External Review ReportofInstitute for Protein Research

2023

March 2024 Issued

Preface
The Institute for Protein Research (IPR) was established in 1958 based on the Faculty of Science andthe Faculty of Medicine of Osaka University as a Joint-use Research Organization under thesupervision of Prof. Shiro Akabori as its first director. Since its establishment, IPR has been leading
protein science, a key field of life sciences based on interdisciplinary research in chemistry, biology,
physics, and medical science. In addition to our research, IPR has been working as a hub of proteinsciences for many laboratories worldwide.
At its establishment, IPR consisted of three divisions: Organic Chemistry, Physical Chemistry, andProtein Metabolism, but with advances in protein science and life science, IPR has expanded to covera broader range of research fields. To respond to the rapid progress of life science in recent years, IPR
reorganized the Research Center for Next-Generation Protein Sciences in October 2020, andestablished the Advanced Data Science Center for Protein Research in October 2022, aiming to serve
as a core center for life sciences based on protein structural information. Now IPR has grown into anorganization consisting of 16 laboratories in five research divisions (including the Endowed Chair),five laboratories in the Research Center for Next-Generation Protein Sciences, and five laboratories
in the Advanced Data Science Center for Protein Research.
Since its establishment, IPR has been active as a Joint-use Research Organization where many
researchers can visit and conduct research by sharing IPR’s facilities, equipment, and research knowhow from all over Japan. In April 2010, IPR was certified as a Joint Usage / Research Center forProtein Research by the Ministry of Education, Culture, Sports Science and Technology. IPR continues
its invigorate activities and is committed to contributing to the protein research community IPR’s
activities involve programs such as “Domestic Collaborators,” “International Collaborative Research,”and “IPR Fellows” that promote research activities, “IPR Seminars” that support organizing seminars
to provide a place for forming a community and exchanging information, the programs that support
the use of the forefront large facilities such as SPring-8 synchrotron radiation beamline, high-magnetic
field NMR machines, and cryo-electron microscopes. IPR also operates a protein structural database(Protein Data Bank) that is fundamental for protein research. IPR continues to serve as a research
center for life sciences, focusing on protein science.
The database project, PDBj (Protein Data Bank Japan) serves as one of the three regional data centersof the Worldwide Protein Data Bank (wwPDB) organization, registers data and provides various
services in Asia and Oceania. Additionally, the Synchrotron Radiation Beamline has been promoting
various international collaborative research activities, such as the formation of an Asia-Oceania

structural biology network through an academic agreement with the National Synchrotron Radiation
Research Center in Taiwan, as well as other international collaborative research programs.
IPR has international academic exchange agreements with 17 research institutions and has increased
its presence.
While conducting cutting-edge research, IPR faculty members actively provide lectures and practicaltraining to 120 students from the Faculty of Science, Faculty of Medicine, Faculty of Engineering,
Graduate School of Science, Graduate School of Medicine, Graduate School of Frontier Biosciences,and Graduate School of Engineering, Osaka University. In addition, about 30 postdoctoral researchers
are involved in various research projects.
For the projects that IPR carried out from FY2016 toFY2021, we received the highest rating of
Category S with the following comments:
As a core center for protein science, IPR makes its facilities, equipment, materials, and data
available for shared use, including the world's most powerful cryo-electron microscope,
instruments essential for protein structure analysis, and the operation of protein databases, andactively conducts collaborative use activities. IPR has achieved excellent research results,
including numerous publications, and is making efforts to further improve its core competence
as a research center by promoting interdisciplinary research, reorganizing researchorganizations, and forming an international joint laboratory, as well as by responding to theinterim evaluation results. In the future, further efforts are expected to be made to focus on
specific areas of research to make the facility unique, and to conduct advanced research in proteinscience using computational science and data science, such as prediction of 3D structures.
IPR has conducted external reviews in the past at critical times when it was deemed necessary toreview its research activities and structure. This external review was conducted prior to the interim
evaluation of the Joint Usage / Research Center scheduled for FY2024, to obtain an external evaluationof the activities of IPR, as well as the Advanced Data Science Center for Protein Research (ASPiRE)
which was launched in 2022 to promote advanced protein science research. This external review was
conducted from December 2023 to March 2024 with the dedicated cooperation of 12 academic experts
inside and outside Japan.
IPR conducted the External Review Committee Meeting (on-site and online) on January 29-30, 2024,
and received evaluations from the following perspectives regarding the status of activities andfunctions related to the IPR's Joint Usage / Research Center.
[Evaluation Items]
1. Research Activities

For the laboratories responsible for the review, are the goals of the research and the research
themes and methods based on those goals appropriate?
2. Budget and Organization
Is the management of the Joint Usage / Research Center properly organized? And is its support
system functioning properly?
3. The Joint Usage / Research Center Activities
Are the activities of the Joint Usage / Research Center appropriately implemented?
4. Education
Is IPR engaging in fostering its undergraduate/graduate students, young researchers, and foreign
researchers by utilizing the programs of the Joint Usage / Research Center?
5. External funding and other research expenses
Is IPR making efforts to secure the necessary research funding for research activities?
6. Information Disclosure and Social Relationships
Is IPR offering information about its research activities sufficiently to society?
7. International Exchanges
As a university-affiliated research institute and as a Joint Usage / Research Center, does IPR
engage in sufficient international exchange activities?
[General Discussion]Are IPR’s research activities and organization appropriate, including the recent reorganization?

Is IPR’s future direction orientated toward protein or life science prospects?

This review report summarizes the above external evaluation and describes IPR’s future actions. We
will take these evaluations and recommendations made by the committee members seriously and incorporate them into our future efforts.
March 2024

Professor, Mariko Okada
Director, Institute for Protein Research

Professor, Atsushi Nakagawa
Chair, Review Committee of IPR

外部評価にあたって
蛋白質研究所は、1958 年に大阪大学の理学部と医学部が母体となり全国共同利用の附置研究所
として、赤堀四郎先生を初代所長として大阪大学に設置されました。設立当初から、化学、生物学、物理学、医学の研究者が集まり、生命活動を担う重要な分子である蛋白質を核に学際的な研究を展開し、分子レベルから個体レベルで生命現象を理解していくことを目指した研究を続けるとともに、共同利用研究所としての活動を通して国内外の蛋白質科学研究をリードしてきたと自負しています。
設立時には、蛋白質有機化学研究部門、蛋白質溶液学研究部門、蛋白質代謝部門の３つの部門（研究室）のみから構成されておりましたが、蛋白質科学、生命科学の進歩とともにより幅広い分野を研究対象として発展してきました。2020 年 10 月には近年の生命科学の急速な進歩に対応するために、「附属蛋白質次世代構造解析研究センター」の改組を、2022 年 10 月には蛋白質構造情報を基盤とする生命科学研究拠点の核となることを目指した「附属蛋白質先端データ科学研究センター」の設置を行い、現在では、5 研究部門 16 研究室（寄附研究部門を含む）、附属蛋白質
次世代構造解析センター5 研究室、附属蛋白質先端データ科学研究センター5 研究室からなる組織に発展しています。
創設時から、全国より多くの研究者が来所され、研究所の施設・装置や研究のノウハウを共有して研究を行うことができる全国共同利用研究所として活動してきましたが、共同利用制度の改革により 2010 年 4 月からは、蛋白質研究共同利用・共同研究拠点に選ばれて、蛋白質研究のコ
ミュニティにより一層貢献できる体制を作り、さらに活発に活動を続けています。この活動では、共同研究員、国際共同研究、客員フェローといった研究活動を推進するための事業、研究者コミ
ュニティの形成や情報交換の場を提供する蛋白質研究所セミナーの開催と支援、SPring-8 の放射光ビームライン、超高磁場核磁気共鳴（NMR）装置群、最新鋭のクライオ電子顕微鏡などの大型装置の利用支援、蛋白質研究の基礎となる蛋白質構造データベースの構築と公開などが行われており、蛋白質科学を中心とする生命科学の研究拠点として活動を続けています。特に、データベース事業においては、蛋白質構造データバンク（PDB）の世界 3 拠点の一つとして日本蛋白質構
造データバンク（PDBj）を運営し、アジア・オセアニア地区のデータ登録や種々のサービスを行
うとともに、PDBj－BMRB（生体分子磁気共鳴データバンク）として生体系 NMR データバンク
を米国 BMRB と共同で運営しています。また、放射光ビームラインでは、台湾国立放射光科学研究センターとの共同研究協定を通じたアジア・オセアニアの構造生物学ネットワーク形成を進めるなどの国際共同研究制度とともに、様々な国際的な共同利用・共同研究活動を進め、現在、17の研究機関と学術国際交流協定を結んで国際的にもプレゼンスを示しています。
蛋白質研究所の教員は、先端的な研究を進める一方で、それらの研究に裏打ちされた講義や実習を、大阪大学理学部、医学部と工学部、および大学院理学研究科、医学系研究科、生命機能研
究科、工学研究科の学生に対して積極的に行っており、特に、学部生と大学院生あわせて約 120
名前後の学生が、蛋白質研究所で教育を受け、研究を行っています。さらに、30 人程度の博士研究員が様々な研究プロジェクトに関与して、日夜研究を進めています。

2016 年度から 2021 年度に本研究所が実施した蛋白質研究共同利用・共同研究拠点の事業に対しては、「蛋白質科学に関する中核的拠点として、世界最高性能のクライオ電子顕微鏡をはじめ蛋

白質の構造解析に不可欠な装置や蛋白質に関するデータベースの運用等、施設、設備、資料及びデータを共同利用に供し、活発に共同利用・共同利用活動を行うとともに、多数の論文発表等優れた研究成果を上げ、分野融合研究の推進や研究組織の改組、国際ジョイントラボの形成に向けた取組を実施するなど、中間評価結果への対応を通じて拠点としての中核性を更に向上するために取り組んでいることは非常に高く評価できる。今後は、特定の領域にフォーカスするなど研究施設の特色を出すような活動や、立体構造の予測等の計算科学やデータサイエンスの活用による
先端的な蛋白質科学の研究に向けた更なる取組が期待される。」という評価コメントとともに評価
区分Ｓという最高ランクの評価を受けることができました。
蛋白質研究所ではこれまで、その研究活動や研究体制の見直しが必要と思われる重要なタイミ
ングで外部評価を行っております。今回の外部評価は、令和 6 年度に予定されている共同利用・共同研究拠点の中間評価に先立ち、2022 年に立ち上げた「附属蛋白質先端データ科学研究センター（ASPiRE）」を中心として生命科学の核となる先端的な蛋白質科学研究を進める蛋白質研究所の活動について、外部から評価をいただくために実施いたしました。
この外部評価は、2023 年 12 月から 2024 年 3 月にわたり、国内外の学識経験者 12 名の先生方にご協力頂き実施いたしました。改めて委員の先生方にお礼申し上げます。2024 年 1 月 29 日から 30 日に蛋白質研究所において外部評価委員会を開催し、研究所の共同利用・共同研究拠点に関する取り組みや機能の状況に関して、以下の視点から評価をいただきました。
【評価項目】
１．研究活動研究の目標とそれに基づく研究テーマの設定および研究方法は適切か。
２．組織体制
共同利用・共同研究拠点の運営は適切に行われ、支援体制が適切に機能しているか。
３．拠点活動共同利用・共同研究拠点の活動は適切に実施されているか。
４．教育
共同利用・共同研究事業を活かした人材養成の取組や、蛋白質研究所の学部生・大学院
生、ポスドク等の若手、および外国人研究者の育成に取り組んでいるか。
５．外部資金等の研究経費
研究活動に必要な研究経費の確保に努めているか。
６．情報公開・社会連携
研究所の活動を十分に社会に発信しているか。
７．国際交流大学附置研究所として、また共同利用・共同研究拠点として、十分な国際交流活動を行っているか。

【総合討論】
１．研究所の活動状況と組織構成は適切であるか。
２．研究所の将来について、蛋白質科学、生命科学等の将来展望を見据えた方向性が示されているか。
本評価書は、以上の外部評価をまとめ、今後の研究所の対応も記載いたしました。評価委員の先生方にいただいた評価や提言を真撃に受け止め、今後の研究所の発展を期したいと考えております。

2024 年 3 月
大阪大学蛋白質研究所所長 教授 岡田眞里子
評価委員会委員長
教授 中川敦史

EXECUTIVE SUMMARY
This is the executive summary for the final report of the 2023 External Review (ER2023) of theInstitute for Protein Research (IPR), Osaka University, organized by the External Review Committee
consisting of 12 distinguished international and domestic researchers in protein science.
During the two-day on-site visit to the IPR in Osaka, the ER2023 committee members extensively had
in-depth reviews and discussions with the directors of the IPR, its affiliated research centers, and PIs
in all research groups to examine their recent activities. The ER2023 committee mainly focused on
the following activities and their performances from April 2019 to December 2023 from the viewpointof the IPR’s roles as a leading research institute and a Joint Usage / Research Center.
Main topics of this external evaluation by the ER2023 committee:
1.

Research Activity

2.

Activities as a Joint Usage / Research Center

3.

Education

4.

Information Disclosure and Social Relationship

5.

International Exchange

The evaluation also provides observations (comments, thoughts), suggestions, and recommendations
for each topic. Overall, ER2023 committee members conclude that:
Research Activity:
The IPR demonstrates excellent international presence, research accomplishments, and strategic
initiatives. The committee recommends maintaining a proactive approach to adapting to emerging
research trends, investing in emerging areas, enhancing internal collaboration, establishing a futureplanning committee, and balancing tradition with cutting-edge research. The launch of ASPiRE is seen
as a proactive approach to adapting to emerging research trends, although its outcomes need further
evaluation.
Activities as a Joint Usage / Research Center:
The Joint Usage / Research Center of IPR, as a core for protein research in Japan, operates as a
successful Joint Usage / Research Center, acknowledged for its significant achievements and proper
functionality with well-established management and user support systems. The committee admires thecenter's exemplary performance and recommends further expanding collaborations forgroundbreaking discoveries in these facilities.

1

SPring-8 and PDBj are the examples of the IPR's outstanding assets. They are also acting as the assets
for global collaborations and the provision of research platforms for high-end protein research.
However, concerns include a decreasing trend in collaborations after 2018 and the need for constantfunding for high-end facilities. The committee appreciates IPR's efforts but raises budgetary concernsand suggests the consideration of charging systems for facility usage to supplement government
support, aligning with current practices at many universities.
Education:
The committee praises the IPR's commendable efforts in cultivating the intellectual landscape ofyoung scientists in the intricate field of protein life science. Its effective programs have educated andsuccessfully nurtured the budding talents that form the backbone of the scientific community. The
committee also acknowledges and commends the IPR's steadfast commitment to student education,
citing a noteworthy increase in student numbers over the preceding four years.
Recognizing the potential for further advancement, the committee puts forth insightful
recommendations. These include augmenting scholarships for Ph.D. students through collaborative
initiatives with Osaka University, ensuring a robust influx of promising doctoral candidates. Moreover,
an imperative call is made to broaden the horizons of the postdoctoral research program, with a keen
focus on fostering diversity among international fellows.

This strategic expansion is pivotal forsustaining a vibrant and globally representative community of researchers.
While acknowledging the enriching seminar milieu conducive to on-site learning, the committee
underscores the necessity for diplomatic negotiations with the Faculty of Science. This effort is crucial
to address perceived limitations in assigning undergraduates to IPR and to promote an inclusive
educational environment.
Information Disclosure and Social Relationship:
The committee appreciates the uniqueness of IPR's outreach activities but propose more inclusive
endeavors transcending generational boundaries for broader societal impact. Additionally, thecommittee emphasizes the need for participant feedback to ensure program satisfaction. Furthermore,
the committee suggests that IPR could enhance transparency and public perception by adopting an
open election system for director and professor positions, leading to information disclosure.
International Exchange:
The IPR has successfully engaged in collaborative research with researchers from diverse countries,
indicating satisfactory international exchange activities for an affiliated research institute and the Joint

2

Usage / Research Center. The institute's commitment to global scientific cooperation is evident
through its involvement in joint research projects, academic exchange agreements, and international
joint labs. Furthermore, IPR's public offering programs, supporting International Collaborative
Research, non-proprietary usage of Synchrotron Radiation Beamline, and MicroED collaborative
research, exemplify its dedication to fostering international scientific exchange and development.
Although the IPR has an outstanding role in facility usage and database access, there is a notableconcentration of international beamline allocation to Taiwan. The committee recommends that the IPR
develop close relationships with more countries worldwide for research and human resource exchange
to ensure sustained growth.
Conclusions and Other Recommendations
The committee has acknowledged that the IPR possesses the ambition and potential to establish itself
as a world-leading research institute. The accomplishments of the IPR faculties are highly
commendable and underscore the institute's significant contributions to protein science. However,collaboration within the IPR is relatively limited. The committee suggests encouraging collaborative
research within the institute to develop it further and take advantage of diverse research experts in the
IPR.
IPR boasts an excellent array of facilities crucial for advancing cutting-edge research in proteinsciences. However, the management of most of these facilities is overseen by associate professors,
who ideally dedicate their time and efforts to their research endeavors. Hiring specialized personnel
to manage these resources would alleviate the burden on academic staff and enhance the overall
functionality and utilization of the facilities. Such support would ensure that the equipment ismaintained at optimal performance levels and is readily available for researchers, thereby maximizing
the investment and contributing to more robust and efficient scientific outcomes. The government
must recognize the importance of funding the purchase of such high-caliber equipment and ensuring
adequate resources for its ongoing management. A more sustainable management model of IPR's
facility infrastructure, supported by adequate government funding, is needed to provide the longevity
and effectiveness of these valuable resources.
Acknowledgments:
The ER2023 committee members acknowledge all the IPR members for helpful, clear, comprehensive
interviews, documentation, presentations, and answers to follow-up questions. As far as the ER2023
committee members could assess, the IPR was transparent and internally self-consistent. The ER2023
committee members note that logistical support was outstanding—many thanks to Director Mariko
Okada, Prof. Atsushi Nakagawa, and the ER2023 administration office.

