BIOPHYSICAL THEORY AND MODELING |
The Emergence of Scaling in Sequence-based Physical Models of Protein Evolution
Eric J. Deeds 1 and Eugene I. Shakhnovich 1*
1 Harvard University
* To whom correspondence should be addressed. E-mail: eugene{at}belok.harvard.edu.
Submitted on August 14, 2004
Revised on November 13, 2004
Accepted on 1 March 2005
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Abstract |
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It has recently been discovered that many biological systems, when represented as graphs, exhibit a scale-free topology. One such system is the set of structural relationships among protein domains. The scale-free nature of this and other systems has previously been explained using network growth models that, while motivated by biological processes, do not explicitly consider the underlying physics or biology. In the present work we explore a sequence-based model for the evolution protein structures and demonstrate that this model is able to recapitulate the scale-free nature observed in graphs of real protein structures. We find that this model also reproduces other statistical feature of the protein domain graph. This represents, to our knowledge, the first such microscopic, physics-based evolutionary model for a scale-free network of biological importance and as such has strong implications for our understanding of the evolution of protein structures and of other biological networks.
Key Words:
lattice models, protein evolution, protein structure
