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Esirkepov, T. Z.; Pirozhkov, A. S.; 神門 正城; Gallegos, P.*; Ahmed, H.*; Ragozin, E. N.*; Faenov, A.*; Pikuz, T.; 河内 哲哉; 匂坂 明人; et al.
AIP Conference Proceedings 1465, p.172 - 180, 2012/07
被引用回数：0 パーセンタイル：0.13(Physics, Applied)最近の実験で観測されたテラワットレーザーによるXUV領域の高次高調波の発生のメカニズムに関し、カタストロフィー理論を利用した船首波によるメカニズムを考案し、2DPIC計算と3DPIC計算によりその妥当性を確認した。これにより、この高次高調波生成メカニズムに基づいた、新しいXUV光及びX線源を提案した。
岡 潔; 関 健史; 赤津 朋宏
no journal, ,
原子力機構において技術開発を進めてきた複合型光ファイバは、高エネルギーと映像情報の両方を扱うことができる特殊なファイバである。この複合型光ファイバは、核融合炉及び大型原子力施設における保守保全技術開発に役立つ特殊ツールとして誕生した。原子炉内部の燃料集合体や熱交換器の伝熱配管など、本ファイバが役立つ狭隘箇所は数多くある。本技術は汎用性が高いため、現在では、種々の計測機器と統合された診断治療機器として医療分野への応用を積極的に推進中である。本報では、複合型光ファイバの基本構造及び医療分野への応用例について紹介する。
松本 淳; 高木 淳一*; 岩崎 憲治*
no journal, ,
We have developed a new approach to build a 3D atomic model from a single electron microscope (EM) image of a biomolecule. In this approach, the initial structure (X-ray crystal structure or modeled structure) of the molecule is deformed by computational techniques and many atomic models with different conformations are generated. The deformation is performed in such a way that the internal energy of the molecule does not increase so much. For this purpose, the lowest frequency normal modes are used in the deformation. Then, each atomic model is projected to many different directions, and each projection is fitted to the EM image and the fitting-score is calculated. The atomic models with high fitting-scores are the candidates that reproduce the EM image.
岩崎 憲治*; 高木 淳一*; 松本 淳
no journal, ,
受容体や細胞接着分子等、大きな細胞外領域を保有する膜タンパク質の構造は非常に柔軟で、中にはその機能との重要な相関を示唆する、大きなコンフォメーション変化を示すものも多い。こうした分子の構造は、電顕イメージング法では三次元構造を求めるのが非常に困難であり、得られたとしても低分解能で、生化学実験等に比して情報の乏しさは否めないものであった。そこで、二次元であれば、簡便にかつ迅速にその構造を吟味できることを提唱してきたが、その場合見た目に依存した主観的な議論にとどまることが常であった。今回、我々は、より客観的に解釈し、特定のアミノ酸配列についての吟味を可能にする方法を開発したのでここに報告する。電顕イメージに対して、そこに適切に当てはまるようにX線結晶構造解析で得られた原子座標を変化させるためには三次元であれ、二次元であれ解析イメージ自身に高い分解能が要求される。そこで松本らがこれまでに三次元用に開発した、あらかじめ様々に変化させた構造を発生させ、このうち最もよく当てはまるものを選出する方法を応用した。モデルタンパク質としてその詳細な構造と機能の相関が調べられているインテグリンavb3を用いて同方法を行ったところ、これまでの報告と一致する結果が得られた。そこで、異なるタンパク質やインテグリンにも適用し、生化学実験等で得られている結果と併せてその多様な構造が示す機能との相関を探った。
松本 淳; 高木 淳一*; 岩崎 憲治*
no journal, ,
We developed a method for comparing 2-D images to a pool of deformed atomic structures that reduces the susceptibility of subjective interpretation and is more expeditious than 3-D analysis. Firstly, we used normal mode analysis (NMA) in the context of an elastic network model to prepare a pool of deformed structures from coarse-grain (CG) structural models. Then, small deformations were applied to the model along low frequency normal modes. Both NMA and deformation were performed iteratively to build many different deformed atomic structures. 2-D images were then compared to these structures to objectively locate their model of best fit. The fitting-search is performed as a rigid body fitting, which works effectively for very noisy raw images as well as for molecules with a large conformational change. Our most representative example of this hybrid approach of using 2-D EM images and crystal structures has been the study of the integrin cell-adhesion molecules. Our hybrid method has allowed the investigation of the conformationally flexible integrins.