3

External review of Institute for Protein Research (FY2023)

Committee Members

Chairperson
Bong-Jin LEE (Dean of College of Pharmacy, Ajou University, Korea)【Division of Protein Chemistry】*Tatsuya SAWASAKI (Professor, Ehime University)
Keiko SHIMAMOTO (Specially Appointed Manager, Suntory Foundation for Life
Sciences)
Hee-Jung CHOI (Professor, Seoul National University, Korea）【Division of Protein Structural Biology】【Research Center for Next-Generation Protein
Sciences】*Bong-Jin LEE (Dean of College of Pharmacy, Ajou University, Korea)
Yuriko YAMAGATA (President, Shokei University, Shokei University Junior College)
Takeshi MURATA (Professor, Chiba University)【Division of Integrated Protein Functions】*Sen TAKEDA (Professor, Teikyo University)
Tatsumi HIRATA (Professor, National Institute of Genetics)
Jun SUZUKI (Professor, Kyoto University)【Division of Protein Network Biology】【Advanced Data Science Center for Protein
Research】*Shoji TAKADA (Professor, Kyoto University)
Kenta NAKAI (Professor, The University of Tokyo)
Chandra VERMA (Senior Principal Investigator, A*STAR, Singapore)*Overall Review Member

4External Review of Institute for Protein Research (FY2023)

AGENDA
Date: January 29 (Mon) - 30 (Tue), 2024
Venue: 1F Auditorium, 2F Large Meeting Room (#212), 2F Medium Meeting Room (#202),
4F Seminar Room (#415), 7F Seminar Room (#712)

DAY 1
Welcome Speech: Dir./Prof. Mariko Okada
Introduction of Reviewers

10:00 – 10:10

10:10 – 10:35
10:35 – 11:00
11:00 – 11:25
11:25 – 11:50
11:50 – 12:05

Attendees

Moderator: Prof. Atsushi Nakagawa
Room: Large Meeting Room (#212)
Overall Review (15 min presentation + 10 min Q&A)
Room: Large Meeting Room (#212)
Overall activities of IPR
Dir./Prof. Mariko Okada
Activities of Joint Usage / Research Center
Prof. Yoshie Harada
Research Center for Next-Generation Protein Sciences
Prof. Atsushi Nakagawa
Advanced Data Science Center for Protein Research
Prof. Nobuyasu Koga

 All Reviewers
 All PIs

Discussion

12:05 – 12:15

Group Photo (Entrance) All Reviewers

12:15 – 13:30

Lunch Break (Auditorium) All PIs

Review of Research Group Activities (10-15 min presentation & 5 min Q&A)
Division of Protein Chemistry
Moderator: Prof. Toshifumi Takao
Room: 4F Seminar Room (#415)

 EachReviewer

13:30 – 13:50

Laboratory for Protein Organic Chemistry: Prof. Hironobu Hojo

13:50 – 14:10

Laboratory for Nanobiology: Prof. Yoshie Harada Hojo14:10 – 14:30

Laboratory for Protein Synthesis and Expression: Prof. Junichi Takagi

 Harada

14:30 – 14:50

Laboratory for Protein Profiling and Functional Proteomics: Prof. Toshifumi
Takao Suzuki

14:50 – 15:05

Laboratory for Physical Biology: Assoc. Prof. Madoka Suzuki

Division of Protein Structural Biology/Research Center for Next-Generation Protein Sciences
Moderator: Prof. Takayuki Kato
Room: 2F Medium Meeting Room (#202)

 Takao Takagi

 EachReviewer

13:30 – 13:50

Laboratory for Protein Crystallography: Prof. Genji Kurisu

13:50 – 14:10

Laboratory for CryoEM Structural Biology: Prof. Takayuki Kato

 Kurisu

14:10 – 14:30

Laboratory for Supramolecular Crystallography: Prof. Atsushi Nakagawa

 Nakagawa

14:30 – 14:45

Laboratory for Molecular Biophysics: Assoc. Prof. Yoh Matsuki

14:45 – 15:00

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy: Assoc. Prof.
Yohei Miyanoiri

15:00 – 15:15

Laboratory for Biomolecular Analysis: Assoc. Prof. Nobuaki Okumura
5 Kato Matsuki
 Miyanoiri
 OkumuraExternal Review of Institute for Protein Research (FY2023)
Division of Integrated Protein Functions
Moderator: Prof. Akira Shinohara
Room: 7F Seminar Room (#712)

 EachReviewer

13:30 – 13:50

Laboratory for Molecular and Developmental Biology: Prof. Takahisa Furukawa

13:50 – 14:10

Laboratory for Genome and Chromosome Functions: Prof. Akira Shinohara Furukawa

14:10 – 14:30

Laboratory for Advanced Brain Functions: Prof. Takatoshi Hikida

 Nakai

14:30 – 14:45

Laboratory for Organelle Biology: Assoc. Prof. Masato Nakai

 Shinohara

Division of Protein Network Biology/Advanced Data Science Center for Protein Research
Moderator: Prof. Kenji Mizuguchi
Room:2F Large Meeting Room (#212)

13:30 – 13:50

Laboratory for Cell Systems: Prof. Mariko Okada

13:50 – 14:10

Laboratory for Computational Biology: Prof. Kenji Mizuguchi

14:10 – 14:30

Laboratory for Protein Design: Prof. Nobuyasu Koga

14:30 – 14:45

Laboratory for Biomolecular Modeling and Dynamics: Assoc. Prof. Sandhya P.
Tiwari14:45 – 15:00

Laboratory of Protein Databases (PDBj): Prof. Genji Kurisu

 EachReviewer Mizuguchi Okada Koga Sandhya

Break (Auditorium)

15:00 – 15:30
15:30 –

Facility tour (NMR (solid/solution), Cryo-EM)

 Applicant

17:00 –To Senri Hankyu Hotel All Reviewers

17:30 –

Dinner (Senri Hankyu Hotel)

 All PIs

DAY 2
10:00 – 10:40

Session 1: Summary of Reviewers’ Comments
Room: Auditorium
Break

10:40 – 10:50
10:50 – 11:30

 All Reviewers
 Okada Nakagawa
 HojoSession 2: Overall Evaluation of Research Group Activities
Room: Each room

 Eachreviewer Each PI(Presenters)

Break

11:30 – 11:40

Overall Review, Q&A
11:40 – 12:35

Moderator: Prof. Atsushi Nakagawa
Closing remarks: Prof. Atsushi Nakagawa

 All reviewers
 All PIs

Room: Auditorium
Lunch Break (Auditorium)

12:35 – 14:00
14:00

To Senri-Chuo Station

6

 All reviewers
 All PIs

Inside the Meeting (Large Conference Room)
7

Inside the Meeting Room (Auditorium)
8Inside the Meeting (Each Division)
9

Evaluation Sheets for Activities of IPR

External Review FY2023

Evaluation Sheet (Activities of IPR)

Reviewers: Hee-Jung CHOI, Bong-Jin LEE, Tatsuya SAWASAKI, Shoji TAKAD, Sén TAKEDA
Based on the perspectives of:
1. the research activities and performance as the research institute, and2. the functions and activities as the Joint Usage / Research Center,please provide your evaluation and review for each topic described below. If you find any outstanding points,
issues, or recommendations, we highly appreciate your comments. You do not need to fill out all topics, butplease kindly provide as much information as possible.
1. Research Activity[Evaluation Perspective]
Are the IPR’s research activity, performance and the compositionof research divisions appropriate as an internationally-recognizedprotein life science research institute?
Is the current IPR’s vision appropriately set to meet the futureadvances in protein science, life science, etc.?

Above
Average
1

Excellent4

Commentary and Recommendations[Reviewer #1]
In terms of research activities, accomplishments, and the composition of its research departments, the IPR
has demonstrated a strong international presence and sufficient influence. In addition, the current vision of
the institute is established with due consideration given to the future development of protein science and life
sciences. By keeping this quality of activity, the IPR will be able to continue to lead protein research in Japan,
as it is doing now.
[Reviewer #2]
IPR shows an excellent track record of publications in prestigious journals, underlining its significant
contributions to protein science. The institute's provision of state-of-the-art facilities and advanced equipment
further underscores its commitment to maintaining a cutting-edge research environment. A particularly
notable achievement is IPR's strategic response to the evolving landscape of data-driven protein science,
including novel protein design, which is rapidly growing research field globally. The establishment of the
new ASPiRE division is a commendable step. This division, encompassing four new laboratories (Protein
Design, Biomolecular Modeling and Dynamics, Protein Network, Drug Discovery Informatics) along withthe existing Protein Databases lab (previously part of the Research Center for Next-Generation Protein
Sciences), reflects a proactive and flexible approach to organizational structure. This reorganization allows
IPR to stay at the forefront of global research trends and dynamically evolve in response to the shifting10

Evaluation Sheets for Activities of IPR
landscape of protein science.
Looking forward, it is recommended that IPR continues to foster this adaptive approach, particularly by
investing in emerging areas of protein science that show potential for significant impact.
[Reviewer #4]
This reviewer finds the IPR’s overall research activity is obviously above average in terms of scientificperformance. Each division constantly contributes to the progress of protein research in each specific fieldand continues to be productive, verified by high-quality publications over the past years. IPR covers broad
areas in protein science ranging from structural biology to higher brain function of mammals, making it
possible to be a hub for the protein-oriented research both in domestic and international research network.
Moreover, basic research, ideas and concept appear to transform or sublime to be a full-fledged appliedsciences that are buttressed by the traditional and master techniques in protein chemistry that have beendeveloped, refined and handed down during the long history of IPR.
When we take a look at equal opportunity action or diversification of faculty, this reviewer finds the statusquo of IPR copes well with the standard requirements from the society as we can see from the breakdownof faculty recently employed here, though continued efforts are required to maintain and foster a mind ofdiversity.
Whilst my general impression on IPR is a very positive one, there are a couple of advice that would be
ideally reconsidered by a decision-making committee of IPR to improve the performance as well as toassure the sustainability of IPR.
First, it would be better to have in-house research seminar that can expedite collaborative research between
different expertise in IPR thorough exchanging basic ideas. As collaborative research is going quite
actively with external facilities, this reviewer does not find it difficult to have in-house collaborations, ifeach member of IPR bears in mind what in-house collaboration means. It does not necessarily mean that
substantial collaboration on a specific theme through and through, but technical or conceptual collaboration
will do. According to vis-à-vis hearing from not a few staff scientists during my stay in IPR, this reviewer
finds himself noticing that there is no real opportunity such as seminar or retreat that make all affiliates in
IPR know about research contents explained by PIs by themselves of each division. What one can do as anext step is to prepare a platform for promoting in-house collaboration to take advantages of expertiseblanketing broad area of protein research. A good example for that is an initiative of in-house funding
platform taken by Prof. Koga from ASPiRE. This has a great potential to promote internal collaboration in
the long run, while it appears rather reserved now.
Second, it is advisable to have a kind of active future planning committee to set short-, mid-, and long- term
goals of IPR with special references to the recruitment of staff, direction of research, re-organization of

11

Evaluation Sheets for Activities of IPR
division, and financial issues. Committee should include a couple of external members to gather and blush
up proposals and idea that potentially contributes to a continued development of IPR.
Third, perspectives for running the organization in mid-term is very important to balance the tradition andcutting-edge research field. On one hand, IPR should keep heritages of protein chemistry as fundamentals
of institute, such as proteomics and organic chemistry. On the other hand, IPR has to deconstruct andreorganize the current division at least to keep abreast of age, and ideally take an initiative of protein
research globally. This reviewer heard that 8 leading PIs are going to be retired from IPR in the coming 5
years. Taking this into account, it may be high time to reconsider the restructuring of organization by taking
the advantages of this opportunity to foster the development of new research area.
[Reviewer #5]
Evaluating the whole activities of the IPR, I am convinced that the overall research activity of the IPR isoutstanding and at the world-level.
For the long-term direction, I am impressed that the IPR realizes nice balance between the conservation andthe revolution/change. As a single national institute focusing on protein science in Japan, the IPR keeps the
position of the center of protein science, with current focus in structure biology. At the same time, the IPR
keeps changing driven by scientific development. More recently, the IPR launched the data-oriented center,
ASPiRE, which perfectly meets the current need in protein science. As such, this new center, ASPiRE, plays
an important role. Its organization looks good, but obviously, it is too early to assess its outcome.
2. Activities as a Joint Usage / Research Center[Evaluation Perspective]

Are the activity and performance as a Joint Usage / ResearchCenter appropriate?
Are the management and user-support system properly arranged
and functioned as a Joint Usage / Research Center?

Excellent5

Commentary and Recommendations[Reviewer #1]
The IPR has more than enough activities and achievements as the Joint Usage / Research Center, and isfunctioning properly. The IPR is fully functioning as a core for protein research in Japan. The management
system and user support system as the Joint Usage / Research Center have been appropriately established andare functioning properly. If the government adds more budget, I can further expect that this institute will bea driving force in protein research in Japan.
[Reviewer #2]
The Joint Usage/Research Center at IPR has demonstrated exemplary performance, particularly evidenced
by the publication of excellent research results in top-tier journals such as 'Cell' (2021) and 'Nature Structural

12

Evaluation Sheets for Activities of IPR& Molecular Biology' (2019, 2021, 2023). This success is notably attributed to the effective utilization of
IPR’s state-of-the-art facilities, including the X-ray beamline, NMR, and cryo-EM. These tools have been
instrumental in advancing research and fostering collaborative projects with industry partners andinternational scholars, showcasing the center's role as a hub of innovation and practical application.
Moving forward, it is recommended that the center continue to build on these strengths by further expanding
its collaborative endeavors. This could involve establishing more diverse partnerships, both within academia
and across different industry sectors worldwide. Doing so could broaden the scope of research and increase
the potential for groundbreaking discoveries and technological advancements.
Additionally, considering the rapid evolution of scientific technology, regular assessments and upgrades of
the center's equipment and facilities (supported by government) are essential. Keeping pace with the latest
advancements will ensure that the center remains at the forefront of research capabilities.
[Reviewer #4]
To this reviewer’s understanding, there are two outstanding assets in IPR, both of which contribute to theexpertise of protein research: Spring-8 and Protein Databank Japan (PDBj). In addition, series of NMR andcryo-EM instrumentations reinforce the fundamentals of IPR, all of which live up to the reputation of IPR asa center of protein research in Japan. The stats show that those facilities are working very busy, operated not
only by the faculty of IPR, but also by many collaborators around the globe.
In terms of fostering researchers in the field of protein life science, the fundamentals of IPR provide young
scientists with an opportunity to carry out forefront research that will be inaccessible at their own
affiliations. Technically, IPR provides 8 types of platforms for collaborators, which enables them to beeasily accessible to high-end protein research facilities without going through any particular issues inoperating and applying those instrumentation.

