The architectonic fold similarity network in protein fold space
Department of Physics, Wuhan University, Wuhan 430072,
Corresponding author: a firstname.lastname@example.org
Revised: 28 November 2005
Published online: 31 January 2006
By constructing the fold similarity network (FSN), we present an alternative approach to the characteristic and architecture of protein fold space. The degree distribution P(k) of FSN differs far from that of the random network with the same number of nodes and connections. The investigation shows that FSN possesses small-world property and broad-scale feature. In order to access to the assumption of the dynamics behavior for FSN, we design a simple evolutionary dynamics model based on the duplication and variation fashions of protein folds. The simulation network generated by this model is a small-world one and reproduces the broad-scale degree distribution consistent with that of FSN. It seems that this model can be used to depict the divergent evolution and expanding progress of protein fold space.
PACS: 87.15.-v – Biomolecules: structure and physical properties / 87.15.Aa – Theory and modeling; computer simulation / 87.23.Kg – Dynamics of evolution
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag, 2006