Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
BMC Struct Biol. 2007 Nov 19;7:79.

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

Author information

  • 1Laboratoire de Biochimie, Ecole polytechnique, route de Saclay, 91128 Palaiseau Cedex, France. j.noirel@sheffield.ac.uk

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.

PMID:
18021454
[PubMed - indexed for MEDLINE]
PMCID:
PMC2248192
Free PMC Article

Images from this publication.See all images (7)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Write to the Help Desk