Protein research at Osaka University has long been active, and with the mission of elucidating the principles of biological activities through fundamental
protein research, the Institute for Protein Research (IPR) was established asa Joint-use Research Organization in 1958. At the time of its establishment,
IPR consisted of three divisions: Organic Chemistry, Physical Chemistry, andProtein Metabolism, and with the advance of technologies like molecularbiology and computational science, IPR has expanded to cover a wide rangeof life science fields. In 2010, IPR was certified by MEXT as a Joint Usage /Research Center in recognition of its activities since its establishment. Up
until now, through the domestic and international joint use of large facilities
such as SPring-8 Beamline for Biological Macromolecular Assemblies,
Cryo-electron microscopes, and NMR (Nuclear Magnetic Resonance) instruments, as well as through the operation of Protein Data Bank Japan (PDBj),
IPR is dedicated to advancing protein research and encouraging the growthof research communities within and outside of Japan.
In recent years, there has been a significant focus on the new findings generated from the fusion of image analysis and deep learning technologies(such as cryo-electron microscopy and AlphaFold) with the protein structural information, or even the data itself. There is also a
growing need for integrating information technology with genomic and other data to comprehend multi-level networks, from proteins to life. Given this situation, in October 2020, IPR set up the Division of Protein Network Biology and the Research Center for
Next-Generation Protein Sciences to elucidate life phenomena based on protein-protein interactions. Furthermore, based on theactivities of PDBj, IPR established the Advanced Data Science Center for Protein Research (ASPiRE) in October 2022 to promote
data science as well as to create novel functional molecules. Under this structure, IPR is collaborating with related institutions
worldwide to pioneer data-driven research on protein information and to encourage research and educational activities.

Director

IPR, based on its strength of protein structural science, is expanding the scope of its research into the functional analysis of proteins, development of protein synthesis and design technology, protein information science and in-silico drug discovery. We
sincerely appreciate your continued support and guidance.

Protein function
prediction
Three-dimensional (3D) protein structures

Cryo-electron
microscopes

De novo design ofprotein molecules©RIKEN

X-ray
crystallography
at SPring-8

Chemical synthesisof proteins

Understanding integrated
protein functions
Pikachurin

High-magnetic field
solution and solid-state
NMR instruments

Implementation towards
solving social issues
drug discovery, cancer, infections,
neurosciences, molecular design

LassoGraft
Technology

Director
Faculty Meeting
Administrative Council
Panel on Joint Usage / Research
Research Divisions● Division of Protein Chemistry

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Organization●

Laboratory for Protein Organic Chemistry●

Laboratory for Nanobiology●

Laboratory for Protein Synthesis and Expression●

Laboratory for Protein Profiling and Functional Proteomics●

Laboratory for Physical Biology

Division of Protein Structural Biology●

Laboratory for Molecular Biophysics●

Laboratory for Protein Crystallography●

Laboratory for CryoEM Structural Biology●

Laboratory for Supramolecular Crystallography

Division of Integrated Protein Functions●

Laboratory for Molecular and Developmental Biology●

Laboratory for Genome and Chromosome Functions●

Laboratory for Advanced Brain Functions●

Laboratory for Organelle Biology

Division of Protein Network Biology●

Laboratory for Cell Systems●

Laboratory for Computational Biology●

Laboratory for Infection Systems

Special Research Facilities● Research Center for Next-Generation Protein Sciences●●

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy●

Laboratory for Synchrotron Radiation Research●Laboratory for High Resolution Cryo-EM●

Laboratory for Biomolecular Analysis●

Open Space Laboratory for Advanced Protein Science

Advanced Data Science Center for Protein Research●Laboratory for Protein Design●

Laboratory for Biomolecular Modeling and Dynamics●

Laboratory of Protein Databases●

Laboratory for Protein Network●

Laboratory for Drug Discovery Informatics

Division of Donated Fund Research●

Division for Matrixome Research and Application

Technology Division
Administration●

General Affairs Section●

Accounting Section●

Research Support Section

Project Team of Joint Usage / Research Center

Office of Research Strategy and Promotion
Public Relations Office
Library
IPR Alumni Office

