A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein
文献类型：期刊论文
| 作者 | Liu, Wei1; Zhang, Jingfeng1,3; Fan, Jing-Song1; Tria, Giancarlo2; Gruber, Gerhard2; Yang, Daiwen1 |
| 刊名 | BIOPHYSICAL JOURNAL
 |
| 出版日期 | 2016-05-10 |
| 卷号 | 110期号:9页码:1943-1956 |
| 英文摘要 | Structure ensemble determination is the basis of understanding the structure-function relationship of a multi domain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biophysics |
| 研究领域[WOS] | Biophysics |
| 关键词[WOS] | PARAMAGNETIC RELAXATION ENHANCEMENT ; MOLECULAR-STRUCTURE DETERMINATION ; RAY SOLUTION SCATTERING ; NMR-SPECTROSCOPY ; BIOLOGICAL MACROMOLECULES ; CONFORMATIONAL SELECTION ; SACCHAROMYCES-CEREVISIAE ; MULTIDOMAIN PROTEIN ; XPLOR-NIH ; STATES |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000375896400005 |
| 源URL | [http://ir.wipm.ac.cn/handle/112942/9343]  |
| 专题 | 武汉物理与数学研究所_磁共振基础研究部 |
| 作者单位 | 1.Natl Univ Singapore, Dept Biol Sci, Singapore 117548, Singapore 2.Nanyang Technol Univ, Sch Biol Sci, Singapore 639798, Singapore 3.Chinese Acad Sci, Wuhan Inst Phys & Math, State Key Lab Magnet Resonance & Atom & Mol Phys, Wuhan, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Wei,Zhang, Jingfeng,Fan, Jing-Song,et al. A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein[J]. BIOPHYSICAL JOURNAL,2016,110(9):1943-1956. |
| APA | Liu, Wei,Zhang, Jingfeng,Fan, Jing-Song,Tria, Giancarlo,Gruber, Gerhard,&Yang, Daiwen.(2016).A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.BIOPHYSICAL JOURNAL,110(9),1943-1956. |
| MLA | Liu, Wei,et al."A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein".BIOPHYSICAL JOURNAL 110.9(2016):1943-1956. |
入库方式： OAI收割
来源：武汉物理与数学研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。