelity and accuracy in genetic code decoding, presenting and discussing the latest research findings in this field.
June 19 (Thu) 16:00-18:30　[Session Language: English]
WS13 Recent advances in the observation of in vivo phenomena by NMR spectroscopy

Organizer：Takanori Kigawa (RIKEN), Yutaka Ito (Tokyo Metropolitan Univ.)

Speakers：Yutaka Ito (Tokyo Metropolitan Univ.),Masato Katahira (Kyoto Univ.),Takanori Kigawa (RIKEN),Seizo Koshiba (Tohoku Univ.),Noritaka Nishida (Chiba Univ.),Yanaka Saeko (Institute of Science Tokyo)

NMR allows non-invasive observation of not only intracellular proteins, but also membrane-localized proteins, nucleic acids, antibodies, metabolites and other molecules under physiological conditions. Experts in cutting-edge research using NMR will present their latest results and future perspectives in this field.

Day 3 June 20 (Fri)

June 20 (Fri) 8:30-11:00　[Session Language: English]
WS14 Towards Reliable Cryo-EM Structures — Let’s Share Tips for Analysis and Validation Methods!

Organizer：Satomi Inaba-Inoue (Hokkaido Univ.), Toshio Moriya (KEK)

Speakers：Daisuke Miyamoto (Amazon Web Services Japan G.K.),Han Zhu (Purdue Univ),Tsukasa Nakamura (KEK),Yuan-E Lee (ExCELLS, NINS),Yasuomi Miyashita (Chiba Univ.),Oleg Sitsel (OIST)

Since the 2017 Nobel Prize in Chemistry, cryo-EM and cryo-ET structure determination have surged. Shorter data collection times, diverse analysis methods, and accessible software contribute to this growth. Focusing on early-career researchers, this workshop aims to share original idea in analysis and verification techniques, as well as thier automation.
June 20 (Fri) 8:30-11:00　[Session Language: Japanese]
WS15 Unraveling the Ubiquity of Photosynthetic Organisms through Structural Biology and Beyond

Organizer：Akihiro Kawamoto(Osaka Univ.), Takahisa Ikegami(Yokohama City Univ.)

Speakers：Keisuke Kawakami(RIKEN), Atsushi Yamagata(RIKEN), Ritsuko Fujii(Osaka Metropolitan Univ.), Hiroyoshi Matsumura(Ritsumeikan Univ.), Nana Yamamoto(Osaka Univ.), Keisuke Saito(Tokyo Univ.), Masaki Mishima(Tokyo Univ of Pharmacy and Life Sciences)

Photosynthetic organisms have adapted to very diverse environment on Earth, from the tropics to the poles. One key factor enabling this ability to perform photosynthesis anywhere on Earth (photosynthesis ubiquity) is the environmental adaptation of proteins and protein-pigment complexes. In this session, researchers investigating the unique functions of proteins from photosynthetic organisms through a variety of research methods will present their latest findings.
June 20 (Fri) 8:30-11:00　[Session Language: Japanese]
WS16 Element-based Biology: Interactions between diverse elements and proteins in living systems

Organizer：Norifumi Kawakami (Keio Univ.), Yoshiaki Furukawa (Keio Univ.)

Speakers：Norifumi Kawakami (Keio Univ.),Toru Fujiwara (The Univ. of Tokyo),Yoshiaki Furukawa (Keio Univ.),Nobutaka Fujieda (Osaka Metro. Univ.),Michiko Nemoto (Okayama Univ.),Hisaaki Mihara (Ritsumeikan Univ.)

Life is thought to have expanded its use of elements through evolution. One hypothesis suggests that evolutionarily new proteins enabled interactions with previously inaccessible elements, integrating them into physiological processes. We will discuss protein-element interactions, how life’s elemental usage has shifted over time, and the potential for further expansion.
June 20 (Fri) 8:30-11:00　[Session Language: Japanese]
WS17 The latest research on immune-related signal transduction and its application to drug discovery, revealed by cell and structural biology.

Organizer：Yoshikazu Tanaka (Tohoku Univ.), Koki Makabe (Yamagata Univ.), Toyoyuki Ose (Hokkaido Univ.)

Speakers：Koki Makabe (Yamagata Univ.),Kimiko Kuroki (Hokkaido Univ.),Naotaka Tsutsumi (Institute of Science Tokyo),Miku Minami (Hokkaido Univ.),Nobutaka Numoto (Okayama Univ.),Yoshikazu Tanaka (Tohoku Univ.)