松本 淳; 高木 淳一*; 岩崎 憲治*
no journal, ,
We have developed a computational technique to build an atomic model from an electron microscopy (EM) image of a biological molecule. In this technique, many atomic models with different conformations of the molecule are prepared first by deforming the X-ray crystal structure or the modeled structure using a computational technique. Then, each atomic model is projected to many different directions and projection images are obtained. Finally, they are compared to the EM image. The atomic models with the projection images similar to the EM image are regarded as the candidates for the atomic structure of the molecule. This technique was applied to the EM images of integrin. Integrin is a membrane protein with a huge extracellular domain, and participates in cell-cell and cell-extracellular-matrix interactions. The X-ray crystal structure of the molecule is already solved. However, it is often very different form those seen in the EM images. By the conventional computational approach, it is difficult to reach the EM structure from the X-ray structure. Thus, we employed a coarse-grained model to simulate the large-scale conformational change.
河野 秀俊; 櫻庭 俊; 石田 恒
no journal, ,
Eukaryotic genome is compactly stored into a tiny nucleus of cell in the form of protein-DNA complex. This protein-DNA complex is called as nucleosome which is composed of a histone octamer formed by two copies each of the four core histones H3, H4, H2A and H2B and about 150 bp of DNA wrapping almost twice around the octamer. This compact form, however, has to be unwrapped in transcription, DNA duplication and DNA repair processes. To study the detailed molecular mechanism, free energy profiles for unwrapping nucleosomal DNA on several nucleosomes were calculated. So far, we estimated that a cost for unwrapping the outer DNA is 0.1 to 0.4 kcal/mol/1bp, consistent with a value experimentally obtained. In the meeting, we will report the cost for unwrapping the inner DNA.
松本 淳; 高木 淳一*; 岩崎 憲治*
no journal, ,
We have been developing a new computational approach to build a 3D atomic model from an electron microscope (EM) image of a biological molecule. In the usual approach, a 3D-EM model is constructed from many EM images. Then, a 3D atomic model is built mainly by deforming the X-ray crystal structure so that it fits into the 3D-EM model better. Our approach, on the other hand, uses only a single EM image (or an averaged image) and an X-ray crystal structure (or a modeled structure), and has the advantage of being applicable even to flexible molecules, for which it is difficult to construct 3D-EM models. We will report the results about the application to integrins, transmembrane proteins that involved in cell-cell and cell-extracellular matrix adhesions.
松本 淳; 高木 淳一*; 岩崎 憲治*
no journal, ,
We are developing a new computational approach to build a 3D atomic model from an electron microscope (EM) image of a biological molecule. In the usual approach, a 3D-EM model is constructed from many EM images. Then, a 3D atomic model is built mainly by deforming the X-ray crystal structure so that it fits into the 3D-EM model better. Our approach, on the other hand, uses only a single EM image (or an averaged image) and an X-ray crystal structure (or a modeled structure), and has the advantage of being applicable even to flexible molecules, for which it is difficult to construct 3D-EM models. We applied this approach to integrins, transmembrane proteins that involved in cell-cell and cell-extracellular matrix adhesions.
松本 淳
no journal, ,
We have developed a computational approach to build an atomic model from an electron microscopy (EM) image of a biological molecule. In this approach, many atomic models of the molecule with different conformations are prepared first by deforming the X-ray crystal structure or the modeled structure using a computational technique. Then, a variety of orientations is given to each atomic model to obtain projection images. Finally, the projection images are compared to the EM image. The atomic models with the projection similar to the EM image are regarded as the candidates for the atomic structure of the molecule. In the symposium, the application to the giant cadherin proteins, which are involved in the cell adhesion, will be explained.