Joint Usage / Research Center

Joint use of large facilities
The Institute for Protein Research (IPR) was established in 1958 as a Joint-use Research Organization attached to Osaka
University. Since its establishment, IPR has actively collaborated with numerous domestic and international researchers,
and in recognition of its activities, IPR was certified as a Joint Usage / Research Center in April 2010 by the Ministry of
Education, Culture, Sport, Science and Technology (MEXT) of Japan. As one of the main activities of the Joint Usage /Research Center, IPR offers large facilities for protein and life sciences, including SPring-8 synchrotron radiation beamline(IPR beamline, BL44XU), high-magnetic field solution and solid-state NMR machines, and state-of-the-art cryo-electron
microscopes. In addition to these large facilities, IPR also operates PDBj (Protein Data Bank Japan) as one of the membersof the Worldwide Protein Data Bank (wwPDB) organization that manages the PDB archives, the most important andsuccessful database on protein structures. IPR is committed to contributing to the future of life sciences.

Beamline for
Macromolecular Assemblies
SPring-8 is the largest synchrotron
radiation facility in the world. It produces
a high brilliance X-ray beam suitable fordata collection of biological macromolecules. IPR installed a contract beamline
named "Beamline for Macromolecular
Assemblies (BL44XU)” at SPring-8. This
beamline is designed for high-precision
diffraction data measurements from large
biological macromolecular assemblies
and is used for advanced research byresearchers worldwide.

Cryo-electron Microscopes
Cryo-electron microscopy is a type ofelectron microscopy that involves samples
frozen in a vitreous ice and observed
under nearly -190 degrees environment. In
recent years, it has made significant
progress, enabling atomic-level structural
analysis of even non-crystallizedbiomolecules. As the base of cryo-electron
microscopy facilities in Japan, IPR
promotes world-leading research from theinvestigation of sample preparation
methods to data acquisition,
three-dimensional image analysis, andatomic model construction, to contributeto a wide range of research and technicalsupport for industry and academia.

NMR (Nuclear Magnetic
Resonance)
At IPR, a diverse range of NMR instruments, including the world's mosthigh-sensitivity ultra-high field NMR
device, is in operation. Through themaintenance and advancement of these
NMR instruments, we are advancing thestructural analysis of challenging targets,
such as low-concentration proteins andhigh-molecular-weight protein complexes.

©RIKENResearch Divisions and Principal Investigators

Division of Protein Chemistry
Hironobu Hojo

Organic chemistry / Chemical protein synthesis

Chemical synthesis of proteins and functional elucidation of their post-translational modifications

We have established an efficient method for the chemical synthesis of proteins, capable of introducing non-natural aminoacids and post-translational modifications at arbitrary positions in the sequence. Using these chemically synthesized
proteins, we are aiming to elucidate the function of protein modifications as well as to design new proteins and develop
new drugs.

Yoshie Harada

Nanobiology

Measuring the environment of the nano region inside the cell to understand the fields where protein molecules work
Using fluorescent nanodiamonds and fluorescent polymeric thermometers, we analyze the relationship between intracellular local temperature and cellular functions, as well as elucidate the heat-sensing system of cells by local heating of cells.
We are also working on a social implementation of drug discovery and regenerative medicine by using real-time imaging of
bioactive proteins secreted from individual cells.

Junichi Takagi

Structural biology / Protein engineering

Elucidation of the structural mechanism of transmembrane signaling and development of novel biotherapeutics

Our research focuses on understanding cellular signal transduction mechainsm from the structural perspective, using
techniques such as cryo-electron microscopy and X-ray crystallography. Furthermore, we combine our expertise instructural analysis and protein engineering to design proteins with novel functions, aiming at creating innovative biotherapeutics.

Toshifumi Takao

Protein mass spectrometry

Exploring the protein world by mass spectrometry

We have developed mass spectrometric methods for sensitive analysis of the primary structure and post-translational
modifications of peptides and proteins, and software for accurate analysis of mass spectra, and are applying thesemethods to trace proteins obtained from living organisms. In addition, we are also applying these methods to the search fordisease markers in body fluids.

