An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure

Journal of Molecular Biology
Gordon S Whamond, Janet M Thornton

Abstract

We present an analysis of intron positions in relation to nucleotides, amino acid residues, and protein secondary structure. Previous work has shown that intron sites in proteins are not randomly distributed with respect to secondary structures. Here we show that this preference can be almost totally explained by the nucleotide bias of splice site machinery, and may well not relate to protein stability or conformation at all. Each intron phase is preferentially associated with its own set of residues: phase 0 introns with lysine, glutamine, and glutamic acid before the intron, and valine after; phase 1 introns with glycine, alanine, valine, aspartic acid, and glutamic acid; and phase 2 introns with arginine, serine, lysine, and tryptophan. These preferences can be explained principally on the basis of nucleotide bias at intron locations, which is in accordance with previous literature. Although this work does not prove that introns are inserted into genomes at specific proto-splice sites, it shows that the nucleotide bias surrounding introns, however it originally occurred, explains the observed correlations between introns and protein secondary structure.

References

Feb 22, 1979·Nature·C C Blake
Nov 24, 1977·Nature·R BreathnachP Chambon
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·J E Darnell, W F Doolittle
Mar 7, 1989·Journal of Theoretical Biology·D A HickeyS M Abukashawa
May 23, 1985·Nature·T Cavalier-Smith
May 17, 1985·Science·W Gilbert
Jul 8, 1994·Science·A StoltzfusW F Doolittle
Jun 16, 1994·Nature·J M Logsdon, J D Palmer
Dec 10, 1996·Proceedings of the National Academy of Sciences of the United States of America·S J de SouzaW Gilbert
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Feb 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·M LongW Gilbert
Jan 20, 1998·Trends in Biochemical Sciences·R A LaskowskiJ M Thornton
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·S J de SouzaW Gilbert
May 22, 1998·Trends in Genetics : TIG·C N Trotman
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Oct 30, 2003·Journal of Molecular Biology·Bruno Contreras-MoreiraPaul A Bates
Aug 25, 2004·Current Biology : CB·Alexander V SverdlovEugene V Koonin

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Citations

Apr 8, 2011·Nucleic Acids Research·Yuri KapustinNick J Dibb
Oct 13, 2006·BMC Genomics·Henrik Nielsen, Rasmus Wernersson
Jun 21, 2007·Current Opinion in Structural Biology·William R Taylor
Jul 25, 2007·Molecular Biology and Evolution·Danny W De KeeArlin Stoltzfus

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