| 引用本文: | 王 浩,徐利楠,孙玉娜,沈曼莉,薛友林,李 辉,宋有涛.Ydj1p二聚体中β14~β15与domain-III分离的拉伸分子动力学模拟研究[J].生物信息学,2013,11(3):167-171. |
| WANG Hao,XU Li-nan,SUN Yu-na,SHEN Man-li,XUE You-lin,LI Hui,SONG You-tao.Steered molecular dynamics simulation of the binding of β14~β15and domain-III in Ydj1p dimer[J].Chinese Journal of Bioinformatics,2013,11(3):167-171. |
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| Ydj1p二聚体中β14~β15与domain-III分离的拉伸分子动力学模拟研究 |
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王 浩1,徐利楠1,孙玉娜1,沈曼莉2,薛友林3,李 辉1,宋有涛1,2
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(1. 辽宁大学生命科学院, 辽宁 沈阳 110036; ;2. 辽宁大学环境学院, 辽宁 沈阳 110036; ;3. 辽宁大学轻型产业学院, 辽宁 沈阳 110036)
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| 摘要: |
| 分子伴侣Hsp40是一种以二聚体的形式调控非天然多肽折叠的热激蛋白。本文通过拉伸分子动力学研究了酵母Hsp40家族成员Ydj1p二聚体中β14~β15与domain-III的分离过程,深入探讨了影响Ydj1p二聚体稳定性的重要残基和相互作用力。研究表明,残基Thr366、Asp368、Cys370、Leu372和Phe375在Ydj1p二聚体的形成过程中发挥着重要的作用。其中,β14~β15中的残基Thr366和Asp368分别通过与domain-III内的残基Asp291、Trp292和Trp292、Lys294之间形成的氢键,Asp368通过与domain-III内的残基Lys314形成盐桥,Cys370、Leu372和Phe375则是通过与domain-III形成疏水作用力来稳定Ydj1p二聚体结构。 |
| 关键词: 分子伴侣 Hsp40 Ydj1p 二聚体 拉伸分子动力学 |
| DOI：10.3969/j.issn.1672-5565.2013-03.20130302 |
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| 基金项目:国家自然科学基金(30970152),辽宁省教育厅优秀人才项目(2009R26)资助。 |
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| Steered molecular dynamics simulation of the binding of β14~β15and domain-III in Ydj1p dimer |
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WANG Hao1, XU Li-nan1, SUN Yu-na1, SHEN Man-li2, XUE You-lin3, LI Hui1, SONG You-tao1,2
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(1.College of Life Science, Liaoning University, Shenyang 110036, China; ;2.School of Environmental Science, Liaoning University, Shenyang 110036, China; ;3. College of Light Industry, Liaoning University, Shenyang 110036, China)
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| Abstract: |
| The molecular chaperone Hsp40functions as a dimer to regulate non-native polypeptides folding. In this study, we have performed steered molecular dynamics (SMD) simulation to investigate the dissociation process between the β14~β15and domain III in yeast Hsp40homologue Ydj1p C-terminal dimer, and further investigate the important residues and intermolecular interactions that influencing Ydj1p dimer stability. Our data indicate that residues Thr366、Asp368、Cys370、Leu372and Phe375is critical for Ydj1p dimer formation:Residues Thr366and Asp368form hydrogen bond with residues Asp291, Trp292and Trp292, Lys294respectively. Residue Asp368forms salt bridge with residue Lys314, and residues Cys370, Leu37and Residue Cys370、Leu372and Phe375form hydrophobic interaction with certain residues in domain-III to stabilize Ydji1p dimer structure. |
| Key words: Molecular Chaperone Hsp40 Ydj1p Dimer Steered Molecular Dynamics |
