Author: Zhou, Y.; Yang, W.; Kirberger, M.; Lee, H.-W.; Ayalasomayajula, G.; Yang, J.J.
Description: The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N- and C-terminal EF-hands within S100 and S100-like proteins, a new signature profile has been established to allow for the identification of pseudo EF-hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF-hands. Furthermore, using the developed patterns, we have identified zero pseudo EF-hand motif and 467 canonical EF-hand Ca(2+) binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF-hand motifs are phylogenetically younger than canonical EF-hand motifs. Our prediction of Ca(2+) binding motifs provides not only an insight into the role of Ca(2+) and Ca(2+)-binding proteins in bacterial systems, but also a way to explore and define the role of Ca(2+) in other biological systems (calciomics).
Subject headings: Amino Acid Motifs; Amino Acid Sequence; Animals; Bacterial Proteins/chemistry/metabolism; Calcium-Binding Proteins/chemistry; EF Hand Motifs/genetics; Evolution, Molecular; Humans; Models, Molecular; Molecular Sequence Data; Phylogeny; Sequence Alignment
Publication year: 2006
Journal or book title: Proteins
Volume: 65
Issue: 3
Pages: 643-655
Find the full text: http://onlinelibrary.wiley.com/doi/10.1002/prot.21139/abstract
Find more like this one (cited by): https://scholar.google.com/scholar?cites=16259536373594132095&as_sdt=1000005&sciodt=0,16&hl=en
Type: Journal Article
Serial number: 415