Unique peptide identification of RNase A superfamily sequences based on reinforced merging algorithms.
Human ribonuclease A (RNaseA) superfamily consists of eight RNases with high similarity in which RNase2 and RNase3 share 76.7% identity. The evolutionary variation of RNases results in differential structures and functions of the enzymes. To distinguish the characteristics of each RNase, we developed reinforced merging algorithms (RMA) to rapidly identify the unique peptide motifs for each member of the highly conserved human RNaseA superfamily. Many motifs in RNase3 identified by RMA correlated well with the antigenic regions predicted by DNAStar. Two unique peptide motifs were experimentally confirmed to contain epitopes for monoclonal antibodies (mAbs) specifically against RNase3. Further analysis of homologous RNases in different species revealed that the unique peptide motifs were located at the correspondent positions, and one of these motifs indeed matched the epitope for a specific anti-bovine pancreatic RNaseA (bpRNaseA) antibody. Our method provides a useful tool for identification of unique peptide motifs for further experimental design. The RMA system is available and free for academic use at http://bioinfo.life.nthu.edu.tw/rma/ and http://spider.cs.ntou.edu.tw/bioinformatics/RMA.html.
Pai
Tun-Wen
TW
Department of Computer Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung, Taiwan 20224, ROC. twp@mail.ntou.edu.tw
Su
Bo-Han
BH
Wu
Pei-Chih
PC
Chang
Margaret Dah-Tsyr
MD
Chang
Hao-Teng
HT
Fan
Tan-Chi
TC
Liu
Shi-Hwei
SH
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal; D000918:Antibody Specificity; D002417:Cattle; D019295:Computational Biology; D018604:Epitope Mapping / Q000706:statistics & numerical data; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D012259:Ribonuclease, Pancreatic / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D020539:Sequence Analysis, Protein / Q000706:statistics & numerical data
D000911:Antibodies, Monoclonal; D010455:Peptides; D012259:Ribonuclease, Pancreatic