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Coarse-grained Simulation of Azurin Crystal Complex System: Protein–protein Interactions
https://doi.org/10.24517/00011975
https://doi.org/10.24517/00011975004fe658-289f-4ba9-a09f-1b7613a8cdb6
名前 / ファイル | ライセンス | アクション |
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ISCS2013Proceedings-79-86.pdf (455.0 kB)
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Item type | 報告書 / Research Paper(1) | |||||
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公開日 | 2017-10-03 | |||||
タイトル | ||||||
タイトル | Coarse-grained Simulation of Azurin Crystal Complex System: Protein–protein Interactions | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_18ws | |||||
資源タイプ | research report | |||||
ID登録 | ||||||
ID登録 | 10.24517/00011975 | |||||
ID登録タイプ | JaLC | |||||
著者別表示 |
高須, 昌子
× 高須, 昌子× 川口, 一朋× 齋藤, 大明× 長尾, 秀実 |
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書誌情報 |
Recent development in computational science : Selected Papers from the International Symposium on Computational Science - International Symposium on Computational Science Kanazawa University, Japan 巻 4, p. 79-86, 発行日 2013-02-01 |
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ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 2223-0785 | |||||
出版者 | ||||||
出版者 | Kanazawa e-Publishing | |||||
抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | Most of protein function analyses focus mainly on the physical properties of a sin-gle protein. Nevertheless, the environments where proteins perform their biological functions are crowded with macromolecules, such as lipid, nucleic acids, and other proteins. The interactions between macromolecules may be affected by molecular crowding. Therefore, as an initial step we here investigate the protein–protein interactions for gaining insights into molecular crowding effects on protein conformational changes. Computational molecular simulation is one of the useful and important tools to study the protein interactions. Here we develop a coarse-grained model and a topology-based potential interactions to simulate dynamical properties of multiprotein complex crys-tal structure. We apply them to simulate complex crystal structure of Pseudomonas Aeruginosa azurin, a small cupredoxin, which functions as an electron carrier in bacterial respiration. Since electron transfer on azurin plays an important role in the biological system, it is important to cha-racterize the protein interactions in azurin. In our simulation, the interactions between intra- and inter- domains are treated at the residue level with the implementation of the off lattice G¯o-like model. In each domain, bonded interactions between residues are described by bond stretching, bond angle bending, and torsional angle potentials. The non-bonded interactions, which are repre-sented by short range and long range potentials, describe the interactions both among residues and between proteins. We probe the protein–protein interactions by analyzing the protein binding. A simple clustering algorithm is applied to group the bound structures of protein complex. Moreover, we can investigate the importance of the long range interaction on the multiprotein complex system. These studies will serve as valuable insights for further investigation on molecular crowding effects. | |||||
権利 | ||||||
権利情報 | Organizing Committee of ISCS 2013 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |