Mapping protein sequence spaces by recurrence quantification analysis: a case study on chimeric structures

被引:25
作者
Giuliani, A
Sirabella, P
Benigni, R
Colosimo, A
机构
[1] Ist Super Sanita, TCE Lab, I-00161 Rome, Italy
[2] Univ Rome La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy
来源
PROTEIN ENGINEERING | 2000年 / 13卷 / 10期
关键词
chimeric sequences; pattern recognition; primary structures; principal component analysis; recurrence plots;
D O I
10.1093/protein/13.10.671
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Recurrence quantification analysis (RQA) was used to characterize the folding properties of 22 chimeric sequences derived from two parent proteins of similar length but different three-dimensional arrangement. A non-linear relation between sequence data and their RQA representation was revealed, which points to new information carried by this method as compared with classical best-alignment methods. This new information is significantly correlated with the folding properties of the hybrid polypeptide chains, as substantiated by careful statistical analysis of the recurrence plots' numerical descriptors, thus encouraging their systematic use to complement sequence data in both proteomics and protein engineering tasks. Even the direct visual screening of the qualitative graphical features of recurrence plots is shown to provide useful hints to discriminate between different recurrence structures of protein sequences.
引用
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页码:671 / 678
页数:8
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