Analysis of chameleon sequences and their implications in biological processes

作者：Jun‐tao Guo, Jerzy W. Jaromczyk, Ying Xu · 发表于：Proteins Structure Function and Bioinformatics · 年份：2007 · DOI：10.1002/prot.21285 · 被引用次数：52 · 研究领域：Machine Learning in Bioinformatics、Protein Structure and Dynamics、Genomics and Phylogenetic Studies

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.