Topology of small-world networks of protein-protein complex structures.
The majority of real examples of small-world networks exhibit a power law distribution of edges among the nodes, therefore not fitting into the wiring model proposed by Watts and Strogatz. However, protein structures can be modeled as small-world networks, with a distribution of the number of links decaying exponentially as in the case of this wiring model. We approach the protein-protein interaction mechanism by viewing it as a particular rewiring occurring in the system of two small-world networks represented by the monomers, where a re-arrangement of links takes place upon dimerization leaving the small-world character in the dimer network. Due to this rewiring, the most central residues at the complex interfaces tend to form clusters, which are not homogenously distributed. We show that these highly central residues are strongly correlated with the presence of hot spots of binding free energy.


BACKGROUND
ao-mesa@fujirebio.co.jp


BACKGROUND
http://www.fujirebio.co.jp/support/index.php (under construction).
del Sol
Antonio
A
Bioinformatics Research Project, Research and Development Division, Fujirebio Inc., 51 Komiya-cho, Hachioji-shi, Tokyo 192-0031, Japan. ao-mesa@fujirebio.co.jp
Fujihashi
Hirotomo
H
O'Meara
Paul
P
D001665:Binding Sites; D003198:Computer Simulation; D019281:Dimerization; D008954:Models, Biological; D008956:Models, Chemical; D046912:Multiprotein Complexes / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D013329:Structure-Activity Relationship
D046912:Multiprotein Complexes; D011506:Proteins