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

文献类型：期刊论文

作者Liu, Zhi-Ping1; Liu, Shutang1; Chen, Ruitang2; Huang, Xiaopeng3,4,5; Wu, Ling-Yun3,4,5
刊名BMC BIOINFORMATICS
出版日期2017-01-11
卷号18页码:13
关键词RNA-binding pocket Local structure classification Structural alignment Network clustering Structure motif
ISSN号1471-2105
DOI10.1186/s12859-016-1410-1
英文摘要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.
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
语种英语
WOS记录号WOS:000392170800003
出版者BIOMED CENTRAL LTD
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/362]  
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.

入库方式： OAI收割

来源：数学与系统科学研究院

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