Folding Simulations of a De Novo Designed Protein with a beta alpha beta Fold
文献类型：期刊论文
| 作者 | Qi, Yifei; Huang, Yongqi; Liang, Huanhuan; Liu, Zhirong1; Lai, Luhua |
| 刊名 | BIOPHYSICAL JOURNAL
 |
| 出版日期 | 2010-01-20 |
| 卷号 | 98期号:2页码:321-329 |
| ISSN号 | 0006-3495 |
| DOI | 10.1016/j.bpj.2009.10.018 |
| 英文摘要 | beta alpha beta structural motifs are commonly used building blocks in protein structures containing parallel beta-sheets. However, to our knowledge, no stand-alone beta alpha beta structure has been observed in nature to date. Recently, for the first time that we know of, a small protein with an independent beta alpha beta structure (DS119) was successfully designed in our laboratory. To understand the folding mechanism of DS119, in the study described here, we carried out all-atom molecular dynamics and coarse-grained simulations to investigate its folding pathways and energy landscape. From all-atom simulations, we successfully observed the folding event and got a stable folded structure with a minimal root mean-square deviation of 2.6 angstrom with respect to the NMR structure. The folding process can be described as a fast collapse phase followed by rapid formation of the central helix, and then slow formation of a parallel beta-sheet. By using a native-centric Go-like model, the cooperativity of the system was characterized in terms of the calorimetric criterion, sigmoidal transitions, conformation distribution shifts, and free-energy profiles. DS119 was found to be an incipient downhill folder that folds more cooperatively than a downhill folder, but less cooperatively than a two-state folder. This may reflect the balance between the two structural elements of DS119: the rapidly formed a-helix and the slowly formed parallel beta-sheet. Folding times estimated from both the all-atom simulations and the coarse-grained model were at microsecond level, making DS119 another fast folder. Compared to fast folders reported previously, DS119 is, to the best of our knowledge, the first that exhibits a parallel beta-sheet. |
| 语种 | 英语 |
| WOS记录号 | WOS:000273972700016 |
| 出版者 | CELL PRESS |
| 源URL | [http://ir.iccas.ac.cn/handle/121111/69641]  |
| 专题 | 中国科学院化学研究所 |
| 通讯作者 | Liu, Zhirong |
| 作者单位 | 1.Peking Univ, Beijing Natl Lab Mol Sci, State Key Lab Struct Chem Unstable & Stable Speci, Coll Chem & Mol Engn, Beijing 100871, Peoples R China 2.Peking Univ, Ctr Theoret Biol, Beijing 100871, Peoples R China |
| 推荐引用方式 GB/T 7714 | Qi, Yifei,Huang, Yongqi,Liang, Huanhuan,et al. Folding Simulations of a De Novo Designed Protein with a beta alpha beta Fold[J]. BIOPHYSICAL JOURNAL,2010,98(2):321-329. |
| APA | Qi, Yifei,Huang, Yongqi,Liang, Huanhuan,Liu, Zhirong,&Lai, Luhua.(2010).Folding Simulations of a De Novo Designed Protein with a beta alpha beta Fold.BIOPHYSICAL JOURNAL,98(2),321-329. |
| MLA | Qi, Yifei,et al."Folding Simulations of a De Novo Designed Protein with a beta alpha beta Fold".BIOPHYSICAL JOURNAL 98.2(2010):321-329. |
入库方式： OAI收割
来源：化学研究所
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。