title: Large contact surface interactions between proteins detected by time series analysis methods: case study on C-phycocyanins.
abstract: 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.
authors.affiliation: Istituto Superiore di Sanita', Lab. TCE, Rome, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Giuliani
authors.forename: Romualdo
authors.initials: R
authors.lastname: Benigni
authors.forename: Mauro
authors.initials: M
authors.lastname: Colafranceschi
authors.forename: Indu
authors.initials: I
authors.lastname: Chandrashekar
authors.forename: Sudha M
authors.initials: SM
authors.lastname: Cowsik
mesh_terms: 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*
chemical_list: D011506:Proteins; D010798:Phycocyanin