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MBE Advance Access published online on November 23, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl181
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 8, 2006

Letter

Quaternary Structure Constraints on Evolutionary Sequence Divergence

María Silvina Fornasari 1, Gustavo Parisi 1, and Julián Echave 2 *

1 Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Roque Saenz Peña 180, B1876BXD Bernal, Argentina
2 Instituto Nacional de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata, Suc 4 C. C. 16, 1900 La Plata, Argentina

* To whom correspondence should be addressed.
Julián Echave, E-mail: jechave{at}inifta.unlp.edu.ar


  Abstract

The Structurally Constrained Protein Evolution (SCPE) model simulates protein divergence considering protein structure explicitly. The model is based on the observation that protein structure is more conserved during evolution than the sequences encoding for that structure. In previous work, the SCPE model considered only the tertiary structure. Here we show that the performance of the model is enhanced when the oligomeric structure is taken into account. Our results agree with recent evolutionary studies of oligomeric proteins that show that conservation of the quaternary structure imposes additional constraints on sequence divergence. The incorporation of protein-protein interactions into protein evolution models may be important in the study of quaternary protein structures and complex protein assemblies.

Keywords: SCPE; quaternary structure; sequence divergence.
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