No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions

BMC Bioinformatics

Marc N Offman³  Ramil N Nurtdinov¹  Mikhail S Gelfand²  Dmitrij Frishman³ 

[1] Department of Bioengineering and Bioinformatics, Moscow State University, Lab. Bldg. B, Leninskie Gory 1-73, Moscow, 119992, Russia

[2] State Scientific Center GosNIIGenetika, 1st Dorozhny pr. 1, Moscow 117545, Russia

[3] Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany

关键词: protein structure analysis;    alternative splicing;    protein-protein interactions;   

Others  :  1171747
DOI  :  10.1186/1471-2105-5-41

 received in 2004-01-13, accepted in 2004-04-19,  发布年份 2004

【 摘 要 】

Background

Alternative splicing is an efficient mechanism for increasing the variety of functions fulfilled by proteins in a living cell. It has been previously demonstrated that alternatively spliced regions often comprise functionally important and conserved sequence motifs. The objective of this work was to test the hypothesis that alternative splicing is correlated with contact regions of protein-protein interactions.

Results

Protein sequence spans involved in contacts with an interaction partner were delineated from atomic structures of transient interaction complexes and juxtaposed with the location of alternatively spliced regions detected by comparative genome analysis and spliced alignment. The total of 42 alternatively spliced isoforms were identified in 21 amino acid chains involved in biomolecular interactions. Using this limited dataset and a variety of sophisticated counting procedures we were not able to establish a statistically significant correlation between the positions of protein interaction sites and alternatively spliced regions.

Conclusions

This finding contradicts a naïve hypothesis that alternatively spliced regions would correlate with points of contact. One possible explanation for that could be that all alternative splicing events change the spatial structure of the interacting domain to a sufficient degree to preclude interaction. This is indirectly supported by the observed lack of difference in the behaviour of relatively short regions affected by alternative splicing and cases when large portions of proteins are removed. More structural data on complexes of interacting proteins, including structures of alternative isoforms, are needed to test this conjecture.

【 授权许可】

   
2004 Offman et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.

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