Regarding protein informatics, PDBj covers over 30% of world-wide registry of protein databank, whose
entries appears to be on an increasing trend after 2015. Moreover, the number of accessions to PDBj has
been drastically increased, reaching at over 170 million annually in 2022. Taking those stats into account,
IPR can be evaluated as a major joint user research center of protein in the world.
However, when we take a look at the status quo in detail, there are several negative factors that have to beaddressed to sustain and strengthen the leading roles of IPR. First, the total number of collaborations takes
on a decreasing trend after 2018, while the number of international ones is increasing. As for the number ofusers, it remains relatively constant during this period except for 2021, non-collaborative users stay on asame trend. Considering one of the important roles of IPR as a center for joint research, it is advisable toencourage collaborative research to broaden the coverage of research area. Second, international beamline
allocation appears to be deviated to Taiwan accounting for ca. 10%, while the sector for all other countries

13Evaluation Sheets for Activities of IPR
adds up only to 1 %. Although there might be some geographical barrier in collaborating with IPR, it isideal to recruit more countries all over the world from the standpoint expediting multidisciplinary research.
Third, measures to maintain constant funding to maintain the high-end facilities have to be considered in aproactive manner to assure the position of IPR to be a pivot of protein research, such as an introduction of
charging system to the users depending on the affiliation. Considering rapidly exchanging, volatile time weare confronting nowadays, proactive measurements are indispensable to further strengthen the power of
IPR.
[Reviewer #5]
I see that the IPR made tremendous effort to serve as the Joint Usage / Research Center, which I appreciate
to. To maintain the service and keep the facilities top-leveled, the budget is the issue. Government support isdesired, but cannot be too much, either. I thought the IPR can seriously think of charging systems for usageof facilities. I hope it would not be too expensive. But, it can be non-free. Nowadays, many Universities havecharging systems, as far as I know.
3. Education[Evaluation Perspective]In terms of fostering researchers in the field of protein life sciencethrough Joint Usage / Research Center, are the programs
appropriately arranged?
In terms of fostering young researchers (undergraduate students,
graduate students, post-doctoral fellows, and foreign researchers)in the IPR, is the education appropriately provided?

Above
Average3

Excellent2

Commentary and Recommendations[Reviewer #1]
As an institution for fostering researchers in the field of protein life science through the Joint Usage /Research Center, the IPR has established sufficient programs and an appropriate systems, and has
demonstrated a satisfactory achievement.
[Reviewer #2]
IPR significantly contributes to the education and training of the next generation of scientists in the field ofprotein life science, offering a range of programs and opportunities for students and researchers. To further
enhance this educational role, it is recommended that IPR, through Osaka University, provides more
scholarship opportunities for PhD students, to recruit more PhD students.
Additionally, although the IPR New Research Exploration Program is commendable (it is not clear whether
it supports postdoctoral fellows), an expansion of the postdoctoral research program to support theindependent research of both domestic and international postdoctoral fellows would be an excellent step
(Government should provide more funding for this purpose). By nurturing a diverse and dynamic communityof researchers, IPR can continue to make substantial contributions to the field.

14Evaluation Sheets for Activities of IPR[Reviewer #4]
According to the stats, the number of students shows an increasing trend during the COVID19 pandemic,
and the total amount of scholarship increased steadily. Considering the expected roles of IPR as a center for
fostering researcher in protein science of broad meaning, the goals of IPR appears to have been successfully
attained at least during last couple of years in terms of figures. Furthermore, this reviewer witnessed thatquite a few students belong to each lab and contribute to the scientific output to some extent. However, as
there was no detailed information, such as syllabus and course guidebook, given during the review round,
this reviewer is not able to evaluate precisely the quality of education both in terms of lectures and laboratory
course for all sectors of students. Taking the environment of IPR into account, where many seminars are held
every week, students are provided with enough chance to learn the cutting-edge research. In this sense,
educational activities in IPR are likely given on site in each lab and they would be ideal teaching materials
for students, judging from the high-quality scientific products from IPR.
One comment that comes up in my mind is a recruiting system. During my stay in IPR, I’ve heard that there
is a restriction in the number of undergraduates allocated to IPR. The fact that only 8 undergraduates
belonging to Faculty of Science can choose labs in IPR appears to be a kind of enclosure, which should be
ideally changed through negotiation on the basis of educational collaboration and development of IPR.
[Reviewer #5]
The IPR made much effort to education of students in IPR. I am very impressed that the number of students
steadily and markedly increased in the last 4 years. I hope this continues.
I did not see the fostering program of protein science for the community run by the IPR (Possibly, I justmissed it). Summer and/or winter schools for comprehensive protein science, for example, can be great forthe community. Such schools can also be effective as a tool of recruiting students from other Universities.
Once video recorded, lectures in these schools can be delivered via YouTube or others.
4. Information Disclosure and Social Relationship[Evaluation Perspective]Is the IPR sufficiently communicating with the societies about the
IPR’s activities?

Average1

Above
Average
2

Commentary and Recommendations[Reviewer #1]
The IPR has adequate outreach activities to the public, including
academic societies and high school students.

15

Excellent2Evaluation Sheets for Activities of IPR[Reviewer #2]
IPR sufficiently communicates with the societies about the IPR’s activities through its website, both inEnglish and Japanese.
[Reviewer #3]
Not only a lecture for high-school students, but a lecture for general people is needed for PR (promotion) of
IPR for the social relationship. PR of IPR research result is important in increasing the support fromgovernment.
[Reviewer #4]
Regarding the outreach activity, this reviewer feels nothing particular that is superior to other institutions.
While IPR offers special programs and lectures to high school students, more generalized activities notconfined to specific generations should be considered to be recognized as a pro bono institute influencing thesociety. From the standpoint of evaluation, this reviewer would like to give just a brief comment on an
outreach activity to high school students. Although it is highly evaluated to facilitate the participation ofyounger generation to get involved in the protein research, it would be better to know the feedback from theparticipants whether or not they have satisfied with the program.
When it comes to information disclosure, IPR places annual reports and review reports of every four years
open to the public on its website. This is a de facto international standard for universities and research
institutions. IPR can be at the vanguard of information disclosure, if election system of director as well as
professor is open to the public. To this reviewer’s eye, a system for electing Director of IPR though mutual
selection is appealing compared to the candidature system. For academic organization, candidature system
often does not work well, where only those aspiring for power tend to stand for the position.

5. International Exchange[Evaluation Perspective]

Are the IPR’s international exchange activities satisfactory as anaffiliated research institute and a Joint Usage / Research Center?

Above
Average
1

Excellent4

Commentary and Recommendations[Reviewer #1]
The IPR has been conducting collaborative research with researchers in a very diverse range of countries.
These facts indicate that IPR's international exchange activities are satisfactory enough for an affiliatedresearch institute and the Joint Usage / Research Center.
[Reviewer #2]

16

Evaluation Sheets for Activities of IPR
IPR's engagement in a broad spectrum of international collaborations is commendable. Its involvement injoint research projects, academic exchange agreements, and international joint labs demonstrates a strong
commitment to global scientific cooperation. Additionally, IPR's public offering programs, which support
International Collaborative Research, non-proprietary usage of Synchrotron Radiation Beamline, andMicroED collaborative research, are exemplary initiatives that showcase the institute's dedication to fosteringinternational scientific exchange and development.
[Reviewer #4]
As commented in sections 1 and 2, most of the stats shows an outstanding role of IPR both in facility usage
and database access. However, international beamline allocation is concentrated to Taiwan accounting forcirca 10%, whereas that for all other countries account for around 1 %. Possibly, very close relationship of
IPR with Academia Sinica account for this, it is ideal to recruit more countries all over the world to promote
the research and human resource exchange, which will ensure a continued growth of IPR.

[Other]If you have any additional comments or recommendations other than those mentioned above, please describe
them here.
[Reviewer #1]
The IPR is a strong supporter of protein research, especially in Japan. This contribution is very significant,and many domestic researchers have benefited from it. However, because of the amount of effort that isrequired to make up for this, collaboration within the IPR appeared to be relatively limited. For the further
development of this institute, I would like to encourage collaborative research within the institute.
[Reviewer #2]
This review has clearly demonstrated that the Institute of Protein Research (IPR) possesses the ambition andpotential to establish itself as a world-leading research institute. The accomplishments of the IPR faculties
are highly commendable and underscore the institute's significant contributions to the field of protein science.
IPR boasts an excellent array of facilities, which are crucial for advancing cutting-edge research in proteinsciences. However, it is notable that the management of this equipment is currently overseen by associate
professors, who ideally should be dedicating their time and efforts to their own research endeavors.
It is essential that the government recognizes the importance of not only funding the purchase of such highcaliber equipment but also ensuring adequate resources for its ongoing management. This includes covering
expenses related to device repairs, updates, and most importantly, the salaries of dedicated staff members
tasked with facility management. Hiring specialized personnel to manage these resources would alleviate theburden on academic staff and enhance the overall functionality and utilization of the facilities. Such support
would ensure that the equipment is maintained at optimal performance levels and is readily available for17

Evaluation Sheets for Activities of IPR
researchers, thereby maximizing the investment and contributing to more robust and efficient scientificoutcomes.
In summary, this reviewer is highly impressed with the accomplishments of the IPR faculties, but there is aclear need for a more sustainable management model of IPR's facility infrastructure, supported by adequate
government funding, to ensure the longevity and effectiveness of these valuable resources. This reviewer
appreciates the opportunity to have undertaken the review.
[Reviewer #3]
IPR have shown very good activities in the field of protein science. IPR has excellent two centers, such as“Research Center for Next-Generation Protein Science” and “Advanced Data Science Center for Protein
Research”. These two centers have shown good achievement in protein science research.
Because IPR has Synchrotron beam line, high-resolution Cryo-EM, Micro-ED and Ultra-high magnetic field
NMR facilities, IPR could lead protein science in the world. Because these facilities was open to foreignscientists, an international collaboration was increased and this international collaboration greatly contributed
to protein science research in the world. The comments for the future development of IPR are as follows.
Recently, female scientists are increasing in the world and have shown an important role and goodachievement in the scientific field. In IPR, the number of female faculty members has been slightly increasing
until 2022. But the percentage of female faculty members is under 20 %. Therefore, an effort to increase thenumber of female faculty members is needed, Because IPR has excellent facilities and good scientists, morecollaborations with overseas scientists are recommended. International collaboration is one of an importantfactor in the evaluation of institute or university by the rating agency (QS, Times etc.) Development fundraising by alumni or industry is needed for the development of IPR. Also, I recommend Bioventure company
will be founded by IPR faculty members. This company can give a research grant and strong academiaindustry relationship. NMR is very important facility in protein science research. IPR has 950 MHz NMR
machine which is most large NMR in Japan and in Asia. In this year, 1200 MHz (1.2 Giga Hz) machine will
be installed in Korea Basic Science Research Center. Therefore, I recommend that IPR will try to purchasemore larger NMR Machine than 950 MHz machine.
[Reviewer #5]
Regarding the diversity and inclusion initiatives, I am very pleased to see that the ratio of female faculties
increased dramatically, based on the IPR’s several strategies. This would influence, to a good direction, other
Departments and Universities in Japan.
The new center ASPiRE is a promising direction. In its organization, it would be great if the center can recruita proper IT group dedicated to machine-learning. Cross-appointing to Professors in Osaka University can bea possibility, I thought.

18

Evaluation Sheets for Activities of IPR

I saw that the Research Center for Next-Generation Protein Science makes much effort to the service as Joint
Research Center. Some of the laboratories are run by Associate Professors, who can be fixed-term employed,
I guess (I am not very sure, though). Especially in this case, I thought the IPR should take care of their effort
to the service.
The IPR has many prominent structural biologists who determine new structures quite steadily. Given that, I
thought it would be nicer if there is one group in the IPR dedicated to the state-of-the-art all-atom MD
simulations. As soon as a new protein structure is determined, they can examine its functional dynamics byMD.

19

Laboratory for Protein Organic Chemistry [Hojo Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Organic Chemistry

Name of Reviewers: Hee-Jung Choi, Keiko Shimamoto, Tatsuya Sawasaki
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

The research goals of this laboratory are well-aligned with the objectives of IPR, demonstrating
a clear approach to their scientific inquiries. As a member of a premier institution in protein life
sciences, the lab's research focus is appropriately established to contribute meaningfully to thefield.

-

Synthesis of large size proteins and synthesis of uniquely modified proteins utilizing thistechnology.

Commentary and Recommendations:-This laboratory has made commendable achievements in the field of protein synthesis research,
particularly in areas such as protein synthesis involving glycosylation and phosphorylation, andcyclic peptide synthesis. These areas are critical to advancing our understanding of proteinfunctionality and potential therapeutic applications, so it is recommended to leverage theirresearch outputs to explore and answer complex biological systems through collaborations,which will greatly enhance the impact the lab's research.

-

They have established techniques for the precise chemical synthesis of proteins modified withglycans and lipids. Technical abilities to synthesize such difficult proteins by using combinationof various types of condensation reactions and newly developed protecting groups should behighly evaluated. Lipid-modified peptides and proteins are expected to be powerful tool for
elucidating functions of hydrophobic proteins. However, at this stage, the purpose of synthesis
in life science is not so clear. Supplying functional molecules directing chemical biology, suchas isotope labeling for NMR and the introduction of click/photoresponsible tags for
identification of their target molecules will be expected.

-

This laboratory has very unique peptide synthesis and fusion technologies, and their research isvery promising. However, it is unclear what kind of impact these technologies will have on
research, and what kind of impact they will have on related research fields. It is necessary to
set more clearly defined goals for the research, and further effective utilization of the20

Laboratory for Protein Organic Chemistry [Hojo Lab]technologies of this laboratory is desirable.
2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

The current review reveals no immediate areas requiring urgent attention in terms of researchachievements and contributions.

-

Collaborations with researchers who will actively use this technology to advance science.

Commentary and Recommendations:-

The research output of this laboratory is commendable, with 11 publications as a corresponding
author, and 13 invited lectures both domestically and internationally over the last 5 years. This
reflects good research conducted in their respective fields.

-

Establishing techniques for the chemical synthesis of proteins modified with glycans and lipids,
and supplying synthesized samples to biological experiments contribute to the advancement ofprotein chemistry. However, at this stage, biological studies using these samples seem to belimited. I recommend them to collaborate with cell biologists in the future.

-

The number of research achievements is not a problem at all. I think it is important to develop
more high-impact research in the future. I think this LAB has enough potential to do so. For
this purpose, I think it is important to find research partners from within and outside the institutewho can make good use of this technology.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:-

The current assessment indicates no immediate areas requiring attention in terms of the group's
contribution to the Joint Usage / Research Center.

-

Promoting the technology to researchers in diverse fields.

Commentary and Recommendations:-This laboratory has demonstrated a commendable level of engagement in collaborative efforts,
evidenced by its participation in 10 international collaborations. Such endeavors enhance its
research capabilities through diverse perspectives and expertise. Additionally, the lab's

21

Laboratory for Protein Organic Chemistry [Hojo Lab]

contribution of 6 seminars to IPR is noteworthy. These highlight the lab's active role in engaging
with the scientific community within the framework of the Joint Usage/Research Center.
-

Synthetic proteins with modifications were provided to researchers inside and outside IPR topromote collaborative research. However, these collaborations were personal, and compounds
were not commonly used. It would be even better that their techniques will be widely appealed
to biologists. Since MS facilities will be moved to their Lab from Takao’s Lab, their contribution
to IPR or protein life science communities will be enhanced by the combination of synthesis
and analysis.

-

I have the impression that this laboratory does not have a high level of activity in the Joint
Usage / Research Center’s Programs. Although this may be a limited need, there are probably
researchers who need this laboratory's unique technology, so more active involvement isrequired.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Area(s) that need(s) further attention:-

While this laboratory provides valuable educational opportunities to graduate students, the ratioof doctoral to master's students suggests a potential area for growth. Doctoral students play a
crucial role in advancing research and maintaining academic rigor. Therefore, it's recommended
to implement strategies aimed at increasing the enrollment and retention of doctoral candidates.

-

Consultation with an Intellectual Property Officer.

Commentary and Recommendations:-

The lab's active engagement in providing research guidance to both graduate and undergraduate
students is commendable. In terms of funding, the lab has successfully secured sufficient
resources to support its research endeavors. The lab's active involvement in numerous

22

Laboratory for Protein Organic Chemistry [Hojo Lab]

international joint research projects is another notable achievement. Such international
collaborations broaden the scope and impact of the lab's research, contributing to the global
scientific community.
-

Competitive fundings have been steadily obtained. Although the number of students earning
doctoral degrees is a few, one is working as an assistant professor. Previously enrolled staff has
moved out into an industrial company. Thus, fostering young researchers/students is properly
managed.

-This lab also performs well in education duty. There seems to be little commitment tointellectual property. It is a unique, useful, and good technology that can be sufficiently IPO.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

As a contributing member of IPR, renowned for its status as a world-class institute in protein
life sciences, this laboratory has consistently demonstrated its ability to produce excellent
research outputs. The lab's involvement in a wide array of collaborative projects is a testament
to its dynamic approach and commitment to scientific advancement. Moreover, the lab's clear
and forward-looking vision aligns well with the goals of IPR.

-

Protein synthesis and modification based on organic chemistry is one of the advantages of
IPR. It is desirable to accelerate collaborations with cell biologists, rather than just developing
synthetic methods, to clarify the purpose of synthesis.

-

This laboratory has unique technology for peptide synthesis. This is a wonderful thing, but I
have the impression that the development of their research is limited. In other words, thetechnology of this laboratory should be utilized more. For this purpose, it seems necessary tocommunicate with researchers in various research fields to understand their needs.