Madoka Suzuki

Physical biology

Quantitative imaging and perturbation to understand the role of heat in biological systems

Cells respond to heat using proteins, but it is unclear how the proteins work, or whether the same mechanism responds toheat released by the cell itself. We use quantitative imaging and photothermal conversion to study the role of heat acrossthe scales of biological systems at the molecular, cellular and organismal levels.

Division of Protein Structural Biology
Genji Kurisu

X-ray crystallography

Precise structural analysis of the protein to understand the system of biological reactions

We use X-ray crystallography together with NMR and Cryo-electron microscopy to analyze the working protein moleculesand elucidate their structure-function relationship. Our goal is to understand the mechanism of controlled biologicalreactions in bioenergetics such as photosynthesis or dynein motors. In addition, we are also developing the method ofneutron crystallography or MicroED for precise structural analysis of metal enzymes or bioactive compounds.

Takayuki Kato

Structural biology

Analyzing higher-order structure and function of biomacromolecules by Cryo-EM

We study superior functional mechanisms of living organisms, such as high energy conversion efficiency of molecularmotors, by structural analysis using cryo-electron microscopy. We also develop technology for high-resolution analysis ofprotein structures and establish methods for analyzing thermal fluctuations of proteins using cryo-EM.

Atsushi Nakagawa

Synchrotron radiation protein crystallography

Structure determination of biological macromolecules using X-ray diffraction and cryo-electron microscopy
We aim to elucidate the detailed three-dimensional structures of biological supramolecular complexes, such as protein
complexes and protein-nucleic acid complexes, at the atomic level using X-ray crystallography and cryo-EM in order tounderstand biological phenomena at the atomic level. We also develop methodologies for X-ray crystallography including
the data collection system using the synchrotron radiaion beamline (BL44XU) at SPring-8.

Division of Integrated Protein Functions
Takahisa Furukawa

Developmental neurobiology / Visual science

Understanding central nervous system development from genes to neuronal function and human diseases

How does genetic information programmed in the genome lead to the development of diverse neurons? How does it relate
to the formation of precise neural circuits and the neurophysiological functions of individuals? And how does it relate to thedevelopment of human diseases? We are tackling these questions by using the retina as a model system to explore thecentral nervous system (CNS) development and function with an integrated approach.

Akira Shinohara

Molecular biology

Studying the mechanisms of genome stability and instability in eukaryotes

We are conducting research employing molecular biology, biochemistry, and structural analysis to elucidate the molecular mechanisms ofhomologous recombination and DNA exchange. Our focus is particularly on dynamic changes in protein complexes involved in recombination.
We aim to understand the mechanisms of genome stabilization and pathological conditions, such as the development of cancerous cells due
to genome instability resulting from its breakdown, as well as miscarriages caused by aneuploidy formation in eggs, sperm, and other cells.

Takatoshi Hikida

Neuroscience / Psychiatry

Understanding molecular and circuit mechanisms in brain functions and mental disorders using model mice

Our laboratory studies neural circuit mechanisms underlying various advanced brain functions, such as cognitive learning and decision-making
behaviors, using molecular techniques for neural circuit-specific manipulation. We use several mouse models to reveal molecular pathologies ofneuropsychiatric diseases. In particular, we focus on molecular mechanisms of gene-environment interaction in the pathogenesis of mental disorders.
We also promote translational research for targeting mental disorders in collaboration with clinical departments and pharmaceutical companies.

Masato Nakai

Plant molecular cell biology

Analysis of molecular mechanisms of protein transport in chloroplasts and chloroplast biogenesis

We are investigating the process by which chloroplast proteins are synthesized outside the chloroplast and transported tothe chloroplast, and the process by which the transported proteins are converted into functional molecules. By employing awide variety of organisms ranging from algae to higher plants, we aim to elucidate molecular mechanisms and evolutions ofchloroplast (plastid) biogenesis with techniques of biochemistry, genetics, and cell biology.

Division of Protein Network Biology
Mariko Okada

Systems biology

Understanding a cell, the smallest unit of life, as a dynamic integrated system of molecules

We develop methodologies for analyzing intracellular information using experiments and mathematical models and employ
these methods to elucidate the regulatory rules of gene networks for cell and disease development. We are also working on
the latest cell modeling methods and automated drug design, incorporating natural language processing and deeplearning.