Recently, various methodologies have been developed to study proteins. By integrating these methodologies, we can gain a deeper understanding of previously unexplained biological phenomena and apply them to new technologies. In this workshop, we will discuss the role of protein science research and its future development, including drug discovery research, based on cutting-edge research that has elucidated the molecular mechanisms of signal transduction and induction that are responsible for activation of the immune system by combining cellular and structural biology.
June 20 (Fri) 8:30-11:00　[Session Language: Japanese]
WS18 Proteomic Technologies for Comprehensive Insights into Cellular Regulatory Mechanisms

Organizer：Yoshio Kodera (Kitasato Univ.), Shinya Ohta (Hokkaido Univ.)

Speakers：Tatsuya Sawasaki (Ehime Univ.),Kotani Norihiro (Saitama Medical Univ.),Tatsuya Niwa (Institute of Science Tokyo),Yusuke Kawashima (Kazusa DNA Research Institute),Shin Kawano (Kitasato Univ.),Chisa Shiraishi (Nagoya Univ.)

Proteomics advancements enable efficient and comprehensive analyses of protein expression, post-translational modifications (such as phosphorylation, glycosylation, etc.), and protein localization and interactions. This session will focus on the application of proteomic technologies to understand cellular molecular mechanisms, featuring case studies from the field.
June 20 (Fri) 15:40-18:10　[Session Language: Japanese]
WS19 Protein molecules that generate time: what they really are

Organizer：Hikari Yoshitane (TMIMS), Shuji kiyama (IMS, NINS)

Speakers：Hikari Yoshitane (TMIMS),Tsuyoshi Hirota (Nagoya Univ),Akari Maeda (Nagoya Univ.),Yoshihiko Furuike (IMS, NINS),Atsushi Mukaiyama (Fukui Prefectural Univ.),Koji ODE (The Univ. of Tokyo)

Chrono-proteinology is a field of studies that approach time-measuring mechanism in organisms from the perspective of functions and structures of protein molecules. In this symposium, we will invite researchers leading the chrono-proteinological studies on mammals, plants, and bacteria. Let’s enjoy cross-species discussion on the substance, evolution, and diversity of “protein molecules that generate time”.
June 20 (Fri) 15:40-18:10　[Session Language: English]
WS20 PS- APPA- KPPS-PSSJ joint workshop: Protein Science from classical to latest approaches

Organizer：Young-Ho Lee (Korea Basic Science Institute), Masaki Okumura (Tohoku Univ.), Tomohide Saio (Tokushima Univ.)

Speakers：Jean Baum (Rutgers Univ.), Kurt Krause (Univ. of Otago),Kyung-Jin Kim (Kyungpook National Univ.),Genji Kurisu (Osaka Univ.)

Protein science has been developed by a wide range of technologies, including structural biology, biophysics, and so on. Considering the next era of protein science, it is necessary to learn from the past and latest deep technologies and to actively exchange ideas internationally. In this workshop, we are planning to introduce the latest cutting-edge research, which will lead to the development of protein science in the world.
June 20 (Fri) 15:40-18:10　[Session Language: Japanese]
WS21 Antibody Design through Computational Science

Organizer：Yoko Akazawa (AIST), Tomonari Matsuda (Kyoto Univ.)

Speakers：Mitsuo Umetsu (Tohoku Univ.),Kuroda Daisuke (National Institute of Infectious Diseases),Tomonari Matsuda (Kyoto Univ.),Kaori Fukuzawa (Osaka Univ.),Kuroda Yutaka (Tokyo Univ. of Agriculture and Technology)

The application of computational science to protein engineering has developed rapidly with the advent of AI technology. Antibodies are no exception and are being used for antibody design and elucidation of antibody maturation mechanisms. This workshop will discuss the latest challenges in antibody prediction and design using in silico analysis.
June 20 (Fri) 15:40-18:10　[Session Language: Japanese]
WS22 Understanding of Diverse Bio-molecular regulating molecular mechanisms of signal transduction and enzyme functions by AI methods

Organizer：Yasushige Yonezawa (Kindai Univ.), Yuko Tsuchiya (AIST)

Speakers：Yuko Tsuchiya (AIST),Hiroko X. Kondo (Kitami Institute of Technology),Takuma Shiraki (Kindai Univ.),Naoyuki Miyashita (Kindai Univ.),Yasushige Yonezawa (Kindai Univ.)

AI has been used to create a variety of new scientific knowledge, including in life sciences. However, the “potential and innovation of life sciences using AI” is not sufficiently recognized. We will present cutting-edge AI studies, and deepen our understanding of the use of AI in life sciences.

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