第59回生物物理学会バイオイジックスセミナー

switchSENSE® heliX®:measuring interactions fromsmall molecules to cells
Thursday, November 25 at 12:00-12:50PM
Room : ch3

Alice Soldá, Irene Ponzo, Agnes Marsal, 〇Daisy Paiva
Dynamic Biosensers GmbHswitchSENSE® is an automated, fluorescence-based
biosensor chip technology that employs electricallyactuated DNA nanolevers for the real-timemeasurement of binding kinetics (ka, kd) and affinities(with KD values down to the fM range). The platform
offers an automated ligand density control, which allows
to conveniently discriminate between affinity and avidity
in one single assay. Interactions between proteins,
DNA/RNA, and small molecules can be detected withfemto-molar sensitivity. At the same time,
conformational changes and complex binding events canbe measured using minimal amounts of sample.
Using heliX® instrument and the novel DNA Y-structure,
we made it possible to characterize ternary complex
formation of bifunctional small molecules like PROTACs(Proteolysis targeting chimeras). The E3 ligase as well asa target protein can be functionalized on each separate
end of two FRET pair color-coded Y-arms. The Ystructure closes upon PROTAC binding and thesubsequent ternary complex formation bringing
together the green donor and the red acceptor dye into
a closer, FRET sensitive, distance. The change in red
fluorescence signal intensity directly correlates withternary complex formation kinetics. we show that the Ystructure is an extremely versatile tool for studying any
type of protein-protein complex formations with adissociation constant between 1nM to 10µM.
Moving from small molecules interactions to complex
systems, we present a novel method to capture isolated
cells and to measure the association and dissociation
kinetics of fluorescently labeled antibodies to/from cellsurface antigens in real-time. To this end, flow-permeable,
mesh-like cell cages were designed to accommodate andphysically retain single cells in the microfluidic channel of acommercially available biochip. Suspension or adherent
cells can be loaded into the cages by an automatedworkflow using only a few microliters of sample and aresubsequently exposed to binders under continuous flow.
We validated the method by investigating a number ofdifferent antibody clones against various antigens (CD3,CD1d, CD7 and CD305) expressed on the surface of Tlymphocyte cancer cells. The engagement of antibodies toone or two antigens (affinity vs. avidity) on the cell surface
and ultimately correlate avidity with the antigen expression
level could be determined in a reproducible manner.
In this work we will highlight both recent advancesthat allows investigation of biomolecular interactions
under conditions that are close to in-vivo situations ina highly automated workflow and thus useful for thescreening and characterization of new drugs thatintervene in the different cellular or biochemical
processes..

お問い合わせ先DKSHジャパン株式会社 テクノロジー事業部門
Tel : 03-5730-4510 Fax :03-5730-7605
e-mail: tp.labtyo@dksh.com* This event will be presented in English language.
– S390 –科学機器部

第 59 回日本生物物理学会年会 BP セミナー
2021 年 11 月 26 日 (金) ch2
PDB activities under ongoing Covid-19 situation, and up-to-date information on our
quality improvement and data validation
By Genji Kurisu, Institute for Protein Research, Osaka University
PDBj (PDB Japan, https://pdbj.org/) is an Asian hub for the development of the single global archive for
3D macromolecular structure data as known as PDB, which is accessible freely online.

In this session,

we will talk how promptly we are trying to provide necessary information under the ongoing Covid-19
situation. We will also introduce our various quality improvement activities, and data validation systemutilizing Cambridge Structural Database (CSD) .

PDBj tools and services for analyzing and visualizing structural data.
By Gert-Jan Bekker, Institute for Protein Research, Osaka University
PDBj has developed multiple services for exploring, visualizing and retrieving data from the PDB. In thisseminar, we will introduce some of the new functionality of the main PDBj website to search and explore
PDB data. In addition, we will describe some of the new functionality of our WebGL based molecular
viewer Molmil (https://pdbj.org/molmil2/) and show examples of how advanced visualization
operations can be performed.

Services and databases for 3D electron microscopy data by PDBj and wwPDB
By Hirofumi Suzuki, Waseda UniversityThe rate of increase in the number of electron microscopy (EM) data is still accelerating. EM raw images,
3D density maps, and atomic coordinates are stored in the databanks, EMPIAR, EMDB, and PDB,respectively. The seminar will cover recent trends in EM data in the databanks, new wwPDB activities
such as validation reports for EM data, PDBj database activities, and services and tools for EM, such as
EM Navigator and Omokage search.

