Journal Article

The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families

M. M. Pentony, P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau and M. D. Purugganan

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 3, pages 360-371
Published in print January 2012 |
Published online February 2012 | e-ISSN: 1759-6653 | DOI:

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  • Bioinformatics and Computational Biology
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Despite its importance, relatively little is known about the relationship between the structure, function, and evolution of proteins, particularly in land plant species. We have developed a database with predicted protein domains for five plant proteomes ( and used both protein structural fold recognition and de novo Rosetta-based protein structure prediction to predict protein structure for Arabidopsis and rice proteins. Based on sequence similarity, we have identified ∼15,000 orthologous/paralogous protein family clusters among these species and used codon-based models to predict positive selection in protein evolution within 175 of these sequence clusters. Our results show that codons that display positive selection appear to be less frequent in helical and strand regions and are overrepresented in amino acid residues that are associated with a change in protein secondary structure. Like in other organisms, disordered protein regions also appear to have more selected sites. Structural information provides new functional insights into specific plant proteins and allows us to map positively selected amino acid sites onto protein structures and view these sites in a structural and functional context.

Keywords: adaptation; protein structure; plant evolution; fold prediction

Journal Article.  7493 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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