Nucleic Acids Research Advance Access originally published online on November 30, 2007
Nucleic Acids Research 2008 36(2):550-558; doi:10.1093/nar/gkm1054
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Nucleic Acids Research, 2008, Vol. 36, No. 2 550-558
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Alternative splicing and protein structure evolution
Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany
*To whom correspondence should be addressed. Tel: +49 (0) 89 21804064; Fax: +49 (0) 89 21804054; Email: fabian.birzele{at}bio.ifi.lmu.de Correspondence may also be addressed to Prof. Ralf Zimmer. Email: ralf.zimmer{at}ifi.lmu.de
Received August 13, 2007. Revised October 5, 2007. Accepted November 7, 2007.
Alternative splicing is thought to be one of the major sources for functional diversity in higher eukaryotes. Interestingly, when mapping splicing events onto protein structures, about half of the events affect structured and even highly conserved regions i.e. are non-trivial on the structure level. This has led to the controversial hypothesis that such splice variants result in nonsense-mediated mRNA decay or non-functional, unstructured proteins, which do not contribute to the functional diversity of an organism. Here we show in a comprehensive study on alternative splicing that proteins appear to be much more tolerant to structural deletions, insertions and replacements than previously thought. We find literature evidence that such non-trivial splicing isoforms exhibit different functional properties compared to their native counterparts and allow for interesting regulatory patterns on the protein network level. We provide examples that splicing events may represent transitions between different folds in the protein sequence–structure space and explain these links by a common genetic mechanism. Taken together, those findings hint to a more prominent role of splicing in protein structure evolution and to a different view of phenotypic plasticity of protein structures.
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  G. Csaba, F. Birzele, and R. Zimmer Protein structure alignment considering phenotypic plasticity Bioinformatics, August 15, 2008; 24(16): i98 - i104. [Abstract] [PDF]
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