23

Laboratory for Nanobiology [Harada Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Nanobiology

Name of Reviewers: Hee-Jung Choi, Keiko Shimamoto, Tatsuya Sawasaki
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

The Laboratory of Nanobiology has developed novel technologies for monitoring biomolecules
at the single-cell level. However, an area that requires further focus is the practical application ofthese technologies to actual biological questions. While the technological advancements are
impressive, leveraging them to explore and answer complex biological phenomena could greatly
enhance the impact and relevance of the lab's research.

-

Collaboration with experts in cell differentiation.

Commentary and Recommendations:-

The Laboratory of Nanobiology's development of the real-time single cell secretion assay
platform, alongside its work in quantum biosensing and intracellular temperature measurement,
demonstrates a clear alignment with long-term research goals and an innovative approach. As
mentioned above, it is recommended that the laboratory actively seeks opportunities to apply
them to real-world biological contexts. This could involve understanding disease mechanisms,
cellular communication, or biomolecular processes under various physiological conditions.
Collaborations with other research groups within the institute or partnerships with external
biological research entities are advised to ensure a comprehensive approach to these complex
questions. By extending the application of their technologies to tangible biological research, thelaboratory can enhance its contribution to the field of nanobiology and further cement its position
as a leader in this area.

-

The technology to precisely measure intracellular temperature is very unique and is expected tocontribute to cell biology and biophysics. Further development of measurement and control
technology is expected. However, at this stage, applications are still limited and it has not been
proven whether these phenomena are universal. It would be even better if they could develop
from model cells and find objects whose physiological significance becomes clear.

-

The laboratory has developed a very unique technology that can measure the temperature of a
localized region of a cell. However, because the cells being targeted are limited to neurons, the24Laboratory for Nanobiology [Harada Lab]

generality of the new finding that the temperature changes found affect cell differentiation is
unclear. Therefore, collaboration with a cell differentiation laboratory is needed for further
analysis.
2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

While the current review reveals no immediate areas requiring urgent attention in terms ofresearch achievements and contributions, it is advisable to continuously monitor emerging trends
and challenges in the field of nanobiology.

-

It is desirable to develop research on diseases, for example, whether temperature changes are
occurring in cancer cells.

Commentary and Recommendations:-

The achievement of publishing 18 research papers in the past five years is indeed commendable,
reflecting the lab's active contribution to the field. It is noteworthy that many of these publications
have been made by Professor Madoka Suzuki as the corresponding author, a testament to hissignificant role in this lab's research endeavors. It is also observed that the Harada lab's research,
particularly in the area of intracellular temperature sensing, is transitioning smoothly into the
Suzuki lab. This transition appears to be a strategic move, leveraging the strengths and expertiseof both labs to advance this line of research.
Looking ahead, there is a keen anticipation for the culmination of the ongoing research projects,
especially as Professor Harada approaches retirement. It is hoped that this period will be marked
by successful completion of their accumulated research, thereby cementing the lab's legacy andcontributing significantly to the advancement of their scientific field.

-

By introducing temperature-sensitive fluorescent polymers or nanodiamonds into cells, they havebeen able to visualize the intracellular temperature. They found that suppressing transcription
and translation decreases heat production, and conversely, providing heat increases neurite
outgrowth. It would be interesting to explore whether this is due to general increases in all
reaction rates or acceleration of specific reactions in neurons. They are expected to apply theirtechnology to other cells.

-

I think the laboratory could have more of an impact because of its unique perspective indeveloping research.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /25

Laboratory for Nanobiology [Harada Lab]

Research Center’s programs?
Area(s) that need(s) further attention:-

In the future, it would be beneficial to conduct more collaborative research in connection with
the Joint Usage/Research Center. Leveraging the resources and expertise available through thecenter can enhance the scope and impact of the research, fostering more integrated and innovative
scientific inquiries.

-

A project to introduce this technology is needed.

Commentary and Recommendations:-

Given the nature of the research, it is anticipated that fluorescence microscopy, a shared resource,
is extensively utilized. While there are commendable domestic collaborations in place, expanding
these collaborations to the international level would be highly advantageous. International
collaborations bring diverse perspectives and expertise, which can significantly enrich researchoutcomes and lead to breakthroughs in the field.

-

The development of basic technology for intracellular temperature measurement and one-cell
immune response analysis is being promoted through collaborative research. However, researchis conducted between individual laboratories, and the ripple effect on the community is not
remarkable. If physiologically significant research targets are found, collaboration withbiologists can be widely expected.

-

From the current data, I had thought that the needs for this technology did not match the Joint
Usage / Research Center’s Programs, but this lab is conducting a reasonable number of joint
research projects.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.

26

Laboratory for Nanobiology [Harada Lab]

Area(s) that need(s) further attention:-

Consultation with an Intellectual Property Officer.

Commentary and Recommendations:-This laboratory has demonstrated a strong commitment to education by successfully securing andtraining a considerable number of graduate students. The notable accomplishment of guiding
Professor Madoka Suzuki to become an independent researcher further highlights the laboratory's
effective role in nurturing the next generation of scientists. This indicates a significant
contribution to the field in terms of educational impact and mentorship.
Additionally, the bilingual organization of the laboratory's website in both English and Japaneseis commendable. Therefore, information about the lab is shared well internationally. Since
detailed information regarding research funding is missing in this material, no commentary isgiven for research funding.

-Collaborative research with inside and outside the institute is progressing to expand the scope of
research. Students successfully have obtained doctoral degrees. A staff member has beenpromoted and has become independent.

-

This lab also performs well in education duty. There is a lack of explanation regarding intellectual
property efforts. Although intellectual property of this technology may be difficult due to theindustrial application aspect, it would be better to ensure a system for consultation.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

The internal collaboration of this laboratory is commendable and this laboratory has
demonstrated an appropriate vision for its future direction.
As previously mentioned, one of the lab's notable strengths is the development of novel
technologies. It is highly recommended that these technologies be further applied to broader
biological systems. Doing so could greatly enhance the practical and real-world impact of thelaboratory's work. Collaborations, both domestic and international institutions, will be key inachieving this application. Such collaborative efforts can provide new insights, access to diverse
expertise, and opportunities to test and refine these technologies in various biological contexts.
In summary, while the laboratory is well-positioned with its effective internal collaboration andclear future vision, maximizing the application of its novel technologies in biological systems

27

Laboratory for Nanobiology [Harada Lab]

through collaborative research should be a primary focus. This approach will ensure thelaboratory continues to thrive and make significant contributions to the scientific community.
-

Dr. Suzuki has become independent, but they have a good collaborative relationship in researchand education. They can continue to promote projects focusing on intracellular thermal
measurement.

-

Since this lab has a unique perspective and approach, it is most important to find a good research
partner who can utilize this technology and develop it broadly and deeply for future research
directions.

28

Laboratory for Protein Synthesis and Expression [Takagi Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Synthesis and Expression

Name of Reviewers: Hee-Jung Choi, Keiko Shimamoto, Tatsuya Sawasaki
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

The three missions presented by this laboratory align well with the objectives of IPR and arebeing effectively pursued. These missions represent appropriate and well-defined research goals,
demonstrating the lab's commitment to contributing to the scientific objectives of IPR.

-

It is enough to promote the research that is underway, without giving any advice.

Commentary and Recommendations:-Protein production is an important step in structural biology and in vitro biochemistry research,and this laboratory has demonstrated commendable expertise in addressing the challenges
associated with protein production. Their proficiency in this area has facilitated significant
research into the mechanisms of signaling pathways, showcasing their ability to apply technicalknow-how to complex biological problems.
Furthermore, the lab's utilization of protein engineering techniques, particularly the innovative
LassoGraft technology, in designing novel protein drugs is noteworthy. This approach not only
exemplifies the laboratory's skill in protein engineering but also its potential for making impactful
contributions to therapeutic development.

-

Three research missions of the Lab, the supply of required proteins, elucidation of the structureand function of complex receptor proteins, and the development of proteins with new functions,are very clear and being vigorously promoted. They should be highly evaluated as cutting-edge
and high-level research in the world class.
The know-how to overcome difficulties in protein synthesis/expression has certainly been
accumulated. LassoGraft technology, in which functional peptides obtained with the RaPID
system are incorporated into antibodies or other proteins, is being industrially applied as a
powerful biomedical strategy of easily adding new functions to antibodies.

-This LAB has three missions as its research pillars: technology development, basic research, andapplied research, and they work in tandem to advance research based on very good research
management. I hope that the lab will continue to proceed research with this quality, and I am

29

Laboratory for Protein Synthesis and Expression [Takagi Lab]

confident that this will contribute greatly to the advancement of this institute.
2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

The current review reveals no immediate areas requiring urgent attention in terms of researchachievements and contributions.

-

I have nothing to advise you, as you have been more than adequate in your perspectives andvision in addressing protein research as well as technology development.

Commentary and Recommendations:-

The research output of this laboratory is commendable, with publications in prestigious journals
such as Science Translational Medicine, Nature Chemical Biology, and Nature Communications.
This reflects the high quality and impact of the research conducted in their respective fields.

-

Through protein making technology, they significantly contribute not only to academia field but
also to the general public.

-

The contribution of this laboratory in the field of protein life science is very significant.
Especially in protein engineering and protein production, the ideas and know-how from thislaboratory have been widely spread. This laboratory is an opinion leader in the field.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:-

The current assessment indicates no immediate areas requiring attention in terms of the group's
contribution to the Joint Usage / Research Center.

-I feel that the support system regarding the Joint Usage / Research Center’s programs would beeven stronger if this laboratory had additional manpower support, such as technical staff andpost-doctoral fellows.

Commentary and Recommendations:-

The active involvement of this lab in the institutional activities of the Joint Usage / ResearchCenter is commendable. Notably, this lab has been involved in diverse range of collaborative
studies, both domestic and international, further highlighting its commitment to global scientific30

Laboratory for Protein Synthesis and Expression [Takagi Lab]

engagement and interdisciplinary research.
-

A number of high-level collaborative projects are underway.

-

The lab is well advanced in its collaborative research with national and international partners,
and I can judge that the lab is contributing to the Joint Usage / Research Center’s programs to agreater extent than anticipated.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences andmeetings.
Area(s) that need(s) further attention:-

The current review indicates no immediate areas requiring attention in terms of the group's
contribution to education, research funding, information disclosure, and international exchange.

-

The status quo is sufficient.

Commentary and Recommendations:-This laboratory has demonstrated remarkable success in producing outstanding researchers,reflecting its strong commitment to high-quality education and mentorship. The lab's active
engagement in providing research guidance to both graduate and undergraduate students isparticularly commendable. In terms of funding, the lab has successfully secured sufficient
resources to support its research endeavors. This financial stability is crucial for maintaining thelab's research momentum and pursuing innovative projects. The lab's active involvement innumerous international joint research projects is another notable achievement. Such international
collaborations broaden the scope and impact of the lab's research, contributing to the global
scientific community.

-

A large amount of research funding and patents were acquired. Notably, Prof. Takagi, with Prof
Suga of the University of Tokyo, founded a venture company. The company is developing
biopharmaceuticals in new modalities to solve unmet medical needs, with LassoGraft technology.

31

Laboratory for Protein Synthesis and Expression [Takagi Lab]

This will be one of the successful examples of Osaka University-launched venture, which will
attract attentions from general public.
-

The educational activities, acquisition of external funds, international exchanges, and disclosureof information to society have all contributed more than enough to date. I hope that you willcontinue to proceed with these activities for the further progress of the institute.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

As a contributing member of IPR, renowned for its status as a world-class institute in protein
life sciences, this laboratory has consistently demonstrated its ability to produce excellent
research outputs. The lab's involvement in a wide array of collaborative projects is a testament
to its dynamic approach and commitment to scientific advancement. Moreover, the lab's clear
and forward-looking vision aligns well with the goals of IPR.

-

Research is being conducted at a very high level, and they can be evaluated as a laboratorythat can communicate the significance of protein research to the world.

-

As mentioned above, this laboratory is outstanding in its current research quality and future
research vision. Even with the quality as it is, the laboratory will be able to demonstrate asufficient presence in the field of protein life science research. As a comment not on thislaboratory but on this institute, this institute should make better use of the research resources
such as protein engineering and protein expression technologies that this laboratory has,because those technologies that this laboratory has are the foundation of protein research. At
present, this institute does not seem to be making good use of them, so I dare to make thiscomment.

32

Laboratory for Protein Profiling and Functional Proteomics [Takao Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Profiling and Functional Proteomics

Name of Reviewers: Hee-Jung Choi, Keiko Shimamoto, Tatsuya Sawasaki
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

The research goals of this laboratory are well-aligned with the objectives of IPR, demonstrating
a clear approach to their scientific inquiries.

-

Installing high-spec mass spectrometry machines

Commentary and Recommendations:-This laboratory has made achievements in the field of protein Mass Spectroscopic analysis. This
area is important for advancing our understanding of protein function within the cellular context.

-

Conventional LC-MS has become popular in many Labs, but native MS or measurement of posttranslationally modification still requires advanced techniques. This Lab has contributed toprotein science through its development.

-

The research results to date have been highly impactful and industry-leading. However, I havethe impression that it has become difficult to develop research that leads the research field
because the performance of mass spectrometry machines has become outdated. Since the mass
spectrometry machines are very expensive, the positioning of mass spectrometry analysis in IPRshould be clarified.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

The current review reveals no immediate areas requiring urgent attention in terms of researchachievements and contributions.

-Support system as IPR if it is difficult to purchase mass spectrometry equipment.

Commentary and Recommendations:33

Laboratory for Protein Profiling and Functional Proteomics [Takao Lab]-The research output of this laboratory is commendable, with 11 publications as a corresponding
author, and 13 invited lectures both domestically and internationally over the last 5 years. This
reflects good research conducted in their respective fields.

-

Native MS method was applied to capture the complex of enzyme-nucleic acid-metal ion. They
captured unstable enzyme reaction intermediates as complexes by mass spectrometry andanalyzed the reaction mechanism, which is commendable. Unfortunately, the number ofpublished papers as a corresponding author is not so many for these years because he had few
students before his retirement. However, he has contributed to protein identification throughcollaborative works as an expert in mass spectrometry.

-

The Lab has a high previous research record and has reported a number of high impact papers. I
consider the activity in the last few years in this Lab to be not high compared to other labs in theInstitute currently. This may be due to the fact that the boss is approaching retirement, butessentially it seems to be due to the absence of a clear direction in the utilization of mass
spectrometry analysis in this institute.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:-

It seems necessary to consider the position of mass spectrometry in the Joint Usage / ResearchCenter's Programs.

Commentary and Recommendations:-This laboratory's longstanding collaboration with the CIGB in Cuba is a testament to its
commitment to international scientific partnerships. This collaboration has undoubtedly yielded
valuable insights and advancements. However, to further enhance the lab's research scope andimpact, it would be beneficial to explore collaborations with a more diverse array of laboratories.

-

Contribution to protein identification through the Joint Usage / Research Center’s programs as
an expert in mass spectrometry for a long time is obvious. It may be necessary to consider taking
over the advanced MS technology after Professor Takao's retirement. It would be desirable toestablish an MS department in the Research Center for Next-generation Protein Sciences andinvite a new PI.

-

In the Joint Usage / Research Center’s Programs, the analysis of protein modification
identification is active, but the studies presented were not the most recent. Therefore, it was notpossible to understand the activities of the past 5 years.

34

Laboratory for Protein Profiling and Functional Proteomics [Takao Lab]

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Area(s) that need(s) further attention:-

I think it is recognized as a highly regarded research from abroad, given the large number ofstudents from China. I think that this Lab needs to be promoted to other Asian countries as well.

Commentary and Recommendations:-more information needed for comment.

-

Although students who belonged to the Lab were small, international students successfullyreceived Ph.D. They have also won awards for their conference presentations. Thus, educational
activities have been appropriate. It is regrettable that few grants have been awarded.

-

The education through research is being done, as the results of research in which students are thefirst authors can be adequately confirmed.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

As the PI approaches retirement in March, it seems that the lab’s recent research output may not
be as robust as that of other labs. However, it is important to acknowledge the lab's significant
achievements over the years, particularly in the field of mass spectrometry (MS). The lab has acommendable track record of utilizing MS to produce excellent research results. This legacy of35

Laboratory for Protein Profiling and Functional Proteomics [Takao Lab]

high-quality research should not be overshadowed by the natural decrease in output typicallyassociated with the transition period leading up to retirement. The lab's contributions to the field,
especially through its MS-based studies, have laid a strong foundation for future research andhave significantly advanced our understanding in this area. To ensure the continuation of the lab’s
strong legacy in this field, it is hoped that a younger MS expert will be hired.
-

Although this is not the problem with this lab only, measures need to be taken to avoid adecline in activity due to a lack of students in the lab before professor’s retirement. This
problem is particularly acute at the institute, because only a few students come from the faculty.
Is it possible that IPR supports to hire PD or temporary staff?
As mentioned in other items, mass spectrometry is essential for identification of modified
proteins and spatio-temporal analysis. We would like to recommend the addition of the MS
facility (including PI level staff) to the Joint Usage / Research Center.

