Molecular dynamics simulations and free energy calculations of a novel series of protein tyrosine phosphatase 1b difluoromethylenephosphonic acid inhibitors
文献类型：期刊论文
| 作者 | Cui Wei1; Zhang Huai2; Ji Ming-Juan1 |
| 刊名 | Acta physico-chimica sinica
 |
| 出版日期 | 2009-04-01 |
| 卷号 | 25期号:4页码:668-676 |
| 关键词 | Protein tyrosine phosphatase 1b Molecular dynamics simulation Free energy calculation Free energy decomposition Mm/gbsa |
| ISSN号 | 1000-6818 |
| DOI | 10.3866/pku.whxb200904271 |
| 通讯作者 | Ji ming-juan(jmj@gucas.ac.cn) |
| 英文摘要 | Binding models for a series of difluoromethylenephosphonic (dfmp) and difluoromethylenesulfonic (dfms) acids to protein tyrosine phosphatase 1b (ptp1b) were studied by molecular docking, molecular dynamics (md) simulations, and free energy calculations. binding free energies were computed using the molecular mechanics/generalized born surface area (mm/gbsa) methodology based on 1 ns md simulations. the order of affinities for the studied inhibitors can be accurately predicted using previously predicted binding free energies. inhibitor/residue interaction profiles for all inhibitors were systematically generated using mm/gbsa free energy decomposition analysis. inhibitor/residue interaction profiles demonstrated that electrostatic interactions between the negative charge center of dfmp/dfms groups and arg221 of ptp1b are a crucial part of the studied molecule affinities. furthermore, the fluorine atom or other hydrogen bonding donor atoms with appropriate radii will improve inhibitor binding to the primary binding site of ptp1b. |
| WOS关键词 | PTP-1B INHIBITORS ; FORCE-FIELD ; SH3 DOMAIN ; BINDING ; POTENT ; DESIGN ; PTP1B ; DOCKING ; RESISTANCE ; MECHANICS |
| WOS研究方向 | Chemistry |
| WOS类目 | Chemistry, Physical |
| 语种 | 英语 |
| WOS记录号 | WOS:000265197400012 |
| 出版者 | PEKING UNIV PRESS |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2402605 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Ji Ming-Juan |
| 作者单位 | 1.Chinese Acad Sci, Grad Univ, Coll Chem & Chem Engn, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Grad Univ, Lab Computat Geodynam, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Cui Wei,Zhang Huai,Ji Ming-Juan. Molecular dynamics simulations and free energy calculations of a novel series of protein tyrosine phosphatase 1b difluoromethylenephosphonic acid inhibitors[J]. Acta physico-chimica sinica,2009,25(4):668-676. |
| APA | Cui Wei,Zhang Huai,&Ji Ming-Juan.(2009).Molecular dynamics simulations and free energy calculations of a novel series of protein tyrosine phosphatase 1b difluoromethylenephosphonic acid inhibitors.Acta physico-chimica sinica,25(4),668-676. |
| MLA | Cui Wei,et al."Molecular dynamics simulations and free energy calculations of a novel series of protein tyrosine phosphatase 1b difluoromethylenephosphonic acid inhibitors".Acta physico-chimica sinica 25.4(2009):668-676. |
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来源：中国科学院大学
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