Neutral evolution of protein-protein interactions: a computational study using simple models.

Abstract : BACKGROUND: Protein-protein interactions are central to cellular organization, and must have appeared at an early stage of evolution. To understand better their role, we consider a simple model of protein evolution and determine the effect of an explicit selection for Protein-protein interactions. RESULTS: In the model, viable sequences all have the same fitness, following the neutral evolution theory. A very simple, two-dimensional lattice representation of the protein structures is used, and the model only considers two kinds of amino acids: hydrophobic and polar. With these approximations, exact calculations are performed. The results do not depend too strongly on these assumptions, since a model using a 3D, off-lattice representation of the proteins gives results in qualitative agreement with the 2D one. With both models, the evolutionary dynamics lead to a steady state population that is enriched in sequences that dimerize with a high affinity, well beyond the minimal level needed to survive. Correspondingly, sequences close to the viability threshold are less abundant in the steady state, being subject to a larger proportion of lethal mutations. The set of viable sequences has a "funnel" shape, consistent with earlier studies: sequences that are highly populated in the steady state are "close" to each other (with proximity being measured by the number of amino acids that differ). CONCLUSION: This bias in the the steady state sequences should lead to an increased resistance of the population to environmental change and an increased ability to evolve.
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Josselin Noirel, Thomas Simonson. Neutral evolution of protein-protein interactions: a computational study using simple models.. BMC Structural Biology, BioMed Central, 2007, 7, pp.79-93. ⟨10.1186/1472-6807-7-79⟩. ⟨hal-00488197⟩

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