-

Although this lab has made several important biological discoveries using mass spectrometry
analysis, I cannot judge them due to a deficiency in explanation of their commitment tointellectual property. Also, since the lab is closing this March, it is not constructive to discuss the
future of this Lab. The most important thing is for this institute to make a vision for the future of
instrumentation for mass spectrometry analysis.

36

Laboratory for Physical Biology [Suzuki Lab]

External Advisory Committee FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Physical Biology

Name of Reviewers: Hee-Jung Choi, Keiko Shimamoto, Tatsuya Sawasaki
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

I believe that this laboratory should collaborate with other biologists who can share its uniqueperspective on temperature biology.

Commentary and Recommendations:-This lab has been established only a year ago, but its research progress is great. It is recommended
that this lab's progress and development as an independent research group be a focal point in thenext institutional evaluation, ensuring it aligns with the division’s high standards and contributes
uniquely to the field of protein chemistry.

-

Using microscopic temperature observation and control technologies in cells, he has succeededin capturing the physicochemical effects of heat on cells, especially on calcium receptors. His
focus is excellent, including the discovery of heat-induced calcium release. The results obtained
are interesting and have been recognized worldwide. Although this is a theme with great potential
for further development, it is still limited to the observation of specific cases at this stage, so it isnecessary to move in the direction of verifying the generality of the observed phenomena andtheir principles.

-

This laboratory has established a methodology for temperature sensors and temperature control
based on its own technology, and its work toward the creation of a new research field of
thermogenesis and temperature sensing based on this methodology is highly commendable forits originality. However, this is still a nascent research field, and its versatility and biologicalsignificance await further clarification.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?

37

Laboratory for Physical Biology [Suzuki Lab]

Area(s) that need(s) further attention:-

Not Applicable (as the lab has been established for less than a year).

-In order to increase the impact on protein life sciences, I believe that the elucidation of themechanism of temperature generation and, in the case of proteins, the various elements of thisinstitute should be used effectively.

Commentary and Recommendations:-

The research output achieved under the guidance of Professor Harada by this PI is indeed
outstanding, showcasing a strong foundation in scientific inquiry and innovation. The PI's
demonstrated research potential under Professor Harada's mentorship bodes well for his future
as an independent researcher now leading his own lab.
Given this promising background, it is expected that significant independent research results will
emerge from the PI's new lab in the near future. To facilitate this transition to independent
research, it is recommended that the lab focuses on defining its unique research niche andestablishing its own research identity. This could involve pursuing novel research questions thatbuild upon the PI's previous work while also exploring new directions that differentiate the lab's
research from that of Professor Harada's.

-Prior to independence in Harada Lab, he measured intracellular heat conduction withnanodiamonds and published a high impact paper, which should be highly appreciated. It would
be even better if he could measure heat conductance in each organelle. Development of organelledirecting thermometer would be interesting.
Independently, he published a unique phenomenon of heat-induced calcium release fromryanodine receptors. Mutant analysis showed its involvement in malignant hyperthermia.
Structural biological analysis of the mutant proteins is in progress as the molecular basis of thisphenomenon. Although this is an important discovery from a medical point of view, the generalityof such a phenomenon needs to be verified.

-

Since the temperature biology ideas from this laboratory are unique and original, I judge that wehave the potential to generate more high impact papers. For this purpose, I think that collaborative
research with pure biologists, rather than with those in the field of protein life science, would
work effectively.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:

38

Laboratory for Physical Biology [Suzuki Lab]-

Biologist.

Commentary and Recommendations:-

Since this lab has been recently established, it is recommended to evaluate this lab in the next
evaluation period.

-

He has published papers from collaborative research conducted under the IPR program. While
there has been steady progress in national and international collaborative research, the scope ofthese research is individual and its contribution to the IPR as a whole has been limited. Since hehas been independent for only one year, I look forward to his further development.

-

I have concluded that this lab is doing well enough in the Joint Usage and Research Centerprogram, both domestically and internationally. However, since there was no detailed explanationof the content of the collaborative research in the Joint Usage / Research Center's Programs, I did
not understand whether the lab's unique methodology was being utilized.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Area(s) that need(s) further attention:-

It would be good if further student recruitment and post-docs to one PI's lab as an institute could
be considered.

Commentary and Recommendations:-

Since this lab has been recently established, it is recommended to evaluate this lab in the next
evaluation period.

-

International collaborative research is being actively promoted. He is making good progress inexternal publications/presentations and obtaining competitive funding. It is good that he has beenpromoted and obtained an independent position. It is desirable to cooperate with Prof Harada to39

Laboratory for Physical Biology [Suzuki Lab]

ensure a smooth education for her students even after her retirement.
-

Despite the short period of time that the laboratory has been up and running, I think it is doing
well in its educational activities and in obtaining external funding. In particular, the joint researchwith foreign countries is outstanding. I hope that you will continue to promote joint research withforeign countries.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

As mentioned above, it is recommended that this lab should establish its own research identity
by exploring new directions distinct from those of Professor Harada. Fostering collaborations
with other research groups, both within and outside the institution, can provide valuable supportand diverse perspectives during this formative stage. Seeking funding opportunities that cater toearly-career researchers and innovative projects can also aid in establishing the lab's research
agenda. By focusing on these strategies, this PI's lab is well-positioned to make significant
contributions to the field and establish itself as a leading research entity.

-

As a young leader, I expect him to lead IPR and the Japanese Biophysical Society.

-

Even though the laboratory has only been up and running for less than a year, the quality andpotential of the research can be judged to be high. For the future advancement of this lab, I think
it is necessary to have colleagues with whom you can collaborate for a long-term in temperature
biological relationship. I look forward to a good meeting.

40

Laboratory for Supramolecular Crystallography [Nakagawa Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Supramolecular Crystallography

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-This group has achieved world-class results in the field of supramolecular crystallography,
determined the structures of many biologically important proteins, and contributed to theadvancement of research in that field. Furthermore, the group has operated the Spring-8 beamline
and supported the development of protein crystallography in Japan.

-

A new beamline (BL44XU) was constructed to enable the structural analysis of supramolecularcomplexes, and this has led to the successful elucidation of many important and complex protein
structures.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-This group has achieved world-class results in the field of supramolecular crystallography,
determined the structures of many biologically important proteins, and contributed to theadvancement of research in that field. Furthermore, the group has operated the Spring-8 beamline
and supported the development of protein crystallography in Japan. (Same as above comments.)-

In addition to constructing beamlines, development of production technologies for complex andchallenging protein complexes has also been achieved, enabling the successful structural analysis
of many membrane proteins.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /41

Laboratory for Supramolecular Crystallography [Nakagawa Lab]

Research Center’s programs?
Area(s) that need(s) further attention:-

Based on the Spring-8 II project, the establishment of the IPR beamline should be considered.

Commentary and Recommendations:-

They have been involved in the management, operation, and user support of BL44XU for many
years.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-

Large budgets continue to be obtained. The beamline has been well promoted.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-This group has led protein crystallography in Japan.

-

This lab showed good activities in all areas. This lab has shown good competitiveness in theprotein science field. But some activity should be pointed out for the future development of thislab. Output (publications) from the IPR Beamline had increased until 2020. But, during2021~2023, publications were decreased comparing with 2020 publications. PDB deposition was

42

Laboratory for Supramolecular Crystallography [Nakagawa Lab]

also decreased during this period. The reason of this decrease should be analyzed. Also, moreindustry-academia collaboration is needed-

Conducting education for young researchers and students in IPR, which encompasses structural
analysis technologies, is crucial for producing researchers who will carry the future of structural
biology in Japan. Therefore, it is of great importance for IPR to construct and operate the latest
and most advanced X-ray beamlines. Even after your retirement, it is hoped that the unique
BL44XU beamline will continue to be developed and operated sustainably, fostering outstanding
beamline scientists and engineers.

43

Laboratory for Protein Crystallography [Kurisu Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Crystallography

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Structure and function relationship at the atomic level in various types of photosynthesis.

Commentary and Recommendations:-Integrated/hybrid structural research including neutron crystallography is amazing.

-

Research focusing on photosynthetic membrane protein complexes and dyneins has outlined
specific goals, such as elucidating the mechanisms of energy conversion and motility.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-This group can advance its current research.

-

Using correlational structural analysis, detailed mechanisms of photosynthesis-related proteins
have been elucidated. Development of technologies such as MicroED is also being pursued.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:-

Enhancing PDBj

Commentary and Recommendations:-

Not only managing the Protein Data Bank Japan (PDBj), but also overseeing the Cambridge
Crystallographic Data Centre (CCDC)

44

Laboratory for Protein Crystallography [Kurisu Lab]

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-

Prof. Kurisu has obtained the Grant-in-Aid for Transformative Research Areas (A) as a head
investigator.

-

Large budgets continue to be obtained.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-This lab showed good activities in all areas. This lab has shown good competitiveness in theprotein science field. But some activity should be pointed out for the future development of thislab as follows: More industry-academia collaboration is needed.

-

Managing the PDBj in IPR is a pride for Japan. While it may be challenging, it would be greatly
appreciated if the management of the PDBj could continue in IPR.

45

Laboratory for Cryo EM Structural Biology [Kato Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Cryo EM Structural Biology

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-This group has determined the structures of highly impact protein complexes and these results
will contribute to the treatments of infectious diseases in the future.

-

I would have liked to see a vision for the planned main focus on research into olfactory receptors.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

I think it is better that this group choose the target protein complexes newly in addition to
flagella motor of salmonella.

Commentary and Recommendations:-

Outstanding results have been achieved in structural studies of flagella and ADE using cryo-EM.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-This group has determined the structures of protein complexes using cryo-EM, in response torequests from many researchers. And also, the development of cryo-EM technique is ongoing.

-

Vigorously advancing the management, operation, and support of cryo-EM.

46

Laboratory for Cryo EM Structural Biology [Kato Lab]

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-Cryo-EM workshops were organized for research including Company’s ones.

-

Contributing to the development of the field and the education of students by organizing cryoEM workshops.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

The laboratory is starting up smoothly, especially cryo-EM equipment has been installed, andthe number of students is increasing, so I can expect the laboratory to develop in the future.

-

Cryo-EM is very power-pool and important tool in protein science research field. This lab
published many papers in high impact factor journals. Recently, International collaboration isimportant for the evaluation of university or institute. I recommend more international
collaboration to this group because this group has very good cryo-EM facilities. Also, moreindustry collaboration and industry grants are needed for this group. Because IPR does not havethe most high-resolution EM. I recommend that IPR will try to purchase more advanced new
high-resolution EM.

-

Not only the development of grid preparation techniques but also the automation and47

Laboratory for Cryo EM Structural Biology [Kato Lab]

acceleration of analysis, as well as the development of new analytical methods, are anticipatedto significantly advance the field of structural biology. Structural analysis of olfactory receptors
is also expected. Conducting education for young researchers and students in IPR, which
encompasses structural analysis technologies, is crucial for producing researchers who will
shape the future of structural biology in Japan. Therefore, it is very important for IPR to beequipped with the latest and most advanced cryo-electron microscopes to fulfill this role. Please
make every effort to achieve this.

48

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy [Miyanoiri Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-

They are developing new methods and labeling techniques for solution NMR to reduce thelimitations on molecular weight and sensitivity, aiming to enhance the value creation of NMR.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

They have successfully performed structural analysis on large proteins using the RO-SAIL
method.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

They are continuously providing operational and management support for large-scale NMR
facilities.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers

49

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy [Miyanoiri Lab]

(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-Continuously promote the utility of liquid NMR and please make efforts to secure large-scalefunding. This will likely attract students synergistically as well.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

High-field NMR shows very important role in the NMR field and will be more developed in the
future. This NMR technique can broaden application of the bioscience research. Fragment-based
drug discovery by NMR can give a useful information for drug discovery of pharmaceuticalcompany. This lab. has good academia-industry collaboration. The research topics are relatively
large considering the number of lab members. Therefore, the number of lab. members, such as
student numbers, should be increased. Although JMR is a good Journal, I recommend this lab
members try to submit their research result to high impact journal.

-

Conducting education for young researchers and students in IPR, which encompasses structural
analysis technologies, is crucial for producing researchers who will carry the future of structural
biology in Japan. It is important to be installed the latest and most advanced 1.2GHz NMR in IPR,
aiming to nurture researchers who will lead future NMR studies.

50

Laboratory for Biomolecular Analysis [Okumura Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Biomolecular Analysis

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

They actively provide support for techniques like protein sequencing and mass spectrometry.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.

51

Laboratory for Biomolecular Analysis [Okumura Lab]

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

Biomolecular analysis tool, such as MASS can be used to discover biomarker. Therefore, this lab.
can have a good the academia-industry collaboration. Because this lab. does not have students
for research, it is needed to increase student numbers in order to broaden research topics.
Although JMR is a good Journal, I recommend this lab members try to submit their research
result to high impact journal.

-

Conducting education for young researchers and students in IPR, which encompasses structural
analysis technologies, is crucial for producing researchers who will carry the future of structural
biology in Japan. It is important to be installed the latest and most advanced mass spectrometry
in IPR, aiming to nurture researchers who will lead structural studies.

52

Laboratory for Molecular Biophysics [Matsuki Group]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Molecular Biophysics

Name of Reviewers: Yuriko YAMAGATA, Bong-Jin Lee, Takeshi MURATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-This group is highly commendable for its development of solid-state NMR, In Cell NMR, andDynamic Nuclear Polarization (DNP) technique that will be very useful for future advances instructural biology.

-

They are advancing technology development towards the ambitious goal of elucidating the statesof membrane proteins and amyloids within cells using solid-state NMR.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

They have developed a helium-temperature Dynamic Nuclear Polarization (DNP) system andsuccessfully increased its sensitivity by 4000 times.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

Please continue to promote solid-state NMR, aiming to expand its user base.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）

53

Laboratory for Molecular Biophysics [Matsuki Group]･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-Continuously promote the utility of solid-state NMR and please make efforts to secure largescale funding. This will synergistically attract students as well.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

Solid-state NMR plays very important role in the NMR field and will be more developed in the
future. DNP technique can broaden academic application in the bioscience research. This lab. hasgood academia-industry collaboration and industry grant. The research topics are relatively large
considering the number of lab members. Therefore, the number of lab members, such as student
numbers, should be increased. Although JMR is a good Journal, I recommend the lab members
try to submit their research results to high impact journal.

-

Conducting education for young researchers and students in IPR, which encompasses structural
analysis technologies, is crucial for producing researchers who will carry the future of structural
biology in Japan. It is important to develop and operate the latest and most advanced solid-state
NMR and DNP devices in IPR, and to train researchers who are proficient in using nextgeneration solid-state NMR.

54

Laboratory for Molecular and Developmental Biology [Furukawa Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Molecular and Developmental Biology

Name of Reviewers: Jun Suzuki, Sén TAKEDA, Tatsumi HIRATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Structure analysis of identified proteins may help further characterization of their regulation
mechanisms.

Commentary and Recommendations:-

Prof. Furukawa’s research on development of retina and brain has been developed throughidentification of core transcriptional factors to determine the cell types. By combining theirown research tools (mice genetics) with single cell RNAseq analysis, their research has beenfurther developed. In some cases, even ES cells are used to see development of neurons.

-

Each research group sets unique goals, all of which directs towards the fundamental questions
in biology. However, the topics are very diversified covering from molecular level to a higher
brain function and behaviour. Dr. Furukawa’s lab investigates neural function by making themost of retina, which is one of the best systems to cover broad topics of neuroscience fromdevelopment, differentiation to special sensory function. Technically, his topics cover neuronaldifferentiation, synaptic formation, visual function revealed by electrophysiology, and proteintransport with special references to the cilia of photoreceptors. Taking advantages of single cell
analysis of transcriptome, he successfully identified genes critical for determining the cell fate
into photoreceptors or amacrine cells. From another standpoint, knockout of retina-specificgene brought about abnormal visual perception. Taking the facts into account thatneurodevelopmental disorders such as autism spectrum disorders (ASD) show occasionally
hypersensitive to sensory inputs, Dr. Furukawa’s viewpoint has potential to uncover themechanism of ASD through multidisciplinary strategy. Moreover, investigation on theconnecting cilium of photoreceptor reveals the molecular mechanism of ciliary transport, which
would be a target of drug discovery to treat retinal degeneration. His team constantly publishes
high quality papers supported by many graduate students, who are the source of younger
scientists leaving the nest to become full-fledged expert. Though it is a personal interest,
focusing on the retinal ganglion cells may pave the way into clarification of pathogenesis for55

Laboratory for Molecular and Developmental Biology [Furukawa Lab]

glaucoma.
-This group constantly publishes high-quality work in various journals using mouse models.
While their activities appear somewhat wide-ranging, it is likely they will converge towards thefocused research goal in the near future.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

If protein function can be categorized at molecular level, cellular level, and at animal level,
Prof Furukawa’s research is strong and more focused on at cellular and animal levels.
Understanding at molecular level has a space to be developed with collaboration.

