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 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 Smaand-Mad related protein families (Smad). The UPMs generally occupy specif...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Hao-Teng Chang, Tun-Wen Pai, Tan-Chi Fan, Bo-Han Su, Pei-Chih Wu, Chuan Yi Tang, Chun-Tien Chang, Shi-Hwei Liu, Margaret Dah-Tsyr Chang
• Keywords: BMCBI 2006, Protein, Protein Family, Protein Sequence