title: Analysis of chameleon sequences and their implications in biological processes.
abstract: Chameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon-HS (Helix vs. Strand) and chameleon-HE (Helix vs. Sheet), based on known structures in Protein Data Bank. Our survey shows that the longest chameleon-HS is eight residues while the longest chameleon-HE is seven residues. We have done a detailed analysis on the local and global environment that might contribute to the unique conformation of a chameleon sequence. We found that the existence of chameleon sequences does not present a problem for secondary structure prediction programs, including the first generation prediction programs, such as Chou-Fasman algorithm, and the third generation prediction programs that utilize evolution information. We have also investigated the possible implication of chameleon sequences in structural conservation and functional diversity of alternatively spliced protein isoforms.
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.
authors.forename: Jun-Tao
authors.initials: JT
authors.lastname: Guo
authors.forename: Jerzy W
authors.initials: JW
authors.lastname: Jaromczyk
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D015094:3-Hydroxyacyl CoA Dehydrogenases / Q000737:chemistry; D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D009842:Oligopeptides; D015094:3-Hydroxyacyl CoA Dehydrogenases; C108634:HSD17B10 protein, human