Kenji Mizuguchi

Computational biology

From the elucidation of biological mechanisms towards drug discovery applications using computational approaches
We are developing methods to predict protein structure, function, and interaction, while integrating a wide range of data
and building databases, which provide a basis for linking molecular-level events and higher-order biological systems. We
are also applying these databases and computational tools for specific problems in biological data analysis, and health anddrug discovery research.

Yumiko Imai

Infection systems

Identification of higher-order-epigenetic modification machineries and development of potential novel
therapeutics in severe virus infection
Our research is focused on understanding the molecular pathologies of viral infections and the networks involved in theirseverity through the integrated analysis of quantitative bioscientific data. We also apply genome synthesis and editing
technologies in mouse models to develop novel drugs, diagnostics, and preemptive medicine.

Research Center for Next-Generation Protein Sciences
Yohei Miyanoiri

Structural biology / Protein chemistry

Elucidating the structural dynamics of proteins by developing advanced solution NMR methods

Utilizing advanced stable isotope labeling techniques and nuclear magnetic resonance (NMR) methods, we comprehensively analyze thethree-dimensional structure, dynamics, and interactions of proteins at atomic resolution. Our primary focus is on elucidating molecularmechanisms related to molecular motors and neurodegenerative diseases. Additionally, we are advancing drug discovery researchthrough in-cell NMR measurements and the development of NMR measurement technology via joint usage and collaborative research.

Nobuaki Okumura

Biochemistry

Developing sequence-based methods for protein analysis and supporting protein research.

We perform biochemical analysis of proteins and peptides, in particular by mass spectrometry and protein sequencing. We develop
methods for protein identification and quantification using these technologies and apply these to analysis of actual biological samples.
We are also interested in peptide and protein metabolism.

Advanced Data Science Center for Protein Research
Nobuyasu Koga

Protein design

De novo design of protein molecules

The goal of our lab is to develop methodologies that enable us to create protein molecules customized to the desired
function, using computational approaches based on physical chemistry and data science, along with biochemical
experiments.

Sandhya Premnath Tiwari

Computational biology

Investigating the collective motions of proteins via computational modeling and simulations tounderstand their biological function

Our goal is to model the dynamic motions of biomolecules, mainly proteins, and explore their role in biological function. By
integrating existing biophysical and structural data, we model biomolecular structure and dynamics using a variety ofcomputational methods.

Division of Donated Fund Research
Kiyotoshi Sekiguchi

Biochemistry / Cell biology

Uncovering the mechanisms governing homeostasis and dynamics of multicellularity through cell-extracellular matrix interactions
Our long-term goal is to understand the molecular mechanisms that govern the morphogenetic interactions of cells withsurrounding extracellular matrices. We are particularly interested in the role of basement membranes in embryonic development
and tissue homeostasis with an emphasis on the molecular interactions of basement membrane proteins with their receptors
on the cell surface and the resulting signaling events that regulate proliferation, differentiation, apoptosis, and motility of cells.

Development/Management of Databases
Protein Data Bank Japan (PDBj), an Asian data center of the worldwide Protein Data Bank (wwPDB), accepts biological macromolecular structures experimentally determined by crystallography, NMR spectroscopy or cryo-Electron Microscopy (cryo-EM) in Asia.
PDBj processes and validates the deposited data by global standards and distributes them as the single global archive (pdbj.org).
PDBj also processes and provides the cryo-EM map data as the Electron Microscopy Data Bank (EMDB), and curates the NMR
experimental data as the Biological Magnetic Resonance Data Bank Japan (BMRBj) together with the BMRB center in the US.



