Large contact surface interactions between proteins detected by time series analysis methods: case study on C-phycocyanins.
A purely sequence-dependent approach to the modeling of protein-protein interaction was applied to the study of C-phycocyanin alphabeta dimers. The interacting pairs (alpha and beta subunits) share an almost complete structural homology, together with a general lack of sequence superposition; thus, they constitute a particularly relevant example for protein-protein interaction prediction. The present analysis is based on a description posited at an intermediate level between sequence and structure, that is, the hydrophobicity patterning along the chains. Based on the description of the sequence hydrophobicity patterns through a battery of nonlinear tools (recurrence quantification analysis and other sequence complexity descriptors), we were able to generate an explicit equation modeling alpha and beta monomers interaction; the model consisted of canonical correlation between the hydrophobicity autocorrelation structures of the interacting pairs. The general implications of this holistic approach to the modeling of protein-protein interactions, which considers the protein primary structures as a whole, are discussed.
Giuliani
Alessandro
A
Istituto Superiore di Sanita', Lab. TCE, Rome, Italy.
Benigni
Romualdo
R
Colafranceschi
Mauro
M
Chandrashekar
Indu
I
Cowsik
Sudha M
SM
D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D010798:Phycocyanin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013223:Statistics as Topic / Q000379:methods*
D011506:Proteins; D010798:Phycocyanin