PMID: 8962105Dec 10, 1996Paper

Intron positions correlate with module boundaries in ancient proteins

Proceedings of the National Academy of Sciences of the United States of America
S J de SouzaWalter Gilbert

Abstract

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of "linker regions" that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-A modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters ...Continue Reading

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Citations

Jan 11, 2005·Journal of Molecular Evolution·Rolf B EdvardsenDaniel Chourrout
Feb 7, 2007·Genetica·Sigurbjorg GudlaugsdottirJun Ma
Oct 30, 2003·Journal of Molecular Biology·Bruno Contreras-MoreiraPaul A Bates
Jan 1, 1997·Progress in Biophysics and Molecular Biology·S Janecek
Mar 6, 1998·Trends in Biotechnology·S Harayama
Sep 4, 2001·Trends in Genetics : TIG·S W RoyW Gilbert
Jul 1, 1997·Trends in Genetics : TIG·J N Davidson, M L Peterson
Feb 14, 1998·Gene·E Zuckerkandl
Nov 26, 1999·Gene·S W RoyW Gilbert
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Feb 18, 2006·Nature Reviews. Genetics·Scott William Roy, Walter Gilbert
Mar 28, 2002·Nucleic Acids Research·Vivek AnantharamanL Aravind
Jan 11, 2005·Nucleic Acids Research·Mingyi LiuAndrei Grigoriev
Feb 12, 2008·Nucleic Acids Research·Manuel Irimia, Scott William Roy
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Mar 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Stepánka VanácováPatricia J Johnson
Nov 15, 2002·Proceedings of the National Academy of Sciences of the United States of America·Scott William RoyWalter Gilbert
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Dec 15, 2010·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Ryusuke Sawada, Shigeki Mitaku

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