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
 (Protein Data Bank Japan)(Biological Magnetic
Resonance Data Bank Japan)(Immunohistochemical database forbasement membrane proteins)https://pdbj.org

https://bmrbj.pdbj.org/

http://dbarchive.biosciencedbc.jp/
archive/matrixome/bm/home.html

International Academic Exchanges
Country

Year of

Institutionagreement

China

Human Proteome Project 2.0-Proteomics-Driven Precision Medicine (PDPM) and Westlake University

2022

Uruguay

Universidad de la República Uruguay

2022

Indonesia

Airlangga University

2020

Australia

The Australian National University

2020

Italy

Fondazione Istituto Italiano di Tecnologia

2018

Germany

Ruhr University Bochum(RUB)

2017

USA

University of Chicago

2017

India

Indian Institute of Science Education and Research(IISER) Thiruvananthapuram

2017

Ireland

University College Dublin

2017

India

Panjab University

2017

TaiwanNational Tsing Hua University

2015

USA

The State University of New Jersey, Rutgers

2015

Korea

Seoul National University

2015

China

Peking University

2014

India

Indian Institute of Chemical Biology

2009

TaiwanNational Synchrotron Radiation Research Center

2007

Cuba

Center for Genetic Engineering and Biotechnology

2003

History

Key Facts

1956 Set up of a new laboratory in the

Faculty and staff members
Technical Staffs

Faculty of Science for organic
Professors

Male 3
Female 2

Male 13

Female 3

Associate Professors
Male 15TOTAL 95
Male 67
Female 28

Researchers

Female 3

Lecturers
Male 2

Female 1

Assistant Professors
Male 12

Female 7chemical studies of proteins andamino acids (the predecessor of IPR)

Faculty of Sciencesupervised by Prof. Shiro Akabori.

1958 IPR was established as a Joint-use Research Organization,
composed of three divisions: Organic Chemistry, Physical
Chemistry, and Protein Metabolism.

1962 IPR established the Peptide Center.

Male 22
Female 12

Breakdown of foreign faculty and staff:
China (5) South Korea (1) Germany (1)UK (1) Netherlands (1) Taiwan (1)Singapore(1)1972 The crystal structure of bonito
heart ferrocytochrome c wasdetermined by Prof. Kakudo of
IPR for the first time in Japan.

1978 IPR established the Crystallographic Research Center.

Students
Undergraduate
students

1988 IPR established the Research Center for Protein Engineering.
Ph.D. students

Male 9Female 7

Male 35
Female 21*Numbers in theparentheses indicate
overseas students.

Male 44
Female 30

2002 IPR established the Research Center for Structural andFunctional Proteomics.
National Universities under the National University Corpora-Affiliation:
Faculties of Science, Medicine, Engineering
Graduate Schools of Science,
Frontier Biosciences, Medicine, Engineering
Breakdown of overseas students:
USA (1) India (1) Indonesia (4) Egypt (2)Kenya (1) Sri Lanka (1) Thailand (3)Germany (1) Fiji (1) Brazil (1) South Korea (5)China (32)Master’ s students

2000 The Protein Data Bank Japan (PDBj) started its operation.

2004 IPR was transformed into a Research Institute of Japanese

TOTAL 146 (53)Male 88 (26)
Female 58 (27)Atomic model of cytochrome c frombonito hearttion Law.

2010 IPR was certified as a Joint Usage / Research Center by MEXT.
2012 IPR established the Research Center for State-of-the-Art
Functional Protein Analysis.

2016 IPR’ s continued activity as a Joint Usage / Research Center
was approved by MEXT.

2020 The atomic models of Cyto-

Grants and Budgets
Joint research funds with companies and others

Subsidies

20 million yen

30 million yen

Scholarship donations
50 million yen

TOTAL ( FY 2022 )1.27 billion yen

were registered as Chemical
Heritage authorized by the
Chemical Society of Japan.
IPR established the Research Center for Next-Generation

Grants-in-Aid for
Scientific Research
190 million yen

chrome c and Taka-amylase

Protein Sciences.
Management
Expenses Grant
410 million yen

2022 IPR’ s continued activity as a Joint Usage / Research Center
was approved by MEXT.
IPR established the Advanced Data Science Center forProtein Research.

Contract research funds
570 million yen

Institute for Protein Research,
Osaka University
3-2 Yamadaoka,
Suita-shi, Osaka 565-0871, Japan
TEL:+81-6-6879-8594 (General Affairs Section)www.protein.osaka-u.ac.jp/en/

Official Mascot of IPR, Osaka Univ.
Tanpakun & Kimichan
Issue: January 2024