Co‐evolution and co‐adaptation in protein networks

@article{Juan2008CoevolutionAC,
  title={Co‐evolution and co‐adaptation in protein networks},
  author={David de Juan and Florencio Pazos and Alfonso Valencia},
  journal={FEBS Letters},
  year={2008},
  volume={582}
}
A Conserved Mammalian Protein Interaction Network
TLDR
Paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals are analyzed to suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
TLDR
The statistical approach allows us to resolve the previously reported contradictory results on the levels of co-evolution induced by protein-protein interactions and develops suitable statistical resampling schemes that can incorporate these two potential sources of correlation into a single inferential framework.
An integrated view of molecular coevolution in protein-protein interactions.
TLDR
It is argued that both site-specific coevolutionary change and whole-sequence evolution contribute to evolutionary signals in sets of interacting proteins, permitting an integrated view of protein-protein interactions, their evolution, and coev evolution.
Phylogenetic correlations can suffice to infer protein partners from sequences
TLDR
It is found that DCA accurately identifies the pairs of synthetic sequences that only share evolutionary history and in cases with shared evolutionary but without known physical interactions, both methods work with similar accuracy, while for physically interacting systems, methods based on correlated amino-acid usage outperform purely phylogenetic ones.
The Effects of Network Neighbours on Protein Evolution
TLDR
It is confirmed that similar expression levels of neighbours indeed explain their similar evolution rates in protein-protein networks, and it is shown that the same is true for metabolic networks.
Function and evolution of genes in the human protein interaction network
TLDR
It is suggested that most of the protein interactions in human are likely to be conserved in chimpanzee, macaque, mouse, rat, horse, dog and cow, and this suggests they date from at least the point in evolution when placental mammals radiated out.
Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.
TLDR
Predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction, and improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence.
Recent Coselection in Human Populations Revealed by Protein–Protein Interaction Network
TLDR
These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome.
Correlated evolution of interacting proteins: looking behind the mirrortree.
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References

SHOWING 1-10 OF 75 REFERENCES
Modularity and evolutionary constraint on proteins
TLDR
In the yeast Saccharomyces cerevisiae, protein interaction hubs situated in single modules are highly constrained, whereas those connecting different modules are more plastic, which could reflect a tendency for evolutionary innovations to occur by altering the proteins and interactions between rather than within modules.
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
TLDR
This work introduces a new estimator of coevolution that uses the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coev evolutionary context.
Evolutionary Rate in the Protein Interaction Network
TLDR
It is shown that the connectivity of well-conserved proteins in the protein interaction network is negatively correlated with their rate of evolution, confirming one predicted outcome of this process—namely, that interacting proteins evolve at similar rates.
The coordinated evolution of yeast proteins is constrained by functional modularity.
Phylogenetic methodology for detecting protein interactions.
TLDR
A method to estimate correlations of pairwise evolutionary distances, which adjusts for non-independent correlations due to shared evolutionary history is described, which makes the use of less complex substitution models preferable in some circumstances.
Lethality and centrality in protein networks
TLDR
It is demonstrated that the phenotypic consequence of a single gene deletion in the yeast Saccharomyces cerevisiae is affected to a large extent by the topological position of its protein product in the complex hierarchical web of molecular interactions.
In silico two‐hybrid system for the selection of physically interacting protein pairs
TLDR
This work proposes a new method (in silico two‐hybrid, i2h) that directly addresses the detection of physically interacting protein pairs and identifies the most likely sequence regions involved in the interactions.
Co-evolution of proteins with their interaction partners.
TLDR
PGK, an enzyme that forms its active site between its two domains, is used to develop a standard for measuring the co-evolution of interacting proteins, and the correlation coefficient for the trees of the two domains of PGK is calculated, which establishes an upper bound for theCo-Evolution of a protein domain with its binding partner.
Predicting protein domain interactions from coevolution of conserved regions
TLDR
It is demonstrated that the performance of the mirrortree method can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions).
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