Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation
文献类型：期刊论文
| 作者 | Liu SQ1; Shi XF2; Liu CQ2; Sun ZR[*]1 |
| 刊名 | JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM
 |
| 出版日期 | 2004 |
| 卷号 | 673期号:1-3页码:133-143 |
| 关键词 | CCR5 molecular dynamics simulation extracellular domains disulfide bond interaction ligand binding |
| ISSN号 | 0166-1280 |
| 通讯作者 | shuqunliu@tsinghua.org.cn |
| 合作状况 | 其它 |
| 英文摘要 | The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. |
| 收录类别 | SCI |
| 原文出处 | 2004673133.pdf |
| 语种 | 英语 |
| 公开日期 | 2010-08-24 |
| 源URL | [http://159.226.149.42:8088/handle/152453/5321]  |
| 专题 | 昆明动物研究所_其他 昆明动物研究所_细胞与分子进化重点实验室 |
| 作者单位 | 1.Department of Biological Sciences and Biotechnology, Institute of Bioinformatics, Tsinghua University, Beijing 100084, China 2.Cellular and Molecular Evolutionary Key Laboratory, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China |
| 推荐引用方式 GB/T 7714 | Liu SQ,Shi XF,Liu CQ,et al. Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation[J]. JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM,2004,673(1-3):133-143. |
| APA | Liu SQ,Shi XF,Liu CQ,&Sun ZR[*].(2004).Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation.JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM,673(1-3),133-143. |
| MLA | Liu SQ,et al."Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation".JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 673.1-3(2004):133-143. |
入库方式： OAI收割
来源：昆明动物研究所
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