Commentary and Recommendations:-

Currently, it is easier to know comprehensively which genes or protein are expressed atparticular stages or cell types during development. Important points are to clarify how these
proteins function at cellular level. In this meaning, Prof. Furukawa’s group has a strategy toutilize genetic approaches and clearly show their role on development in detailed analysis.

-

As stated in the previous section, most of the labs significantly contribute to the advancementof protein research, which can be evaluated by the list of publication, acquisition of grants andinternational collaborations. Dr. Furukawa’s alumni include quite a few people who joinedindustrial fields. This will expedite interdisciplinary research as well as expand the scopes ofresearch significantly. While my general remarks are excellent, this reviewer thinks the score
fluctuates depending on the team being evaluated.

-

This face-to-face meeting revealed an exciting fact that this group is actively pursuing in-housecollaborations with protein science labs. Their published successes alone would not hint atthese hidden efforts and experimentation, which might have underscored the lab’s activities.
What I mean is that some biologists are genuinely open to exploring protein sciencecollaborations. It is vital for IPR to actively cultivate an environment that fosters these seeds ofcollaboration. For that, efficient communication among labs will be needed. I also feel that thepresentation style can be adjusted to understand each other.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?

56

Laboratory for Molecular and Developmental Biology [Furukawa Lab]

Area(s) that need(s) further attention:-

Because Prof. Furukawa is distinct in the field of retina development, it is encouraged to show
and share his tools with scientists in the field, but currently the tools are not easier to see fromoutside. By having a platform (that might be named as e.g. EyePR, Eye Protein ResearchTools) in IPR, tools are easier to be found and accessed.

Commentary and Recommendations:-Because the group’s strength is mouse genetics, mice tools are shared well with the researchcommunity.

-

Since this division is composed of labs different from those providing IPR with basic analyticaltechniques, informatics or high-end facilities, contribution to joint usage/research seems to be
hard to appreciate. However, 3 departments out of 4 included a power point slide illustrating
their involvement in this subject. While some of those activities would be preferably classified
as collaborations with external facilities, rather than joint usage/research center having
connotation of more assisting or rear-guard position, this reviewer finds the overall activities
are accepted as a favorable factor contributing to the reputation of IPR. This reviewer
recommends all the lab head to include materials that correspond precisely to the evaluation
axis preset by IPR.

-

This group has contributed Joint Usage / Research Center’s programs. They organize IPR
seminars, and provide genetically modified mice globally.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Area(s) that need(s) further attention:-

Although homepage is well designed, unfortunately quality of some member photos is quite
low. It is recommended to replace them with new one. Taking photo outside in sunny days will57

Laboratory for Molecular and Developmental Biology [Furukawa Lab]

show their face expression brighter.
Commentary and Recommendations:-

The group includes two female staff scientists (International and domestic Assistant professors)and international students, thus contributes to the diversity of the institute. Homepage is wellorganized and appealing. CREST and Moonshot should be also recognized.

-

Generally speaking, this reviewer finds that each department fosters young researchers from all
categories and is up to the level of expectations from IPR and Osaka University. When it comesto the acquisition of research funding, some departments do not explicitly state the exact nameof grant they have acquired. As far as this reviewer concerned, Dr. Furukawa’s and Dr.
Shinohara’s group must be financially prosperous by judging from their activities andachievements, though there is no description on this subject at all. Information disclosure andsocial relationship appear to be on average for all the labs. For international exchange, all labs
actively collaborate with foreign countries represented by the number of foreign students.

-

Many students have been educated in this lab.

5. Comprehensive Evaluation[Evaluation Perspective]
A. Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
B. Does each laboratory or department have an appropriate vision and perspective for its future
direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

Prof. Furukawa’s research is distinct enough in the research field. Internal collaboration seems
like not much for this group, but at the same time, internal collaboration happens when eachinterest matches between different groups. It should not be forced by the institute. If it isforced, it becomes service, but not research collaboration. I rather suggest having a framework
to set up some small goals to be achieved by the institute. For instance, “Understand andcontrol photo system”. The plant chloroplasts use light to generate a metabolite while the eyesystem use light to see outside. Light can be also used to control protein functions such as PAGFP and channel rhodopsin. In such framework, scientists from different fields or groups
exchange ideas freely, and this may be more important to facilitate science. I can say,inspiration-based collaboration.

-

Concerning item A, this reviewer’s general impression is that the division seems to be rather
independent from other divisions as applied biology. According to Dr. Furukawa’s explanation,
he was also eager to have a collaboration with other divisions, while joint usage was not

58

Laboratory for Molecular and Developmental Biology [Furukawa Lab]

realized due to discrepancies in mutual research interests. Nowadays, it is often said that we
confront deep valley or obstacles among each highly developed expertise, and they prevent us
from understanding each specialty in detail and make us blind to the field outside one’s
expertise. To overcome this and facilitate collaborations, university research administrators(URA), who liaise with different specialists to achieve effective collaboration, should be placed
properly as shared staff, though this reviewer is familiar with the issue of budget in national
universities. However, URA is able to set a framework of collaboration between division of
integrated protein science and other division focusing on protein analysis, even if an initiative
was not taken by the leaders of integrated protein science. Regarding the item B, most of thedepartments have their own future perspectives that can be evaluated as excellent.
-This group's excellence in their own field is evident. Furthermore, their proactive search forprotein science collaborations elevates their standing. A successful collaboration will holdimmense potential for IPR.

59

Laboratory for Genome and Chromosome Functions [Shinohara Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Genome and Chromosome Functions

Name of Reviewers: Jun Suzuki, Sén TAKEDA, Tatsumi HIRATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Research area is important to be explored, but also classic. Integrating new technologies such as
CRISPR screening and proximity biotin-labeling may facilitate Prof Shinohara’s research by
identifying core components of RAD51.

Commentary and Recommendations:-

Since Prof. Shinohara started to work by cloning cDNA of RAD51, an important gene forhomologous recombination, he has intensively worked on RAD51 to understand molecularmechanisms of the protein on homologous recombination. Research done by this group has beenproceeded well and productivity is enough. Also Prof. Shinohara collaborates with IPR members
to determine protein structure.

-

Each research group sets unique goals, all of which directs towards the fundamental questions inbiology. However, the topics are very diversified covering from molecular level to a higher brain
function and behaviour. Dr. Shinohara’s project sets genome stability as a main topic ofresearch, with an emphasis on the homologous recombination. He is a leading scientist in
genome stability and contributed greatly to this field after he discovered Rad51, a crucial
molecule in recombination over 30 years ago. Based on this molecule, his research has beendeveloped to have a link with various associated proteins, whose function is involved in
immunity and reproductive system. Presentation of unpublished data pertaining to thesemolecules were exciting one, making us convinced that his research is coherent for many
years in terms of protein molecule-based study. This will lead to the elucidation of aetiologyof female infertility. This reviewer would like to emphasize his proactive attitude to have inhouse collaborations with other departments in IPR. For example, with a participation ofProf. Nakagawa and Prof. Kato, Dr. Shinohara has successfully submitted lines of evidence
that dynamic conformational changes are responsible for carrying out precisely homologous
recombination. This reviewer finds him as a role model for facilitating the in-housecollaborations. Regarding the publication and grant acquisition, his group attains great60

Laboratory for Genome and Chromosome Functions [Shinohara Lab]achievements during past 5 years, all of which should be highly appreciated as a great
contributor to IPR. This reviewer would like to know about the appointments of his lab
alumni to any academic position, after leaving his lab.
-

This group has constantly published solid papers in scientific journals and their research goal is
crystal clear. It is also obvious that this group promotes diversity in IPR.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

Through deep understanding of homologous recombination, it will be great if new technology toartificially control the process appears.

Commentary and Recommendations:-

Current trend is to understand the biological phenomenon as network by comprehensive
analysis. On the other hand, understanding mechanisms of specific biological process such as
homologous recombination is also important. In this meaning, the group has advanced theresearch area.

-

As stated in the previous section, most of the labs significantly contribute to the advancement ofprotein research, which can be evaluated by the list of publication, acquisition of grants andinternational collaborations. Dr. Shinohara and Hikida had also an interface with clinical andpharmaceutical area, starting from their target molecules. While my general remarks are
excellent, this reviewer thinks the score fluctuates depending on the team being evaluated.

-

I am particularly impressed by this group's strong drive to integrate protein science into theirresearch. Given the natural synergy between this research field and structural biology,
collaborative efforts within IPR hold immense potential for impactful results. While DNA
research collaborations with structural biology often yield high-impact publications, success is
not guaranteed. Nonetheless, the collaboration between this group's activities and proteinscience makes them prime candidates for investment. Successful in-house collaborations coulddeliver groundbreaking, globally impactful findings, solidifying IPR's leadership. Therefore, I
strongly advocate for IPR to develop support mechanisms for fostering such internal
collaborations.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /61

Laboratory for Genome and Chromosome Functions [Shinohara Lab]

Research Center’s programs?
Area(s) that need(s) further attention:-

One of the ways to contribute to the protein life science communities is to share the researchtools and knowledge for homologous recombination.

Commentary and Recommendations:-

Homologous recombination is an important research area where a lot of senior researchers haveretired. In this meaning, Prof. Shinohara is expected to explore the field by conducting cuttingedge science and to contribute to the society.

-

Since this division is composed of labs different from those providing IPR with basic analyticaltechniques, informatics or high-end facilities, contribution to joint usage/research seems to be
hard to appreciate. However, 3 departments out of 4 included a power point slide illustrating
their involvement in this subject. While some of those activities would be preferably classified
as collaborations with external facilities, rather than joint usage/research center having
connotation of more assisting or rear-guard position, this reviewer finds the overall activities are
accepted as a favorable factor contributing to the reputation of IPR. The degree of contribution
varies with each department, while there was no explicit statement from Laboratory of GenomeChromosome Function. However, taking the multidirectional contributions of this lab into
account, and judging from the on-site presentation during the external review, this reviewer
assumes its active participation in Joint Usage/Research Center’s program. This reviewer
recommends all the lab head to include materials that correspond precisely to the evaluation axis
preset by IPR.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.

62

Laboratory for Genome and Chromosome Functions [Shinohara Lab]

Area(s) that need(s) further attention:-

In the website, it is recommended to put photos so that students/researchers outside can have an
image or atmosphere of laboratory and research life in Japan.

Commentary and Recommendations:-

The group includes two female staff scientists (Associate professor and postdoc) and many
international students, thus contributes to the diversity of the institute.

-

Generally speaking, this reviewer finds that each department fosters young researchers from all
categories and is up to the level of expectations from IPR and Osaka University. When it comesto the acquisition of research funding, some departments do not explicitly state the exact nameof grant they have acquired. As far as this reviewer concerned, Dr, Furukawa’s and Dr.
Shinohara’s group must be financially prosperous by judging from their activities andachievements, though there is no description on this subject at all. Information disclosure andsocial relationship appear to be on average for all the labs. For international exchange, all labs
actively collaborate with foreign countries represented by the number of foreign students.

-

Fostering foreign and female researchers is highly appreciated.

5. Comprehensive Evaluation[Evaluation Perspective]
A. Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
B. Does each laboratory or department have an appropriate vision and perspective for its future
direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

The group has collaborated with structural biologist in the institute to know the protein structure.
In this meaning, internal collaboration is ongoing well. I expect that Prof. Shinohara develops
his curiosity-driven research on homologous recombination and greatly impacts on the research
field.

-

Concerning item A, this reviewer’s general impression is that the division seems to be rather
independent from other division as applied biology except for Dr. Shinohara’s team. His
collaborations with groups for protein structure substantiate the joint usage/research center’s
policy as mentioned above, and therefore is judged as excellent. Nowadays, it is often said that
we confront deep valley or obstacles among each highly developed expertise, and they prevent
us from understanding each specialty in detail and make us blind to the field outside one’s
expertise. To overcome this and facilitate collaborations, university research administrators(URA), who liaise with different specialists to achieve effective collaboration, should be placed63

Laboratory for Genome and Chromosome Functions [Shinohara Lab]

properly as shared staff, though this reviewer is familiar with the issue of budget in national
universities. However, URA is able to set a framework of collaboration between division of
integrated protein science and other division focusing on protein analysis, even if an initiative
was not taken by the leaders of integrated protein science. Regarding the item B, most of thedepartment have their own future perspectives that can be evaluated as excellent.
-

I hope to see a successful collaboration of genome DNA research and protein science in the near
future.

64

Laboratory for Advanced Brain Functions [Hikida Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Advanced Brain Functions

Name of Reviewers: Jun SUZUKI, Sén TAKEDA, Tatsumi HIRATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Compared to neural circuit study, molecular study seems like not much done.

Commentary and Recommendations:-

Prof. Hikida’s group is strong in the research field of decision making. Especially, at neuralcircuit level, Prof. Hikida’s group has explored how decision is made through dopamine
receptors at thalamus when mistakes happened. This research is quite original.

-

Each research group sets unique goals, all of which directs towards the fundamental questions
in biology. However, the topics are very diversified covering from molecular level to a higher
brain function and behaviour. While Dr. Hikida’s selection of research topic is very intriguingin terms of neuroscience, especially higher cognitive function of the brain, it appears to lack aninterface with IPR’s other laboratories and departments. On the other hand, his topic attracts
many young scientists as his research direction is one of the hottest topics in basal ganglia
function of broad meaning, especially in terms of neural circuit for the reward system. He set a
goal of research to dissect the molecular mechanism of psychiatric disorders such as addiction,schizophrenia and so on. Taking advantages of cutting- edge techniques in molecular biology
and optogenetics, his team is going to study a neural circuit for integrating various sensory
modality. This reviewer find that the setting of his research goal directs towards the elucidationof the decision-making process mediated by various sensory inputs, just being similar to thesomatic marker hypothesis proposed by Antonio R. Damasio, while the approaches taken by
Dr. Hikida are original ones. On one hand, his study opens a new avenue in brain function
research. On the other hand, it may be important to think about the strategy how to weave his
team into IPR’s framework of research smoothly.

-This group has published research papers constantly well and received a good track record ofobtaining grants. Therefore, the research goal and topic seem to be quite appropriate as anindividual lab. At the same time, I feel that it is possible that this group steers a little more toward
integration with protein science in collaboration with other labs. Such a research focus could be65

Laboratory for Advanced Brain Functions [Hikida Lab]

greatly beneficial for this division's long-term success.
2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

Dopamine signaling has been studied extensively in the world and structural analysis has been
performed. So, rather, Prof. Hikida may be able to seek the space for protein study to generate
new tools to control neuronal function through designing reporter proteins/systems.

Commentary and Recommendations:-Proteins function in cells, 2. Cells function in tissues, and 3. Tissues function in individual(animal). Prof. Hikida’s research is strong at tissue level, especially how dopamine receptors
regulate behaviors.

-

As stated in the previous section, most of the labs significantly contribute to the advancementof protein research, which can be evaluated by the list of publication, acquisition of grants andinternational collaborations. Dr. Furukawa’s alumni include quite a few people who joinedindustrial fields. This will expedite interdisciplinary research as well as expand the scopes ofresearch significantly. From another standpoint, both Dr. Shinohara and Hikida had also aninterface with clinical and pharmaceutical area, starting from their target molecules. While mygeneral remarks are excellent, this reviewer thinks the score fluctuates depending on the teambeing evaluated.

-

I understand that it is not easy that this research field combines with protein science. However,there are many interesting questions that can be solved by protein science, and this group can
provide these questions in more appealing way to other IPR members. Effective communication
with other IPR members, highlighting how protein science could answer this group’s key
questions, can pave the way for fruitful collaborations within the institute. The current situation,
though productive, may miss opportunities for greater impact. Encouraging exploration ofcollaborative avenues with protein science experts, even without immediate collaboration,
should foster interdisciplinary understanding each other.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?

66

Laboratory for Advanced Brain Functions [Hikida Lab]

Area(s) that need(s) further attention:-

Commentary and Recommendations: It is not clear how Prof. Hikida contributes to Joint Usage
without oral presentation: e.g. tool, knowledge, or mice sharing.

Commentary and Recommendations:-

Prof. Hikida seems like contributing to the protein life science through Joint Usage in terms ofnumbers of collaboration.

