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A reinforced merging methodology for mapping unique peptide motifs in members of protein families

BACKGROUND: Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common ca...

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Autores principales: Chang, Hao-Teng, Pai, Tun-Wen, Fan, Tan-chi, Su, Bo-Han, Wu, Pei-Chih, Tang, Chuan-Yi, Chang, Chun-Tien, Liu, Shi-Hwei, Chang, Margaret Dah-Tsyr
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369005/
https://www.ncbi.nlm.nih.gov/pubmed/16433931
http://dx.doi.org/10.1186/1471-2105-7-38
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author Chang, Hao-Teng
Pai, Tun-Wen
Fan, Tan-chi
Su, Bo-Han
Wu, Pei-Chih
Tang, Chuan-Yi
Chang, Chun-Tien
Liu, Shi-Hwei
Chang, Margaret Dah-Tsyr
author_facet Chang, Hao-Teng
Pai, Tun-Wen
Fan, Tan-chi
Su, Bo-Han
Wu, Pei-Chih
Tang, Chuan-Yi
Chang, Chun-Tien
Liu, Shi-Hwei
Chang, Margaret Dah-Tsyr
author_sort Chang, Hao-Teng
collection PubMed
description BACKGROUND: Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family. RESULTS: We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope. CONCLUSION: Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family.
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spelling pubmed-13690052006-04-21 A reinforced merging methodology for mapping unique peptide motifs in members of protein families Chang, Hao-Teng Pai, Tun-Wen Fan, Tan-chi Su, Bo-Han Wu, Pei-Chih Tang, Chuan-Yi Chang, Chun-Tien Liu, Shi-Hwei Chang, Margaret Dah-Tsyr BMC Bioinformatics Methodology Article BACKGROUND: Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family. RESULTS: We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope. CONCLUSION: Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family. BioMed Central 2006-01-25 /pmc/articles/PMC1369005/ /pubmed/16433931 http://dx.doi.org/10.1186/1471-2105-7-38 Text en Copyright © 2006 Chang et al; licensee BioMed Central Ltd.
spellingShingle Methodology Article
Chang, Hao-Teng
Pai, Tun-Wen
Fan, Tan-chi
Su, Bo-Han
Wu, Pei-Chih
Tang, Chuan-Yi
Chang, Chun-Tien
Liu, Shi-Hwei
Chang, Margaret Dah-Tsyr
A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title_full A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title_fullStr A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title_full_unstemmed A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title_short A reinforced merging methodology for mapping unique peptide motifs in members of protein families
title_sort reinforced merging methodology for mapping unique peptide motifs in members of protein families
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369005/
https://www.ncbi.nlm.nih.gov/pubmed/16433931
http://dx.doi.org/10.1186/1471-2105-7-38
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