The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

	The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains
	Ren, SY; Yang, G; He, YY; Wang, YG; Li, YX; Chen, ZJ
刊名	BMC GENOMICS
	2008
卷号	9 期号:1 页码:452-452
通讯作者	Chen, ZJ (reprint author), Chinese Acad Sci, Inst Biochem & Cell Biol, State Key Lab Mol Biol, Shanghai, Peoples R China.,rsysjtu@hotmail.com ; gyang@sibs.ac.cn ; yyhe@sibs.ac.cn ; wangyg@sibs.ac.cn ; yxli@sibs.ac.cn ; zjchen@sibs.ac.cn
英文摘要	Background: Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Results: Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion: The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.
学科主题	Biotechnology & Applied Microbiology; Genetics & Heredity
类目[WOS]	Biotechnology & Applied Microbiology ; Genetics & Heredity
关键词[WOS]	EUKARYOTIC PROTEINS ; REFERENCE DATABASE ; TYROSINE KINASE ; WIDE PREDICTION ; SRC KINASE ; PHOSPHORYLATION ; ACTIN ; PHOSPHATASES ; SPECIFICITY ; DISCOVERY
收录类别	SCI
语种	英语
WOS记录号	WOS:000260678100002
内容类型	期刊论文
版本	出版稿
源URL	[http://202.127.25.143/handle/331003/1487]
专题	上海生化细胞研究所_上海生科院生化细胞研究所
推荐引用方式 GB/T 7714	Ren, SY,Yang, G,He, YY,et al. The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains[J]. BMC GENOMICS,2008,9(1):452-452.
APA	Ren, SY,Yang, G,He, YY,Wang, YG,Li, YX,&Chen, ZJ.(2008).The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.BMC GENOMICS,9(1),452-452.
MLA	Ren, SY,et al."The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains".BMC GENOMICS 9.1(2008):452-452.