Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).
BACKGROUND
Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes.


RESULTS
We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: (1) eukarya had significantly more hub families than archaea and bacteria and (2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led to the evolution of interactomes and seemed to have played a key role in species diversification.


BACKGROUND
http://interactomics.org.
Park
Daeui
D
Object Interaction Technologies Inc., CMS Building 705, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
Lee
Semin
S
Bolser
Dan
D
Schroeder
Michael
M
Lappe
Michael
M
Oh
Donghoon
D
Bhak
Jong
J
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D013329:Structure-Activity Relationship
D020543:Proteome