B

計算生物物理研究室

研究室

タンパク質中の熱・エネルギー移動機構Florence Tama教授* Florence Tama 教授

倭剛久

木村明洋

准教授

Takahisa YAMATO, Assoc. Prof.

助教

Akihiro KIMURA, Assist. Prof.

Overview of Computational Biophysics Labiophysics is a field of study that aims to understandbiological phenomena using the principles and toolsof physics. Every living organism must be following
the laws of physics; however, our understanding ofbiological systems is still limited due to their complexity.
B laboratory focuses on studying biomolecules suchas proteins and nucleotides that perform many vital
cellular functions, and whose dysfunctions result insevere diseases. To understand diseases and develop
treatments, the functional mechanisms of these complex
biomolecules must be elucidated. A crucial step in thisprocess is the characterization of their structures anddynamics. We use computational techniques, often incollaboration with experimental groups, to study thesebiomolecules.
Our current research focuses on:

B木村明洋助教倭剛久准教授biological molecules). Such dynamics are essential for
their functions; however, at the atomic level, direct
observation of their motions is still difficult with current
experimental techniques. Molecular dynamics simulation
is a powerful computational technique to obtain
additional insights as it can provide atomistic level
details of molecular motions. In this approach, a potential
energy function represents the physicochemical
properties of biomolecules. Newton’s equation of motionis then numerically solved using high-performancecomputers to obtain a complete description of atomic
motions. We study biomolecules using molecular
dynamics simulations to discover new insights that are
not accessible from experimental studies. Recent studiesinclude circadian clock proteins as well as multipleenzymes.

Florence Tama, Prof.

生きている細胞の中では，沢山の生体分子たちが休むことなく働き，生命活動を支えています．遺伝子の設計図に基づいてポリペプチド鎖が合成されると，タンパク質は天然構造に折り畳まり，アミノ酸残基はお互いに相互作用をし始めます．B研究室では，この相互作用を理解することでタンパク質の動作原理を追求しています．凝縮系物理学と生物物理学の概念を融合するユニークな手法を用いて，タンパク質中の熱・エネルギーの移動機構を調べ，アミノ酸残基の間のコミュニケーションの様子を探っています．独自のコンピュータープログラムを駆使して，これまでに，タンパク質がシグナルを伝達するメカニズム等の問題を解明してきました．この分野では欧州や米国のチームと並んで世界の研究を牽引しています．「物理の言葉で生命を語る」をモットーにして，新しい生物物理学を生み出す「特異点」を目指しています．

biomolecules. Each experimental technique has its own
strengths and weakness. Therefore, the integrativeuse of multiple experimental data is essential for an
in-depth understanding of biomolecular dynamicalmechanisms under physiological conditions. We develop
new computational modeling techniques, which utilize
concepts of mechanics in physics and combine themwith various experimental data (hybrid approach) tomodel the structure and dynamics of biomolecules.
Multi-scale modeling, which describes the system
at different levels of detail, is used to study various
biological systems. Accurate descriptions of molecularmechanics and computational algorithms for efficient
sampling are critical components to these projects.

光合成反応初期過程の研究
生物が生物らしく活動する力の源は，生体エネルギー変換というダイナミックな働きが重要になります．地球に降り 注ぐ太陽光が生物界で最も基本的なエネルギー源であり，光合成生物はそれを吸収し，集め，電子移動反応という化学反応によって，電気化学エネルギーという生物が利用できるエネルギーに変換します．B研では，光合成反応の初期過程である，光エネルギーを吸収し電子を取り出すまでに発生する，励起エネルギー移動/電子移動反応に焦点を当てて，そのメカニズムの解明を行っています.
これらの反応はすべて光合成反応中心タンパク質中で起こります．そこで，反応中心タンパク質の構造情報を基に，溶液中などで起こる化学反応論や非平衡統計物理学を駆使して，光合成反応の特徴を明らかにします．B研究室は，この分野では世界的に実績ある理論的研究を進めています.

Hybrid Approaches - Computational Modelingand Experimental Data
Information on the 3-dimensional (3D) structures anddynamics of biomolecules is essential to understand theirfunctions’mechanisms. X-ray crystallography and cryoelectron microscopy (cryo-EM) provide 3D structuresof protein complexes. However, such 3D structures
represent frozen snapshots of the molecule and cannot
alone provide all the information on the conformational
dynamics responsible for biological functions. Other
experimental techniques can provide information closer
to physiological conditions, room temperature, and insolution (Small Angle X-ray Scattering, Atomic ForceMicroscopy, Fluorescence Energy Transfer, X-ray Free
Electron Lasers); however, the resolution of the data is
still limited for constructing detailed atomic models of

Molecular Dynamics Simulation to study
Biological Functions
Biomolecules are highly dynamics due to theirinteractions with other molecules (small chemical or

https://sites.google.com/view/b-lab-nagoya-university*連絡先 florence.tama.y5@f.mail.nagoya-u.ac.jp
教授：1／准教授：1／助教：1／ DC：2／ MC：5

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