Protein Data Bank Japan
https://pdbj.org

PDBj 事務局
565-0871 大阪府吹田市山田丘 3-2
大阪大学蛋白質研究所プロテインデータバンク研究室
TEL: 06-6879-4311 (事務局) 8634 (登録事務局)* This event will be presented in English language.
– S391 –第 59 回日本生物物理学会年会
サーモフィッシャーサイエンティフィック
バイオフィジックスセミナー◆ 日時：2021 年 11 月 26 日（金）12:00-12:50◆ 会場：ch3
クライオトモグラフィーで実現する生体三次元構造解析の新時代:
生体分子構造から機能解析へ
甲斐 翼
サーモフィッシャーサイエンティフィック
The New Era of Advanced Structural and Functional Analysis of Biological Systems
Driven by Cryo Tomography
Tsubasa Kai
Thermo Fisher Scientific
細胞やオルガネラ、タンパク質複合体の三次元微細構造の解析は、生体内で起こる事象を理解するうえで重要な役割を担っている。細胞内でのタンパク質の局在状態やオルガネラとの相関、タンパク質複合体の細胞内での状態を分子レベルで詳細に三次元観察することができれば、これまで明らかでなかったタンパク質の細胞内での機能環境を知る手がかりを得ることができる。
細胞内やタンパク質複合体の微細構造は電子顕微鏡を用いることで観察することが可能である。現在、タンパク質の立体構造解析法の一つとして、試料を液体窒素温度で観察するクライオ電子顕微鏡を用いた単粒子解析法が大きな注目を集めているが、クライオ電子顕微鏡のアプリケーションはそれだけにとどまらない。その一つであるクライオトモグラフィー法は、細胞内のオルガネラや微細構造の詳細な三次元観察を可能とする革新的な手法である。急速凍結によりアモルファス状の氷に包埋した細胞試料はその自然に近い状態を保ったまま、クライオ電子顕微鏡観察に用いることができる。クライオトモグラ
フィー法を用いることで、自然状態に近い細胞内の様子を数 nm～数百 nm スケールの高分解能で三次元観察を実現できる。つまり、クライオトモグラフィー法によって、各タンパク質やその複合体の独立した立体構造だけでなく、それらが相互作用し、機能している環境の様子までを詳細に三次元観察することで、これまでにない視点から生体内の機能解析することが可能となる。本セミナーでは、クライオトモグラフィー法のワークフローを最新のアプリケーション事例とともに紹介する。

※このイベントは日本語で開催します。
* This event will be presented in Japanese language.
– S392 –  ਸ਼  ৚঩মে੟੟৶৾ভফভ 崸崌崒崽崋崠崫崗崡崣嵇崲嵤ৰ੠峕ু峕਄峍峐峩峉崛崊嵎崳崫崰ଲષ‫ع‬৸ખೝዓ୾௴௄岴峲峝ઁଳ৙੗಍ཝ௴௄峕峎岮峐‫ع‬৅਀঩‫ ؟‬া  ঩ ଅ  t   ৖ો୞ಀ‫ ؟‬FK崟崘嵆୾ਃ峘崛崊嵎崳崫崰ଲષ峙岝ে੟੟৶৾ভ৩岶ਝੑ峁峉岝ে੟੟৶峘峉峫峘୾৾ႀ๶ྰঢ়৴ଲષ峑峃岞৾ে峬ੂੱ঻峬岝ஆঽ峘୾৾௺峼௫峁峩峔岶峳岝岴峬峁峷岮ଢ଼஢峼৫ิ峃峵峉峫峘ৗଲષ岶岝০ফ峬ਯ੗岹岬峴峨峃峘峑岝岴஫岲峁峉岮岽峒岶௥ൗ峑峃岞ఠଢહ岾ງஂ৿઺峙 KWWSV\RXWXEHG/8S4:O/IF 峨峉峙        ০৚峙ੂ峫峐岝岴ઞ岮ຘ岮峉্‫ر‬峕ৰ੠峘஘৕峼岾൥౰峁峐ຘ岹岽峒峕峔峴峨峁峉岞শਚ峬ಢਚ峬அ峫峉ଲષ峘ઞ৷૎峒ુ峕岝ৗ峁岮崌嵉嵤崠嵛崘ৰୡ峮峇峘૭ચਙ峔峓峕峎岮峐岾ງஂຘ岷峨峃岞ઢਉ ჟ৕ ၳઇ౸ਕદ ඤপ 岿峽 0 শળૼ୒ఐ৾প৾嵣ে੟ਃચੵ৾ 岣৸ખೝႀ๶ྰ峼ੂଡണ峁峐ዓ୾崊崗崩嵛峼௴峵岤ె੩ ௏੘ ઇ౸পଚপ৾嵣ਓ঵ఐ৾ଢ଼஢ਚ 岣6(0$7(5$6 峑崟嵛崖嵍嵑嵒崮崋峼ኇ岲峵‫آ‬岤 崟崘嵆୾ਃઙૄভ঺‫ূ ٿ‬਎੃ႅিય෤ 
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※このイベントは日本語で開催します。
* This event will be presented in Japanese language.
– S393 –