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Open Access Research article

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

Marc N Offman1, Ramil N Nurtdinov2, Mikhail S Gelfand34 and Dmitrij Frishman1*

Author Affiliations

1 Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany

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

3 Institute for Problems of Information Transmission, Russian Academy of Sciences, Bolshoy Karetny per. 19, Moscow, 127994, Russia

4 State Scientific Center GosNIIGenetika, 1st Dorozhny pr. 1, Moscow 117545, Russia

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BMC Bioinformatics 2004, 5:41  doi:10.1186/1471-2105-5-41

Published: 19 April 2004



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.


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.


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.

protein-protein interactions; alternative splicing; protein structure analysis