Journal Article

Positive Selection Differs between Protein Secondary Structure Elements in <i>Drosophila</i>

Kate E. Ridout, Christopher J. Dixon and Dmitry A. Filatov

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 166-179
Published in print January 2010 |
Published online February 2010 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evq008

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Different protein secondary structure elements have different physicochemical properties and roles in the protein, which may determine their evolutionary flexibility. However, it is not clear to what extent protein structure affects the way Darwinian selection acts at the amino acid level. Using phylogeny-based likelihood tests for positive selection, we have examined the relationship between protein secondary structure and selection across six species of Drosophila. We find that amino acids that form disordered regions, such as random coils, are far more likely to be under positive selection than expected from their proportion in the proteins, and residues in helices and β-structures are subject to less positive selection than predicted. In addition, it appears that sites undergoing positive selection are more likely than expected to occur close to one another in the protein sequence. Finally, on a genome-wide scale, we have determined that positively selected sites are found more frequently toward the gene ends. Our results demonstrate that protein structures with a greater degree of organization and strong hydrophobicity, represented here as helices and β-structures, are less tolerant to molecular adaptation than disordered, hydrophilic regions, across a diverse set of proteins.

Keywords: positive selection; protein secondary structure; dN/dS ratio; Drosophila

Journal Article.  10084 words.  Illustrated.

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

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