-

Since this division is composed of labs different from those providing IPR with basic analyticaltechniques, informatics or high-end facilities, contribution to joint usage/research seems to be
hard to appreciate. However, 3 departments out of 4 included a power point slide illustrating
their involvement in this subject. While some of those activities would be preferably classified
as collaborations with external facilities, rather than joint usage/research center having
connotation of more assisting or rear-guard position, this reviewer finds the overall activities
are accepted as a favorable factor contributing to the reputation of IPR. The degree ofcontribution varies with each department, while there was no explicit statement fromLaboratory of Genome-Chromosome Function. However, taking the multidirectional
contributions of this lab into account, and judging from the on-site presentation during theexternal review, this reviewer assumes its active participation in Joint Usage/Research Center’s
program. This reviewer recommends all the lab head to include materials that correspondprecisely to the evaluation axis preset by IPR.

-

This group contributes to collaborations with people outside IPR and gives IPR seminars
frequently. These activities can be regarded as institutional activities of the Joint Usage/
Research Center.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.

67

Laboratory for Advanced Brain Functions [Hikida Lab]

Area(s) that need(s) further attention:-

Without availability in web site, it is not easy to judge.

Commentary and Recommendations:-

Prof. Hikida seems like obtaining enough budgets from different funding agency such as JSPS,
AMED, and private foundations. Also contributing the diversity by hiring an international
Assistant professor.

-

Generally speaking, this reviewer finds that each department foster young researchers from all
categories and is up to the level of expectations from IPR and Osaka University. When it comesto the acquisition of research funding, some departments do not explicitly state the exact nameof grant they have acquired. Information disclosure and social relationship appear to be on
average for all the labs. For international exchange, all labs actively collaborate with foreigncountries represented by the number of foreign students.

-

There seems to be many students in the lab. I am actually surprised to hear that the PI comes tothe lab only once a week to manage the lab activities. It may be efficient but not the best way to
run the lab. I hope that the lab will return back to normal operation soon.

5. Comprehensive Evaluation[Evaluation Perspective]
A. Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
B. Does each laboratory or department have an appropriate vision and perspective for its future
direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

As you know, protein functions in animal. In this meaning, having Prof. Hikida in the instituteis meaningful. It is because protein scientists often see only proteins but not to see animals. On
the other hand, animal scientists often see only animals but not see proteins. There is often a
big gap in these two research fields. Considering protein aggregation, both scientists can easily
work together because protein aggregation is process for protein assembly and aggregatedproteins control cell/tissue behaviors in animals. In the case of Prof Hikida’s research, theinstitutional small goal might be “Understand and control photo system”. Channel rhodopsin in
can control brain function and GFP-reporter system can visualize neuronal activity. Using brain
as an output, cross-boundary collaboration might be possible.

-

Concerning item A, this reviewer’s general impression is that the division seems to be rather
independent from other division as applied biology. Nowadays, it is often said that we confront
deep valley or obstacles among each highly developed expertise, and they prevent us from68

Laboratory for Advanced Brain Functions [Hikida Lab]

understanding each specialty in detail and make us blind to the field outside one’s expertise. To
overcome this and facilitate collaborations, university research administrators (URA), who
liaise with different specialists to achieve effective collaboration, should be placed properly asshared staff, though this reviewer is familiar with the issue of budget in national universities.
However, URA is able to set a framework of collaboration between division of integrated
protein science and other division focusing on protein analysis, even if an initiative was nottaken by the leaders of integrated protein science. Regarding the item B, most of thedepartment have their own future perspectives that can be evaluated as excellent.
-

Because the homepage is closed and the ResearchMap is not updated, evaluating the lab activities
solely based on the submitted PowerPoint file was very challenging.

69

Laboratory for Organelle Biology [Nakai Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Organelle Biology

Name of Reviewers: Jun SUZUKI, Sén TAKEDA, Tatsumi HIRATA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Prof. Nakai’s work is mainly about protein complexes for protein import. This kind of research
will have more impact on research fields with structural analysis.

Commentary and Recommendations:-

Mainly with graduate students without professional researchers, the group’s achievement isenough, I think. Especially, Prof. Nakai has explored the field of protein import into chloroplastby identifying new proteins.

-

Each research group sets unique goals, all of which directs towards the fundamental questions
in biology. However, the topics are very diversified covering from molecular level to a higher
brain function and behaviour. First, plant biology by Dr. Nakai is a kind of showcase of IPR’s
that has a unique position and policy in protein research field as his research focuses on plant
cells, while most of the research topics in IPR and other institutions are usually animals. Since
his group is rather small compared to others, explicit research goal is somewhat restricted,
ʻElucidation of protein transport to chloroplast and their evolutionary historyʼ. The topic
appears to be an authentic protein research bridging protein function to structural biology,
which has potential to accelerate in-house collaborations. However, while his group publishes
high-quality papers, the number of publications is relatively low, especially in recent years.
Although this reviewer does not know the details of his team as there was no on-sitepresentation by himself, I dare to point out that more achievements are required to be qualified
enough as a member of IPR.

-

I find that this group is active in research; articles have been published in top journals lately
after a little fruitless period of time. Their research seems to be appreciated globally inscientific community. I am surprised to know that this group is run by only one faculty
member.

2. Research achievements and resultant contributions to specific research area(s) in protein life70Laboratory for Organelle Biology [Nakai Lab]science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Area(s) that need(s) further attention:-

Protein import is a classical field of research and therefore it is hard to know what the missing
piece or big question in the field is, without oral presentation.

-

Laboratory for Organelle Biology

Commentary and Recommendations:-

Prof. Nakai seems like exploring the filed by identifying components of the protein importcomplex in chloroplasts.

-

As stated in the previous section, most of the labs significantly contribute to the advancementof protein research, which can be evaluated by the list of publication, acquisition of grants andinternational collaborations. Regarding Dr. Nakai’s team, this reviewer could not find out clear
future direction of study at all. This should have been explicitly stated in the documents
delivered before the review round. While my general remarks are excellent, this reviewer
thinks the score fluctuates depending on the team being evaluated.

-

I cannot identify current activities explicitly combining with protein science. Because thisresearch field and protein science are a very good match, exploring avenues for suchcollaboration could be highly beneficial for both.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Area(s) that need(s) further attention:-

It is difficult to know what kind of Joint usage (material or knowledge sharing) was conductedwithout oral presentation.

Commentary and Recommendations:-

At least, outcome for research activity is apparent/obvious by judging from publication in thegroup.

-

Since this division is composed of labs different from those providing IPR with basic analyticaltechniques, informatics or high-end facilities, contribution to joint usage/research seems to be
hard to appreciate. However, 3 departments out of 4 included a power point slide illustrating
their involvement in this subject. While some of those activities would be preferably classified
as collaborations with external facilities, rather than joint usage/research center having

71

Laboratory for Organelle Biology [Nakai Lab]

connotation of more assisting or rear-guard position, this reviewer finds the overall activities
are accepted as a favorable factor contributing to the reputation of IPR. The degree ofcontribution varies with each department. This reviewer recommends all the lab head to include
materials that correspond precisely to the evaluation axis preset by IPR.
-

I cannot find contribution of this group through the Joint Usage / Research Center’s programs.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Area(s) that need(s) further attention:-

Blog is a nice idea to communicate with people including students from outside, but currently
available only in Japanese.

-

Laboratory for Organelle Biology

Commentary and Recommendations:-

Blog is a nice idea to communicate with people from outside.

-

Generally speaking, this reviewer finds that each department foster young researchers from all
categories and is up to the level of expectations from IPR and Osaka University. When it comesto the acquisition of research funding, some departments do not explicitly state the exact nameof grant they have acquired. However, it is hard to judge whether Dr. Nakai’s lab is funded byexternal sources. This reviewer does not take it for granted that research funding is more
important than achievements, sustainability for basic research would be guaranteed by constantfundings. Moreover, a source from external funding supports IPR’s activity. In this meaning,
this reviewer is rather curious about the financial status of Dr. Nakai’s lab. Information
disclosure and social relationship appear to be on average for all the labs. For international
exchange, all labs actively collaborate with foreign countries represented by the number offoreign students.

72

Laboratory for Organelle Biology [Nakai Lab]-The number of students in the lab has increased lately. If the papers are published by students,
education effort of young researchers can be more highly recognized.

5. Comprehensive Evaluation[Evaluation Perspective]
A. Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
B. Does each laboratory or department have an appropriate vision and perspective for its future
direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-Publication is enough in this smaller group consisting of only PIs, technical staff, and students.
Research focus on protein complex involved in protein import is clear, and in this topic,
internal collaboration in structural analysis seems like adequate in the future. However, as I
described previously in Prof. Furukawa’s part, it happens when two teams are interested in the
project. Without oral presentation and Q&A, it is not easy to evaluate as excellent in total.

-

Concerning item A, this reviewer’s general impression is that the division seems to be rather
independent from other division as applied biology. Nowadays, it is often said that we confront
deep valley or obstacles among each highly developed expertise, and they prevent us fromunderstanding each specialty in detail and make us blind to the field outside one’s expertise. To
overcome this and facilitate collaborations, university research administrators (URA), who
liaise with different specialists to achieve effective collaboration, should be placed properly asshared staff, though this reviewer is familiar with the issue of budget in national universities.
However, URA is able to set a framework of collaboration between division of integrated
protein science and other division focusing on protein analysis, even if an initiative was nottaken by the leaders of integrated protein science. Regarding the item B, most of thedepartment have their own future perspectives that can be evaluated as excellent except forLaboratory for Organelle Biology.

-

The lack of face-to face meeting made a comprehensive evaluation challenging. Despite such
limitation, this group's recent publications show a commendable level of activity.

73Laboratory for Cell Systems [Okada Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Cell Systems

Name of Reviewers: Kenta NAKAI, Chandra VERMA, Shoji TAKADA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Area(s) that need(s) further attention:-

Integration with the structural models.

Commentary and Recommendations:-This group is exploring new fields of protein research. I like it.

-

Excellent goal to integrate information at the cellular level. The PI is certainly excellent andqualified to continue making significant contributions in the field of systems biological approachto cell fate decisions. This is a world leading effort. PI is exploring a novel extension to the work:
to use her models to report on post-translational modifications in the cell which will be a major
contribution to the field and complement the in-cellulo experimental methods being developed.
Indeed experimentally it is difficult to get time resolved data which the PIs systems approach ofmathematical modelling of signalling networks should be able to report on and this will asignificant advance in understanding intracellular biomolecular dynamics. Absolutely worldclass as evident from high impact publications. In addition, the NLP based modelling is boundto break new boundaries.

-

The integrated approach of system biology to cell signaling in Okada lab is extremely impressive.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

Relatively few ‘big’ works in the last few years(?)-

The mathematical modelling of cell fate, signalling networks, NLP based models, use of ML/AI
methods etc are world class efforts and clearly are opening up new vistas not only in fundamental
understanding of intracellular landscapes, but also opens up the route to discovering new biology,

74

Laboratory for Cell Systems [Okada Lab]new regulatory mechanisms and clearly has already translated into areas as diverse as dentistry,skin, drug targets and patient stratification. Has significant number of research publications ininternational peer reviewed journals with high impact. This has resulted in a wide variety ofcollaborations – local and international and in a diverse range of topics reflecting the significanceof the fundamental and necessary nature of the work of the PI.
3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

I think this group is a typical model for desired interdisciplinary research in the center.

-

A significant number of activities including domestic and international collaborations, visiting
researchers and exchanges etc has emerged as a result of the PI’s work.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-

Accepting many international students.

-

As for the educational activities, excellent team has been assembled – faculty and graduate
students and also an undergraduate student. In addition, has a diverse group of collaborators
across the world in applying these fundamental methods to a range of problems from basic toclinical. Carried out considerable teaching and supervision of undergrad and grad students andalso mentors international interns.

75Laboratory for Cell Systems [Okada Lab]-As for the research funding, the group has successfully achieved significant funding, covers a
range of topics from basics to applied from organizations ranging from JSST, JSPS, Uehara
Foundation.

-

As for the international exchanges, it is quite significant and diverse. Excellent in enabling
international and national collaborations. This is also associated with several international
exchanges.

-

It is notable that the group has full of funding.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

Close to the ‘Excellent’ level. I have an impression that the collaboration between the labs in IPR(or even ASPIRE) has not begun fully.
As a general comment, I think that the construction of the ASPIRE center was very nice (while
the other center looks also promising). These organizations should become driving forces of theentire IPR in the future. It is too early to criticize its outcome. Work hard to prove these newattempts are indeed successful.

-

Overall, excellent in all domains. Both as director of IPR and member of ASPIRE, has provided
great leadership, mentoring in research, education and liaison. Is further expanding operations
and making many more significant contributions with greater interdisciplinary efforts planned.
These will emerge from both internal to APSPIRE/IPR, domestic and international
collaborations.
Has excellent vision among perspective of future directions. I would encourage continuing
support and effort to further integrate across some aspects of different research groups. For
example one area which can provide unique insights and be world leaders would be to integrate
across the groups individual abilities that can illustrate at atomic level, how the intracellularsignalling networks function in space and time and be modulated by post-translational
modifications by integrating the functional dynamics of proteins and their interactions and how
they will change with SNPs in different protein components of the network. This could reallybe a major milestone in the world and the current ASPIRE team has excellent capability toachieve this.

-I thought the recruitment of students in Okada Lab is very successful among other groups. I hope76

Laboratory for Cell Systems [Okada Lab]the successful cycles can be transformed to other groups in IPR.

77

Laboratory for Computational Biology [Mizuguchi Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Computational Biology

Name of Reviewers: Kenta NAKAI, Chandra VERMA, Shoji TAKADA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-This group mainly focuses on computational research in the drug-discovery-related field/medical
applications. I think this is a very promising approach.

-The research group is using database development, data integration, AI, machine learning andother modelling and simulations to lead a world class effort in protein life sciences. The research
topics are clearly well thought out and very important including predicting toxicities ofnanoparticles, ADMET properties of drugs, TCR-pMHC interaction predictions etc. Each ofthese has resulted in resources and/or high impact publications.

-Integration of data-driven science, AI, and simulations for drug discovery is truly a desired
direction to go. This group covers broad range of bioinformatic analysis and modeling for the
drug discovery and is very valuable.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

They keep high productivity, though there may not be many ‘remarkable’ achievements so far.

-Achievements of the group are excellent at an international level and has established the groupwith an excellent international reputation. Among the many projects, the excellent achievementsof the PI in their ability to predict toxicity and ADME properties is of great significance to drug
development and the MHC-peptide work for vaccine design. Nanoparticles toxicity prediction
has great potential because of the huge interest in the world for drug delivery purposes and thePIs achievement is very notable and would be of significant interest to academics and industry.
The development of DruMAP will be a great resource for the worldwide community. In addition,

78

Laboratory for Computational Biology [Mizuguchi Lab]

critical analysis of their findings has resulted in the PI expanding the scope of investigations by
for example inclusion of structural data. The research has been published in many internationallypeer reviewed journals with high impact and several invited lectures.
3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

The lab shows representable activities in ASPIRE because their activities are based on theanalyses of massive data.

-

Several collaborations every year both national and international with a significant number from
IPR, thus contributing significantly to the protein life science communities. Several international
exchange students and staff and attracts many students with many resulting collaborations.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-This group accepted many students, including those from overseas. Successful collaboration withindustries.

-

As for the educational activities, the group has established an excellent reputation internationally.
Mentors a significant number of international students and postdocs. Additionally gets several
visiting researchers from the world. The group has also been mentoring an ASPIRE member Dr
Tiwari by encouraging her to work with staff in his group.

79Laboratory for Computational Biology [Mizuguchi Lab]-As for the research funding, the group has significant industry partnerships: Technopro, Astra
Zeneca KK; the work is of great significance in the prediction of toxicity/ADME.

-As for Information Disclosure and Social Relationships, the group has given 36 invited lectures.

-

As for the international exchange, the group has several collaborative research projects bothnationally and internationally and with industry. The group has given 36 invited lectures.

-

The group is having fairly many graduate students, but the majority is foreign students. It would
be nicer if the group can recruit more Japanese students as well.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

Considering that the group has started their activity rather recently, their activity is rather
impressive. I hope that they will tighten their links with industrial people because I believe that
this will show a new model for the future of IPR.

-

Excellent performance all round: research, mentorship, collaborations, outreach, industry
collaborations. PI has great vision as is exemplified by excellent basic and applied research,
including the plans for integrating work with others in ASPIRE has the potential to create somereally groundbreaking discoveries and make significant contributions to basic andapplied/translational sciences. The integration of resources developed by PI with those fromother members of ASPIRE has excellent potential to result in a world leading platform.

-

Dr. Mizuguchi joined the IPR relatively recently. We have to wait some years to see how theachievement done at IPR can lead to real drug discovery.

80Laboratory for Protein Design [Koga Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Design

Name of Reviewers: Kenta NAKAI, Chandra VERMA, Shoji TAKADA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-

I believe that this lab would become an iconic symbol of the new IPR.

