Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces

doi:10.1186/s12859-016-1410-1

CSpace > 应用数学研究所

	Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces
	Liu, Zhi-Ping 1; Liu, Shutang 1; Chen, Ruitang 2; Huang, Xiaopeng 3,4,5; Wu, Ling-Yun3,4,5
	2017-01-11
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	18 页码:13
摘要	Background: Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recognition mechanisms and benefit complementary structural design in bioengineering. RNA-binding events often take place at pockets on protein surfaces. The structural classification of local binding pockets determines the major patterns of RNA recognition. Results: In this work, we provide a novel framework for systematically identifying the structure motifs of protein-RNA binding sites in the form of pockets on regional protein surfaces via a structure alignment-based method. We first construct a similarity network of RNA-binding pockets based on a non-sequential-order structure alignment method for local structure alignment. By using network community decomposition, the RNA-binding pockets on protein surfaces are clustered into groups with structural similarity. With a multiple structure alignment strategy, the consensus RNA-binding pockets in each group are identified. The crucial recognition patterns, as well as the protein-RNA binding motifs, are then identified and analyzed. Conclusions: Large-scale RNA-binding pockets on protein surfaces are grouped by measuring their structural similarities. This similarity network-based framework provides a convenient method for modeling the structural relationships of functional pockets. The local structural patterns identified serve as structure motifs for the recognition with RNA on protein surfaces.
关键词	RNA-binding pocket Local structure classification Structural alignment Network clustering Structure motif
DOI	10.1186/s12859-016-1410-1
语种	英语
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13040600] ; National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences ; National Natural Science Foundation of China (NSFC)[61533011] ; National Natural Science Foundation of China (NSFC)[61572287] ; National Natural Science Foundation of China (NSFC)[31100949] ; National Natural Science Foundation of China (NSFC)[11131009] ; National Natural Science Foundation of China (NSFC)[11631014] ; National Natural Science Foundation of China (NSFC)[91330114] ; Shandong Provincial Natural Science Foundation of China[ZR2015FQ001] ; Fundamental Research Funds of Shandong University[2014 TB006] ; Fundamental Research Funds of Shandong University[2015QY001] ; Fundamental Research Funds of Shandong University[2016JC007] ; Scientific Research Foundation for Returned Overseas Chinese Scholars, Ministry of Education of China
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000392170800003
出版者	BIOMED CENTRAL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/363
专题	应用数学研究所
通讯作者	Wu, Ling-Yun
作者单位	1.Shandong Univ, Sch Control Sci & Engn, Dept Biomed Engn, Jinan 250061, Shandong, Peoples R China 2.Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA 3.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing 100190, Peoples R China 4.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Liu, Zhi-Ping,Liu, Shutang,Chen, Ruitang,et al. Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces[J]. BMC BIOINFORMATICS,2017,18:13.
APA	Liu, Zhi-Ping,Liu, Shutang,Chen, Ruitang,Huang, Xiaopeng,&Wu, Ling-Yun.(2017).Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces.BMC BIOINFORMATICS,18,13.
MLA	Liu, Zhi-Ping,et al."Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces".BMC BIOINFORMATICS 18(2017):13.