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The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains
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 s...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576256/ https://www.ncbi.nlm.nih.gov/pubmed/18828911 http://dx.doi.org/10.1186/1471-2164-9-452 |
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author | Ren, Siyuan Yang, Guang He, Youyu Wang, Yiguo Li, Yixue Chen, Zhengjun |
author_facet | Ren, Siyuan Yang, Guang He, Youyu Wang, Yiguo Li, Yixue Chen, Zhengjun |
author_sort | Ren, Siyuan |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2576256 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25762562008-10-31 The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains Ren, Siyuan Yang, Guang He, Youyu Wang, Yiguo Li, Yixue Chen, Zhengjun BMC Genomics Research Article 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. BioMed Central 2008-10-01 /pmc/articles/PMC2576256/ /pubmed/18828911 http://dx.doi.org/10.1186/1471-2164-9-452 Text en Copyright © 2008 Ren et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Ren, Siyuan Yang, Guang He, Youyu Wang, Yiguo Li, Yixue Chen, Zhengjun The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title | The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title_full | The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title_fullStr | The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title_full_unstemmed | The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title_short | The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
title_sort | conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576256/ https://www.ncbi.nlm.nih.gov/pubmed/18828911 http://dx.doi.org/10.1186/1471-2164-9-452 |
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