Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol

doi:10.1039/d0cp05003b

	Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol
	Shang, Xu 1; Guan, Zhen 1; Zhang, Shuai 1,2; Shi, Lulin 1,2; You, Haihang 1
	2021-03-28
发表期刊	PHYSICAL CHEMISTRY CHEMICAL PHYSICS
ISSN	1463-9076
卷号	23 期号:12 页码:7066-7079
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.
DOI	10.1039/d0cp05003b
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[11801541]
WOS研究方向	Chemistry ; Physics
WOS类目	Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS记录号	WOS:000635798200048
出版者	ROYAL SOC CHEMISTRY
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/16709
专题	中国科学院计算技术研究所期刊论文_英文
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.