ENGLISH
2024.04

Innovative Life Science Research with Proteins
Institute for Protein Research (IPR) is conducting cutting-edge and highly
original research in the life sciences, based on chemistry, physics,
biology, medicine, and informatics, which other institutes can rarely do. At
the same time, IPR is expected to serve as a hub for contributing to thedomestic and international community by upgrading large-scaleequipment that would be difficult for researchers to install by themselves,
such as ultra-high-field NMR, synchrotron beamline, cryo-EM, andcryo-FIB/SEM. In addition, as the Asian hub of the Protein Data Bank, oneof the major international databases, we continue to work as aninternational data center.
The environment surrounding our research field has changed dramatically

Directorover the past several years. New research results integrated with data or
information science have been produced utilizing AI with conventional
research methods. In recognition of this revolutionary situation, IPR has
been strengthening data-driven research. We intend to continue this trend
and promote innovative life science research from molecular level tocellular network information. Your continuous support and encouragement
are very much appreciated.

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 Membrane Systems Biology●

Laboratory for Physical Biology●

Laboratory for Cell Function Design

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

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 (ASPiRE)●

Laboratory for Protein Design●

Laboratory for Biomolecular Modeling and Dynamics●

Laboratory of Protein Databases●

Laboratory for Protein Network●

Laboratory for Drug Discovery Informatics

Endowed Chair●

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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.

Taki Nishimura

Protein engineering / Cell biology

Create highly functional artificial proteins and understand the membrane systems present in living organisms

Biological membranes, such as the plasma membrane and organelle membranes, dynamically change their structure and biophysical properties
in response to changes in nutrient conditions and stress. Using our remarkable screening technology and machine learning, we are developing
artificial proteins capable of sensing subtle alterations in biological membranes. By employing this innovative tool, we aim to understand themolecular mechanisms underlying membrane changes, elucidate their physiological significance, and generate new leads for drug discovery.

Madoka Suzuki

Physical biology

Imaging and manipulating heat flow: Understanding heat in biological systems

Cells are sensitive to heat. What is the response of proteins to this mechanism? Cells release heat by themselves. Does
that heat also play an important role in cellular function? We are developing techniques that combine physicochemical
concepts such as quantitative imaging and photothermal conversion to visualize and manipulate the flow of heat within thecell. We then aim to understand the role of heat flow across spatial scales and complexity in biological systems.

Satoshi Toda

Synthetic biology

Synthesis of cell functions by design to understand biological systems

Cells communicate with each other to organize complex tissue morphologies and regenerate after injury, which are uniquefunctions of life. We are developing technologies to design cell behavior and investigating how cells self-organize andmaintain multicellular structures. Furthermore, we are applying the technologies to develop therapeutic cells for intractablediseases.

Division of Protein Structural Biology
Genji Kurisu

Concurrent PI in ASPiRE

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 metalloenzymes or bioactive chemical compounds.

Takayuki Kato

Concurrent PI in Research Center for Next-Generation Protein Sciences

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

Concurrent PI in ASPiRE

Systems biology

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

We develop methods for analyzing intracellular information using experiments and mathematical models, and apply thesemethods to elucidate the regulatory rules of gene networks for cell and disease development. We are also working on thelatest methods in cell modeling and automated drug design, incorporating natural language processing and deep learning.

Kenji Mizuguchi

Concurrent PI in ASPiRE

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.

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 (ASPiRE)
Nobuyasu Koga

Protein design

De novo design of novel proteins and understanding mechanisms of protein folding and function

The protein sequence space is enormously vast, but naturally occurring proteins have only explored a tiny fraction of it. We
aim to develop methodologies for designing protein molecules using both computational and experimental approaches,
and to discover novel proteins from this vast and unexplored sequence space. We also aim to understand mechanisms ofprotein folding and function through de novo design.

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.

Endowed Chair
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.

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 inrecognition 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 theselarge facilities, IPR also operates PDBj (Protein Data Bank Japan) as one of the members of the Worldwide Protein Data Bank
(wwPDB) organization that manages the PDB archives, the most important and successful database on protein structures.
In April 2022, IPR received its second approval to continue as a Joint Usage / Research Center by MEXT. We have initiated newactivities towards becoming a global hub for multiscale structural life sciences, including the commencement of joint usage andresearch on MicroED, a technique for analyzing nano crystals in powder samples using electron microscopes. 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.
©RIKEN

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.

Development/Management of Databases
Protein Data Bank Japan (PDBj), an Asian data center of the worldwide Protein Data Bank (wwPDB), accepts the structure data of biological macromolecules 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) collaborating with the BMRB center in the US.

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
(Protein Data Bank Japan)(Biological Magnetic
Resonance Data Bank Japan)

https://pdbj.org

https://bmrbj.pdbj.org(Immunohistochemical database forbasement membrane proteins)
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

Website

Key Facts(English)Faculty and staff members

Students

Professors

Undergraduate
students

Male 15
Female 3

TOTAL 159
Male 77
Female 82

Male 4
Female 16(Twitter)

Male 15
Female 3

Male 7
Female 30

Technical
StaffsMale 35
Female 21

Male 9Female 7

Associate
Professors

Administrative
Staff

Ph.D. students

Researchers

Lecturers

TOTAL 146 (53)Male 1
Female 2

Male 88 (26)
Female 58 (27)Assistant
Professors
Male 9Female 7

Male 26
Female 21*Numbers in theparentheses indicate
overseas students.

Master’ s students
Male 44
Female 30

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)(There figures include the Specially Appointed positions,full-time and part-time positions.)
Breakdown of foreign faculty and staff:
China (5) South Korea (1) Germany (1) Italy (1)Netherlands (1) Singapore(1) Taiwan (1) Thailand (1) UK (1)Tanpakun &Kimichan(Official Mascot of
IPR, Osaka Univ.)

History
1956 Set up of a new laboratory in the Faculty of Science

Tanpakunfor organic chemical studies of proteins and amino

Kimichanacids (the predecessor of IPR) supervised by Prof.
Shiro Akabori.

Faculty of Science

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

(Twitter)Tanpakunofficial account1962 IPR established the Peptide Center.
1972 The crystal structure of bonito heart ferrocyto-(Twitter)

Kimichanofficial accountchrome c was determined by Prof. Kakudo of IPR
for the first time in Japan.

Atomic model of cytochrome c frombonito heart

1978 IPR established the Crystallographic Research Center.
1988 IPR established the Research Center for Protein Engineering.
2000 The Protein Data Bank Japan (PDBj) started its operation.
2002 IPR established the Research Center for Structural and Functional
Proteomics.

2004 IPR was transformed into a Research Institute of Japanese National
Universities under the National University Corporation 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 Cytochrome c andTaka-amylase were registered as Chemical
Heritage authorized by the Chemical Societyof Japan.IPR established the ResearchCenter for Next-Generation Protein Sciences.

2022 IPR’ s continued activity as a Joint Usage / Research Center was approved
by MEXT.
IPR established the Advanced Data Science Center for Protein Research(ASPiRE).

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