Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures

BMC Research Notes

Takeshi Kikuchi²  Masatake Sugita²  Masanari Matsuoka¹ 

[1] Japan Society for the Promotion of Science (JSPS) Research Fellow DC2, Tokyo, Japan;Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, Japan

关键词: Protein G;    Protein A;    IgG binding protein;    Sequence tendency;    Conservation analysis;    Inter-residue average distance statistics;    Sequence analysis;    Chameleon sequence;    Artificial homologues;   

Others  :  1129378
DOI  :  10.1186/1756-0500-7-654

 received in 2014-07-29, accepted in 2014-09-05,  发布年份 2014

【 摘 要 】

Background

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem.

Results

It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation.

Conclusions

The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

【 授权许可】

   
2014 Matsuoka et al.; licensee BioMed Central Ltd.

【 图 表 】

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