-

PI is clearly very good at designing novel proteins. The plan is very well thought out and will bevery relevant to industry-pharma, sustainability, materials etc.

-

Dr Koga has been so successful for designing protein structures, including oligomerization. Next
challenge would be to design function in broad sense. Obviously, a hard target is to design
enzyme activity. Combining with evolutionary approach seems promising.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

Excellent achievements are accumulating although they are performed at the group’s previous
affiliations.

-

PI has been publishing (and undoubtedly will continue to publish) in high impact journals andalso will contribute to innovations which clearly have been of great interest to industry. Will
make significant contributions to life sciences especially in the areas of biomarker discovery,
novel therapeutics etc.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:81Laboratory for Protein Design [Koga Lab]-

Obviously, it would be too early to evaluate their contributions; however, as I noted above,owning a lab for protein design would attract much attention to the center.

-

There is excellent potential to engage with the other members. A collaboration with Dr Tiwari
for example is planned which could illuminate significantly the role of intramolecular flexibility
and complex formation as there is a vast resource of designed proteins that the PI has constructed.
Feedback from the models of Dr Tiwari could point to new design principles. The work of the PI
increasingly will also attract many more industries and research groups.

-

Since it is a very new group, it is too early to assess this point.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-

My suggestion is that they plan to boost a new avenue of protein-based industry (probably bylaunching a venture company).

-

As director of ASPIRE, he oversees the various activities of ASPIRE which has witnessed several
visiting students, researchers, collaborations of the team members in ASPIRE.

-

The PI has attracted significant interest and funds from industry.

-

As for the ASPIRE activity, a plan for collaboration with more than two groups would be a greatidea. Especially, formation of a long-term team including young PIs is great.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly82

Laboratory for Protein Design [Koga Lab]

share them with us.
Commentary and Recommendations:-

The high score is given not to their activities after coming to this institute but to my great hopefor their future activities.

-

The PI undoubtedly is excellent and the work that is emerging is amongst the best worldwide in
the area of protein design. In addition, once the PI starts including ML/AI/LLM methods, theproject will achieve a much higher level of applications and novel discoveries. In addition,
there is immense potential of integrating the work both as director of ASPIRE and his own
platforms with those of others in IPR to advance scientific research and directing an integrationin his role as Director of ASPIRE. For example, combining the designs of proteins andassemblies with Dr. Tiwari’s platforms to relate protein flexibility to functional motions andinteractions and then to combine forces with the work on SNPs with Dr. Mizuguchi and finallyto decorate the signalling networks of Dr. Okada could result in a fantastic integrated resourcethat can inform upon intracellular processes in unprecedented detail. The information would
feedback into designing proteins with modified and unnatural amino acids too which will be ofanother great benefit to the international community.

-

Recent outcomes from Koga’s lab are fantastic, but most of them are from the previous position.
We look forward to seeing the achievement done at IPR.

83

Laboratory for Biomolecular Modeling and Dynamics [Tiwari Lab]

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Biomolecular Modeling and Dynamics

Name of Reviewers: Kenta NAKAI, Chandra VERMA, Shoji TAKADA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-

I think that their goal is appropriate but the PI should hurry up in recruiting new members toachieve the goal: how many staff can she employ?

-

PI has just started but has a very good research plan. The plan will undoubtedly evolve with timeand collaborations. The two main streams are modelling with analysis of SAXS, XFEL data;
Understanding protein flexibility, allostery etc in the context of function. Both have immense
potential to inform protein life science research.

-

Dr. Tiwari just joined the IPR as a new PI so it is too early to judge her research in normal manner.
It was not clear exactly what is her major research goal. She has many reasonable and promising
themes planned as collaborations, but her own goal was not emphasized. It is very important tofind a backbone research plan, a sort of dream, in the coming years.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

Of course, it is too early to discuss the achievements of this group. However, I could not recognize
excellence in their approach.

-Currently the PI has already developed an IPR collaboration and an external collaboration with
Hiroshima University. The PI has also written one review and several manuscripts are in progresswith ASPIRE and external people. The results of these will be crucial in establishing a benchmark
for the use of the PIs computational tools in advancing proteins life science research.

-

Again, it is too early to assess this point. All atom molecular dynamics (MD) simulation is apotentially very valuable approach in the IPR because of many structural biologists who needs

84Laboratory for Biomolecular Modeling and Dynamics [Tiwari Lab]MD analysis associated with the structure determination and because of lack of MD specialists
in IPR.
3. Contribution of the group to the institutional activities of the Joint Usage / Research Center[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

Considering the number of staff, I think that the PI is actively seeking collaborations (though
they may not be through the programs of IPR).

-

The PI already has been lecturing, serving as Masters thesis examiner, participating in Prof
Mizuguchi’s lab activities. PI is working on manuscripts with members of ASPIRE (Mizuguchilab). The PI has plans to exploit and mine the vast resource of designed proteins with the Kogalab.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-

These points are not bad, but considering the scale of the lab, the PI should not expand theirmiscellaneous activities at this stage, perhaps.

-

Educational activities: PI has been working with postdoc in the Mizuguchi lab and has developed
collaborations with Univ or Bergen, Universite Paris-Saclay and IIT Gandhinagar.

-

Research finding: PI has received New Field Research Grant and has also been recipient ofsupercomputing hours at Cybermedia and TSUBAME

85

Laboratory for Biomolecular Modeling and Dynamics [Tiwari Lab]-

Information Disclosure and Social Relationships: PI is organizer of IPR/ASSPIRE seminars andis on the organizing committee of IPR Retreat 2023.

-

International exchanges: PI has already visited France, presented a poster at a conference foryoung modellers in Tolouse and gave an invited seminar in Paris. PI has organized the joint
collaboration visit of Prof Nathalie Reuter from Norway.

-

PI has begun to engage with students in the group of Prof Mizuguchi with his kind approval andmentoring. PI is exploring several routes to attract students. PI is participating in international
conferences.

5. Comprehensive Evaluation[Evaluation Perspective]
Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

I hope that this lab will be able to establish a solid position in ASPIRE/IPR soon.

-

The PI is a recent addition but is already embarking on multiple projects both within
ASPIRE/IPR and externally. The PIs platforms have excellent potential to inform upon thelinks between protein dynamics and function. Integrating her method with the designed
proteins of the Koga lab, the SNPs of the Mizuguchi lab and inform upon the protein networks
in signalling pathways from the Okada lab has excellent potential to advance protein life
science research. It will attain much more momentum once the group is staffed towards which
the PI is applying for grants and students. In addition, PI is developing collaborations withinternational partners.

-

The group has no other members at the moment, which is a bit difficult situation especially as ayoung PI. To boost her group activity, it would be great if she can have at least one post-doc fora few years supported by the IPR.

86

Laboratory for Protein Databases (PDBj)

External Review FY2023

Evaluation Sheet (Research Group Activity)
Name of the research group:

Laboratory for Protein Databases (PDBj)

Name of Reviewers: Kenta NAKAI, Chandra VERMA, Shoji TAKADA
1. Research Goal and approach(s)[Evaluation Perspective]
Does the research group set an appropriate research goal, select relevant research topic(s), and takeappropriate approach(s) as a member of IPR, that is a world-class institute for protein life sciences?
Commentary and Recommendations:-This lab could be a “raison d‘etre” of the data science-based center.

-

An amazing and excellent effort for maintaining the PDB and associated databases to enable thecommunity to mine and exploit structural biology research – its value to the relevant scientificcommunity for advancing protein life sciences is beyond measure. There are significant plans inprogress to link the PDB data with other data resources which will be quite a significant resource.

-This group has a special mission of managing the PDB, which is largely a service to thecommunity. As users of PDB, I would really appreciate the effort of this group.

2. Research achievements and resultant contributions to specific research area(s) in protein life
science[Evaluation Perspective]
Do the achievements of the group contribute to the advancement of protein life science?
Commentary and Recommendations:-

I appreciate their effort in achieving the 31% contribution in wwPDB. However, we cannot be
optimistic because this figure may be dropped significantly after PDBc goes smoothly.

-

The achievements of this effort are tremendous and excellent. Research has focused on improved
biocuration which has resulted in tremendous increase in deposited structures, increased
efficiency; there was no impact of COVID-19 on the work which is an excellent testimony to thesignificance and robustness of this project. In addition there has been a tremendous effort in
improving the quality of models of structures deposited which is very good for the communityof users. The development of RDF to integrate across different databases will be an extremely
useful resource for the community.

3. Contribution of the group to the institutional activities of the Joint Usage / Research Center87Laboratory for Protein Databases (PDBj)[Evaluation Perspective]
Does the research group contribute to the protein life science communities through the Joint Usage /Research Center’s programs?
Commentary and Recommendations:-

The current situation may change drastically in the future.

-

An increasing number of data submissions and its usage over the years. This is the aim of thedata service and it is being accomplished in an excellent manner.

4. Others
Please give your comments and/or suggestions on other points as shown below,(Educational activities）･Fostering young researchers, including graduate students, post-doctoral fellows, and foreign
researchers(Research Funding from External Sources)
Research funding acquisition status, such as Grants-in-Aid for Scientific Research (KAKENHI),
contracted research, industry-academia collaboration, etc.
(Information Disclosure and Social Relationship)･Activities for updating the IPR website, lectures, public courses, etc.
(International Exchange)･Activities for international joint research, organizing/participating in international conferences
and meetings.
Commentary and Recommendations:-so far so good-Two young members have joined PDBj as lead annotator and annotation/validation servers for
PDB China.

-

Concerning “Information Disclosure and Social Relationship”, the PDB is constantly updated
and the worldwide effort includes workshops, lectures etc and has been an ongoing and extremely
successful effort for years.

-

International exchanges are a crucial part of the world wide PDB effort.

-

The group owes major effort by specially-appointed people. I am not sure about their career path.
Can they be permanently employed? In the near future, it would be more and more difficult tofind great technical staffs. Stable employment would be desired.

5. Comprehensive Evaluation[Evaluation Perspective]

88Laboratory for Protein Databases (PDBj)

Are internal collaboration and/or IPR framework nicely utilized in the group’s research?
Does each laboratory or department have an appropriate vision and perspective for its future direction?
If you have any opinions or suggestions regarding the future directions of their research, please kindly
share them with us.
Commentary and Recommendations:-

In the post-AlphaFold2 era, the expected role of PDB will change significantly. If the PDBj teamwants to have its independent policy from the one with its partners, they should propose it assoon as possible. In addition, the probable rise of PDBc is also a concern. I believe that the staffof PDBj should share a sense of crisis.

-This is a very critical part of protein life science research and it is a major public service. It
consists of a significant number of staff from ASPIRE and IPR. It is continuing the momentumof its aims and their accomplishments. The RDF will incorporate other databases with othermembers including Mizuguchi and Koga labs. The development of OneDep system has clearly
been a tremendous success. With the appropriate development of mining tools, ML/AI
methods, it will be a great resource to include and enable integration of the models of the
KOGA lab with the dynamics of the Tiwari lab and insights from the Mizuguchi lab and finally
into the systems analysis of the Okada group. Has a fantastic potential of a well-integrated
resource for the world wide community to efficiently mine and accelerate discoveries

89External Review FY2023
Comments from the Reviewers on the Division of Protein Network Biology and the ASPiRE
Overall the output is quite amazing in terms of the science industry collaborations, outreach efforts
The science is excellent and certainly at the leading and competitive edge in the world.
Division of Protein Network Biology
Laboratory for Cell Systems led by Dr. Mariko Okada focuses on system biology of cell fate decision
mechanisms integrating experimental measurement and computational modeling. Laboratory for
Computational Biology led by Dr. Kenji Mizuguchi works for drug discovery by database-driven andAI based approaches. Both labs show extremely high-level research activities. Notably, a good balance
between academic and basic researches and collaborations with academic groups and industries isimpressive.
We would like to suggest the following possibilities:
1) Increase links with local clinicians to perhaps be able to use their capabilities to help clinicaldecision making – especially with regards to SNPs in the local populations and their effects on
drugs; maybe initiate this coupling into a national Precision Diagnosis/Medicine Program (if one
does not exist)
2) Increase center links with biotech and industry along with those already arising out of individual
networks that already are excellent (maybe have open days and invite biotech/pharma)
3) Explore joint PhD students with other countries (model could be the ARAP program offered by
ASTAR, Singapore) and explore whether pharma would be interested in joint PhD students (model
could be CASE studentships in the UK)
ASPiRE
ASPiRE aims at putting forward protein-centric data-driven studies, which perfectly meets the current
need in protein science. As such, this new center, ASPiRE, plays a key role in the IPR. Its organization
looks good overall: The five groups cover rational protein design, analysis of protein dynamics andprotein network, drug discovery, and building/managing protein database.
The most exciting aspect we find is the potential for integrating across scales in space and time ranging
from protein structures (SNPs), dynamics to cellular pathways (brings together all the 5 presentations)is very exciting because the tools are uniquely in place at ASPIRE and the integration capabilities exist– this will excitingly inform upon things such as post-translational modifications (PTMs) and theirinfluence on structures, associations and phenotypes – thus opening new avenues in drug discovery –90

which so far has not really been able to include the effects of PTMs. This will be a great defining
unique character of ASPIRE which will certainly be world leading and guiding. It is an effort thatcertainly would blossom with as long-term assurance of funding.
We would like to suggest the following going forward:4) It would be great if the center can recruit a proper IT group dedicated to machine-learning /AI.
Cross-appointment to other Schools in Osaka University can be a possibility.
5) Keep an eye on developments in Quantum Computing especially in the field of structure
manipulations in biology; keep talking with industry leaders in this area to keep updated with
developments, especially in Quantum ML-AI. While these are long term, innovations can happen
and the dynamic may suddenly change91Organaizaion
Director 所長
Faculty Meeting

教授会

Administrative Council

運営協議会

Panel on Joint Usage/Research

専門委員会

Research Divisions

研究部門● Division of Protein Chemistry

蛋白質化学研究部門

Laboratory for Protein Organic Chemistry

蛋白質有機化学研究室

Laboratory for Nanobiology

蛋白質ナノ科学研究室

Laboratory for Protein Synthesis and Expression

分子創製学研究室

Laboratory for Protein Profiling and Functional Proteomics

機能・発現プロテオミクス研究室

Laboratory for Physical Biology

蛋白質物理生物学研究室● Division of Protein Structural Biology

蛋白質構造生物学研究部門

Laboratory for Molecular Biophysics

機能構造計測学研究室

Laboratory for Protein Crystallography

蛋白質結晶学研究室

Laboratory for CryoEM Structural Biology

電子線構造生物学研究室

Laboratory for Supramolecular Crystallography

超分子構造解析学研究室● Division of Integrated Protein Functions

蛋白質高次機能学研究部門

Laboratory for Molecular and Developmental Biology

分子発生学研究室

Laboratory for Genome and Chromosome Functions

ゲノム-染色体機能研究室

Laboratory for Advanced Brain Functions

高次脳機能学研究室

Laboratory for Organelle Biology

オルガネラバイオロジー研究室● Division of Protein Network Biology

蛋白質ネットワーク生物学研究部門

Laboratory for Cell Systems

細胞システム研究室

Laboratory for Computational Biology

計算生物学研究室

Laboratory for Infection Systems

感染病態システム研究室

Special Research Facilities

附属施設● Research Center for Next-Generation Protein Sciences

蛋白質次世代構造解析センター

Laboratory for Ultra-High Magnetic Field NMR Spectroscopy

高磁場NMR分光学研究室

Laboratory for Synchrotron Radiation Research

高輝度放射光結晶解析研究室

Laboratory for High Resolution Cryo-EM

高分解能クライオ電子顕微鏡研究室

Laboratory for Biomolecular Analysis

生体分子解析研究室Open Space Laboratory for Advanced Protein Science

産学・国際連携研究室● Advanced Data Science Center for Protein Research

蛋白質先端データ科学研究センター

Laboratory for Protein Design

蛋白質デザイン研究室

Laboratory for Biomolecular Modeling and Dynamics

生体分子動態モデリング研究室

Laboratory of Protein Databases

蛋白質構造データバンク構築研究室

Laboratory for Protein Network

蛋白質ネットワーク研究室

Laboratory for Drug Discovery Informatics

創薬インフォマティクス研究室

Division of Donated Fund Research

寄附研究部門● Division for Matrixome Research and Application

マトリクソーム科学（ニッピ）寄附研究部門

Office of Research Strategy and Promotion (URA)

研究戦略推進室 (URA)

Technology Division

技術部

Administration

事務部

General Affairs Section

庶務係

Accounting Section

会計係

Project Team of Joint Usage / Research Center

拠点プロジェクト班

Research Support Section

研究支援係

Public Relations Office

広報室

Library

図書室

IPR Alumni Office

卒業生担当室92