Prediction of Protein-Glycan Structure Complex with Low Binding Affinity
| Project/Area Number |
25540138
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| Research Category |
Grant-in-Aid for Challenging Exploratory Research
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| Allocation Type | Single-year Grants |
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| Research Field |
Life / Health / Medical informatics
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
SUGITA Yuji 独立行政法人理化学研究所, 杉田理論分子科学研究室, 主任研究員 (80311190)
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| Co-Investigator(Kenkyū-buntansha) |
RE Suyong 理化学研究所, 杉田理論分子科学研究室, 研究員 (50390670)
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| Co-Investigator(Renkei-kenkyūsha) |
YAMAGUCHI Yoshiki 理化学研究所, 糖鎖構造生物学研究チーム, チームリーダー (90323451)
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| Project Period (FY) |
2013-04-01 – 2014-03-31
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| Project Status |
Completed (Fiscal Year 2013)
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| Budget Amount *help |
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2013: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
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| Keywords | 分子シミュレーション / 糖鎖複合体 / 自由エネルギー計算 / 分子認識 / レクチンOS9 / タンパク質ーリガンド認識 / 低親和性複合体構造予測 / 糖鎖 / レクチン / レプリカ交換分子動力学法 / CMAP補正 |
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| Research Abstract |
Protein-ligand interaction is essential for numerous biological functions. We focused on the biding of a flexible ligand as glycan and built a computational basis for the prediction of weekly bound protein-ligand complexes. We have developed the CMAP correction for glycans based on the original CHARMM force field and tested for small models using the replica-exchange umbrella sampling method. The results show that new CMAP correction gives better description of glycan conformations compared with the original CHARMM force field. We have also examined the N-glycan binding of OS9 lectin by using the conventional molecular dynamics simulation. The results show the importance of WW motif as suggested by the experiment, but imply the presence of other factors governing the binding affinity of OS9-glycan interactions. These outcomes are all relevant to develop the computational method for the prediction of weekly bound protein-ligand complex structures.
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Report
(2 results)
Research Products
(12 results)
