Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol | |
Shang, Xu1; Guan, Zhen1; Zhang, Shuai1,2; Shi, Lulin1,2; You, Haihang1 | |
刊名 | PHYSICAL CHEMISTRY CHEMICAL PHYSICS |
2021-03-28 | |
卷号 | 23期号:12页码:7066-7079 |
ISSN号 | 1463-9076 |
DOI | 10.1039/d0cp05003b |
英文摘要 | Aptamers (small single strand DNA/RNAs) such as SYL3C are considered as ideal alternatives to antibodies in cancer related research studies. However, 3D structure predictions for aptamers and aptamer-protein complexes are scarce due to the high cost of experimental measurements and unreliable computer-based methods. Thus aptamers' diagnostic and therapeutic applications are severely restricted. To meet the challenge, we proposed a Martini-based aptamer-protein complex prediction protocol. By combining the base-base contact map from simulation and secondary structure prediction from various tools, improved secondary structure predictions can be obtained. This method reduced the risk of providing incorrect or incomplete base pairs in secondary structure prediction. Thus 3D structure modeling based on the secondary structure can be more reliable. We introduced the soft elastic network to the hairpin folded regions of the Martini ssDNAs to preserve their canonical structure. Using our protocol, we predicted the first 3D structure of the aptamer SYL3C and the SYL3C-EpCAM complex. We believe that our work could contribute to the future aptamer-related research studies and medical implications. |
资助项目 | National Natural Science Foundation of China[11801541] |
WOS研究方向 | Chemistry ; Physics |
语种 | 英语 |
出版者 | ROYAL SOC CHEMISTRY |
WOS记录号 | WOS:000635798200048 |
内容类型 | 期刊论文 |
源URL | [http://119.78.100.204/handle/2XEOYT63/16708] |
专题 | 中国科学院计算技术研究所 |
通讯作者 | You, Haihang |
作者单位 | 1.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100190, Peoples R China |
推荐引用方式 GB/T 7714 | Shang, Xu,Guan, Zhen,Zhang, Shuai,et al. Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol[J]. PHYSICAL CHEMISTRY CHEMICAL PHYSICS,2021,23(12):7066-7079. |
APA | Shang, Xu,Guan, Zhen,Zhang, Shuai,Shi, Lulin,&You, Haihang.(2021).Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol.PHYSICAL CHEMISTRY CHEMICAL PHYSICS,23(12),7066-7079. |
MLA | Shang, Xu,et al."Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol".PHYSICAL CHEMISTRY CHEMICAL PHYSICS 23.12(2021):7066-7079. |
个性服务 |
查看访问统计 |
相关权益政策 |
暂无数据 |
收藏/分享 |
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。
修改评论